Starting phenix.real_space_refine on Tue Sep 24 18:37:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdi_33148/09_2024/7xdi_33148.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.048 sd= 5.514 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 168 5.16 5 C 35777 2.51 5 N 8218 2.21 5 O 9506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 53669 Number of models: 1 Model: "" Number of chains: 6 Chain: "0" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "1" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 996 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "2" Number of atoms: 1443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1443 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 14, 'TRANS': 170} Chain: "3" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3680 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 18, 'TRANS': 437} Chain breaks: 4 Chain: "4" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Chain: "5" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 516 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 4, 'TRANS': 64} Restraints were copied for chains: 6, C, I, O, U, c, 7, D, J, P, V, d, 8, E, K, Q, W, e, 9, F, L, R, X, f, A, G, M, S, Y, a, B, H, N, T, Z, b Time building chain proxies: 13.35, per 1000 atoms: 0.25 Number of scatterers: 53669 At special positions: 0 Unit cell: (196.85, 196.85, 135.89, 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 168 16.00 O 9506 8.00 N 8218 7.00 C 35777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.33 Conformation dependent library (CDL) restraints added in 5.3 seconds 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12824 Finding SS restraints... Secondary structure from input PDB file: 210 helices and 56 sheets defined 62.2% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 15 through 32 Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE A 36 " --> pdb=" O LEU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 83 Proline residue: A 63 - end of helix Proline residue: A 74 - end of helix removed outlier: 3.665A pdb=" N ARG A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 45 Proline residue: B 34 - end of helix Processing helix chain 'B' and resid 53 through 82 Proline residue: B 63 - end of helix Proline residue: B 74 - end of helix Processing helix chain 'C' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Proline residue: C 34 - end of helix Processing helix chain 'C' and resid 53 through 83 Proline residue: C 63 - end of helix Proline residue: C 74 - end of helix Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 36 through 44 Processing helix chain 'D' and resid 60 through 96 Processing helix chain 'D' and resid 101 through 125 Processing helix chain 'E' and resid 136 through 159 Processing helix chain 'E' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA E 165 " --> pdb=" O PRO E 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 178 " --> pdb=" O ILE E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL E 188 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 45 Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 80 through 82 No H-bonds generated for 'chain 'F' and resid 80 through 82' Processing helix chain 'F' and resid 85 through 99 Processing helix chain 'F' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR F 612 " --> pdb=" O LEU F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR F 635 " --> pdb=" O GLN F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 658 Processing helix chain 'F' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER F 664 " --> pdb=" O ASN F 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN F 665 " --> pdb=" O THR F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 903 through 921 Processing helix chain 'F' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU F 926 " --> pdb=" O ASN F 922 " (cutoff:3.500A) Processing helix chain 'F' and resid 975 through 989 Processing helix chain 'F' and resid 990 through 1003 Processing helix chain 'F' and resid 1030 through 1046 Processing helix chain 'F' and resid 1164 through 1187 Processing helix chain 'F' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR F1193 " --> pdb=" O ASN F1189 " (cutoff:3.500A) Processing helix chain 'F' and resid 1211 through 1233 Processing helix chain 'G' and resid 15 through 32 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 83 Proline residue: G 63 - end of helix Proline residue: G 74 - end of helix removed outlier: 3.665A pdb=" N ARG G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 45 Proline residue: H 34 - end of helix Processing helix chain 'H' and resid 53 through 82 Proline residue: H 63 - end of helix Proline residue: H 74 - end of helix Processing helix chain 'I' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE I 23 " --> pdb=" O LEU I 19 " (cutoff:3.500A) Proline residue: I 34 - end of helix Processing helix chain 'I' and resid 53 through 83 Proline residue: I 63 - end of helix Proline residue: I 74 - end of helix Processing helix chain 'J' and resid 3 through 20 Processing helix chain 'J' and resid 36 through 44 Processing helix chain 'J' and resid 60 through 96 Processing helix chain 'J' and resid 101 through 125 Processing helix chain 'K' and resid 136 through 159 Processing helix chain 'K' and resid 160 through 178 removed outlier: 3.824A pdb=" N ALA K 165 " --> pdb=" O PRO K 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE K 178 " --> pdb=" O ILE K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL K 188 " --> pdb=" O TYR K 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 45 Processing helix chain 'L' and resid 67 through 79 Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 85 through 99 Processing helix chain 'L' and resid 598 through 612 removed outlier: 3.669A pdb=" N TYR L 612 " --> pdb=" O LEU L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR L 635 " --> pdb=" O GLN L 631 " (cutoff:3.500A) Processing helix chain 'L' and resid 640 through 658 Processing helix chain 'L' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER L 664 " --> pdb=" O ASN L 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN L 665 " --> pdb=" O THR L 661 " (cutoff:3.500A) Processing helix chain 'L' and resid 903 through 921 Processing helix chain 'L' and resid 922 through 936 removed outlier: 3.854A pdb=" N LEU L 926 " --> pdb=" O ASN L 922 " (cutoff:3.500A) Processing helix chain 'L' and resid 975 through 989 Processing helix chain 'L' and resid 990 through 1003 Processing helix chain 'L' and resid 1030 through 1046 Processing helix chain 'L' and resid 1164 through 1187 Processing helix chain 'L' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR L1193 " --> pdb=" O ASN L1189 " (cutoff:3.500A) Processing helix chain 'L' and resid 1211 through 1233 Processing helix chain 'M' and resid 15 through 32 Processing helix chain 'M' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE M 36 " --> pdb=" O LEU M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 83 Proline residue: M 63 - end of helix Proline residue: M 74 - end of helix removed outlier: 3.664A pdb=" N ARG M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 45 Proline residue: N 34 - end of helix Processing helix chain 'N' and resid 53 through 82 Proline residue: N 63 - end of helix Proline residue: N 74 - end of helix Processing helix chain 'O' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE O 23 " --> pdb=" O LEU O 19 " (cutoff:3.500A) Proline residue: O 34 - end of helix Processing helix chain 'O' and resid 53 through 83 Proline residue: O 63 - end of helix Proline residue: O 74 - end of helix Processing helix chain 'P' and resid 3 through 20 Processing helix chain 'P' and resid 36 through 44 Processing helix chain 'P' and resid 60 through 96 Processing helix chain 'P' and resid 101 through 125 Processing helix chain 'Q' and resid 136 through 159 Processing helix chain 'Q' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA Q 165 " --> pdb=" O PRO Q 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE Q 178 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) Processing helix chain 'Q' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL Q 188 " --> pdb=" O TYR Q 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 45 Processing helix chain 'R' and resid 67 through 79 Processing helix chain 'R' and resid 80 through 82 No H-bonds generated for 'chain 'R' and resid 80 through 82' Processing helix chain 'R' and resid 85 through 99 Processing helix chain 'R' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR R 612 " --> pdb=" O LEU R 608 " (cutoff:3.500A) Processing helix chain 'R' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR R 635 " --> pdb=" O GLN R 631 " (cutoff:3.500A) Processing helix chain 'R' and resid 640 through 658 Processing helix chain 'R' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER R 664 " --> pdb=" O ASN R 660 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN R 665 " --> pdb=" O THR R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 903 through 921 Processing helix chain 'R' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU R 926 " --> pdb=" O ASN R 922 " (cutoff:3.500A) Processing helix chain 'R' and resid 975 through 989 Processing helix chain 'R' and resid 990 through 1003 Processing helix chain 'R' and resid 1030 through 1046 Processing helix chain 'R' and resid 1164 through 1187 Processing helix chain 'R' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR R1193 " --> pdb=" O ASN R1189 " (cutoff:3.500A) Processing helix chain 'R' and resid 1211 through 1233 Processing helix chain 'S' and resid 15 through 32 Processing helix chain 'S' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE S 36 " --> pdb=" O LEU S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 83 Proline residue: S 63 - end of helix Proline residue: S 74 - end of helix removed outlier: 3.665A pdb=" N ARG S 83 " --> pdb=" O TYR S 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 16 through 45 Proline residue: T 34 - end of helix Processing helix chain 'T' and resid 53 through 82 Proline residue: T 63 - end of helix Proline residue: T 74 - end of helix Processing helix chain 'U' and resid 16 through 45 removed outlier: 3.637A pdb=" N PHE U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Proline residue: U 34 - end of helix Processing helix chain 'U' and resid 53 through 83 Proline residue: U 63 - end of helix Proline residue: U 74 - end of helix Processing helix chain 'V' and resid 3 through 20 Processing helix chain 'V' and resid 36 through 44 Processing helix chain 'V' and resid 60 through 96 Processing helix chain 'V' and resid 101 through 125 Processing helix chain 'W' and resid 136 through 159 Processing helix chain 'W' and resid 160 through 178 removed outlier: 3.824A pdb=" N ALA W 165 " --> pdb=" O PRO W 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE W 178 " --> pdb=" O ILE W 174 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL W 188 " --> pdb=" O TYR W 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA W 194 " --> pdb=" O LEU W 190 " (cutoff:3.500A) Processing helix chain 'X' and resid 31 through 45 Processing helix chain 'X' and resid 67 through 79 Processing helix chain 'X' and resid 80 through 82 No H-bonds generated for 'chain 'X' and resid 80 through 82' Processing helix chain 'X' and resid 85 through 99 Processing helix chain 'X' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR X 612 " --> pdb=" O LEU X 608 " (cutoff:3.500A) Processing helix chain 'X' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR X 635 " --> pdb=" O GLN X 631 " (cutoff:3.500A) Processing helix chain 'X' and resid 640 through 658 Processing helix chain 'X' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER X 664 " --> pdb=" O ASN X 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN X 665 " --> pdb=" O THR X 661 " (cutoff:3.500A) Processing helix chain 'X' and resid 903 through 921 Processing helix chain 'X' and resid 922 through 936 removed outlier: 3.854A pdb=" N LEU X 926 " --> pdb=" O ASN X 922 " (cutoff:3.500A) Processing helix chain 'X' and resid 975 through 989 Processing helix chain 'X' and resid 990 through 1003 Processing helix chain 'X' and resid 1030 through 1046 Processing helix chain 'X' and resid 1164 through 1187 Processing helix chain 'X' and resid 1189 through 1207 removed outlier: 3.601A pdb=" N THR X1193 " --> pdb=" O ASN X1189 " (cutoff:3.500A) Processing helix chain 'X' and resid 1211 through 1233 Processing helix chain 'Y' and resid 15 through 32 Processing helix chain 'Y' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE Y 36 " --> pdb=" O LEU Y 32 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 83 Proline residue: Y 63 - end of helix Proline residue: Y 74 - end of helix removed outlier: 3.664A pdb=" N ARG Y 83 " --> pdb=" O TYR Y 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 45 Proline residue: Z 34 - end of helix Processing helix chain 'Z' and resid 53 through 82 Proline residue: Z 63 - end of helix Proline residue: Z 74 - end of helix Processing helix chain '0' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Proline residue: 0 34 - end of helix Processing helix chain '0' and resid 53 through 83 Proline residue: 0 63 - end of helix Proline residue: 0 74 - end of helix Processing helix chain '1' and resid 3 through 20 Processing helix chain '1' and resid 36 through 44 Processing helix chain '1' and resid 60 through 96 Processing helix chain '1' and resid 101 through 125 Processing helix chain '2' and resid 136 through 159 Processing helix chain '2' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA 2 165 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE 2 178 " --> pdb=" O ILE 2 174 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL 2 188 " --> pdb=" O TYR 2 184 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA 2 194 " --> pdb=" O LEU 2 190 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 45 Processing helix chain '3' and resid 67 through 79 Processing helix chain '3' and resid 80 through 82 No H-bonds generated for 'chain '3' and resid 80 through 82' Processing helix chain '3' and resid 85 through 99 Processing helix chain '3' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR 3 612 " --> pdb=" O LEU 3 608 " (cutoff:3.500A) Processing helix chain '3' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR 3 635 " --> pdb=" O GLN 3 631 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 658 Processing helix chain '3' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER 3 664 " --> pdb=" O ASN 3 660 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN 3 665 " --> pdb=" O THR 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 903 through 921 Processing helix chain '3' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU 3 926 " --> pdb=" O ASN 3 922 " (cutoff:3.500A) Processing helix chain '3' and resid 975 through 989 Processing helix chain '3' and resid 990 through 1003 Processing helix chain '3' and resid 1030 through 1046 Processing helix chain '3' and resid 1164 through 1187 Processing helix chain '3' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR 31193 " --> pdb=" O ASN 31189 " (cutoff:3.500A) Processing helix chain '3' and resid 1211 through 1233 Processing helix chain '4' and resid 15 through 32 Processing helix chain '4' and resid 32 through 45 removed outlier: 3.770A pdb=" N ILE 4 36 " --> pdb=" O LEU 4 32 " (cutoff:3.500A) Processing helix chain '4' and resid 52 through 83 Proline residue: 4 63 - end of helix Proline residue: 4 74 - end of helix removed outlier: 3.665A pdb=" N ARG 4 83 " --> pdb=" O TYR 4 79 " (cutoff:3.500A) Processing helix chain '5' and resid 16 through 45 Proline residue: 5 34 - end of helix Processing helix chain '5' and resid 53 through 82 Proline residue: 5 63 - end of helix Proline residue: 5 74 - end of helix Processing helix chain '6' and resid 16 through 45 removed outlier: 3.637A pdb=" N PHE 6 23 " --> pdb=" O LEU 6 19 " (cutoff:3.500A) Proline residue: 6 34 - end of helix Processing helix chain '6' and resid 53 through 83 Proline residue: 6 63 - end of helix Proline residue: 6 74 - end of helix Processing helix chain '7' and resid 3 through 20 Processing helix chain '7' and resid 36 through 44 Processing helix chain '7' and resid 60 through 96 Processing helix chain '7' and resid 101 through 125 Processing helix chain '8' and resid 136 through 159 Processing helix chain '8' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA 8 165 " --> pdb=" O PRO 8 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE 8 178 " --> pdb=" O ILE 8 174 " (cutoff:3.500A) Processing helix chain '8' and resid 184 through 204 removed outlier: 3.624A pdb=" N VAL 8 188 " --> pdb=" O TYR 8 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA 8 194 " --> pdb=" O LEU 8 190 " (cutoff:3.500A) Processing helix chain '9' and resid 31 through 45 Processing helix chain '9' and resid 67 through 79 Processing helix chain '9' and resid 80 through 82 No H-bonds generated for 'chain '9' and resid 80 through 82' Processing helix chain '9' and resid 85 through 99 Processing helix chain '9' and resid 598 through 612 removed outlier: 3.668A pdb=" N TYR 9 612 " --> pdb=" O LEU 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 614 through 636 removed outlier: 3.560A pdb=" N TYR 9 635 " --> pdb=" O GLN 9 631 " (cutoff:3.500A) Processing helix chain '9' and resid 640 through 658 Processing helix chain '9' and resid 660 through 677 removed outlier: 4.502A pdb=" N SER 9 664 " --> pdb=" O ASN 9 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN 9 665 " --> pdb=" O THR 9 661 " (cutoff:3.500A) Processing helix chain '9' and resid 903 through 921 Processing helix chain '9' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU 9 926 " --> pdb=" O ASN 9 922 " (cutoff:3.500A) Processing helix chain '9' and resid 975 through 989 Processing helix chain '9' and resid 990 through 1003 Processing helix chain '9' and resid 1030 through 1046 Processing helix chain '9' and resid 1164 through 1187 Processing helix chain '9' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR 91193 " --> pdb=" O ASN 91189 " (cutoff:3.500A) Processing helix chain '9' and resid 1211 through 1233 Processing helix chain 'a' and resid 15 through 32 Processing helix chain 'a' and resid 32 through 45 removed outlier: 3.769A pdb=" N ILE a 36 " --> pdb=" O LEU a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 83 Proline residue: a 63 - end of helix Proline residue: a 74 - end of helix removed outlier: 3.664A pdb=" N ARG a 83 " --> pdb=" O TYR a 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 16 through 45 Proline residue: b 34 - end of helix Processing helix chain 'b' and resid 53 through 82 Proline residue: b 63 - end of helix Proline residue: b 74 - end of helix Processing helix chain 'c' and resid 16 through 45 removed outlier: 3.638A pdb=" N PHE c 23 " --> pdb=" O LEU c 19 " (cutoff:3.500A) Proline residue: c 34 - end of helix Processing helix chain 'c' and resid 53 through 83 Proline residue: c 63 - end of helix Proline residue: c 74 - end of helix Processing helix chain 'd' and resid 3 through 20 Processing helix chain 'd' and resid 36 through 44 Processing helix chain 'd' and resid 60 through 96 Processing helix chain 'd' and resid 101 through 125 Processing helix chain 'e' and resid 136 through 159 Processing helix chain 'e' and resid 160 through 178 removed outlier: 3.825A pdb=" N ALA e 165 " --> pdb=" O PRO e 161 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE e 178 " --> pdb=" O ILE e 174 " (cutoff:3.500A) Processing helix chain 'e' and resid 184 through 204 removed outlier: 3.625A pdb=" N VAL e 188 " --> pdb=" O TYR e 184 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA e 194 " --> pdb=" O LEU e 190 " (cutoff:3.500A) Processing helix chain 'f' and resid 31 through 45 Processing helix chain 'f' and resid 67 through 79 Processing helix chain 'f' and resid 80 through 82 No H-bonds generated for 'chain 'f' and resid 80 through 82' Processing helix chain 'f' and resid 85 through 99 Processing helix chain 'f' and resid 598 through 612 removed outlier: 3.669A pdb=" N TYR f 612 " --> pdb=" O LEU f 608 " (cutoff:3.500A) Processing helix chain 'f' and resid 614 through 636 removed outlier: 3.559A pdb=" N TYR f 635 " --> pdb=" O GLN f 631 " (cutoff:3.500A) Processing helix chain 'f' and resid 640 through 658 Processing helix chain 'f' and resid 660 through 677 removed outlier: 4.501A pdb=" N SER f 664 " --> pdb=" O ASN f 660 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN f 665 " --> pdb=" O THR f 661 " (cutoff:3.500A) Processing helix chain 'f' and resid 903 through 921 Processing helix chain 'f' and resid 922 through 936 removed outlier: 3.855A pdb=" N LEU f 926 " --> pdb=" O ASN f 922 " (cutoff:3.500A) Processing helix chain 'f' and resid 975 through 989 Processing helix chain 'f' and resid 990 through 1003 Processing helix chain 'f' and resid 1030 through 1046 Processing helix chain 'f' and resid 1164 through 1187 Processing helix chain 'f' and resid 1189 through 1207 removed outlier: 3.600A pdb=" N THR f1193 " --> pdb=" O ASN f1189 " (cutoff:3.500A) Processing helix chain 'f' and resid 1211 through 1233 Processing sheet with id=1, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=2, first strand: chain 'E' and resid 25 through 27 Processing sheet with id=3, first strand: chain 'E' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU E 73 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR E 57 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'E' and resid 120 through 124 Processing sheet with id=5, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=6, first strand: chain 'F' and resid 1005 through 1007 Processing sheet with id=7, first strand: chain 'F' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE F1088 " --> pdb=" O PHE F1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA F1055 " --> pdb=" O GLN F1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN F1086 " --> pdb=" O ALA F1055 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'F' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE F1063 " --> pdb=" O TYR F1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR F1078 " --> pdb=" O ILE F1063 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'J' and resid 47 through 50 Processing sheet with id=10, first strand: chain 'K' and resid 25 through 27 Processing sheet with id=11, first strand: chain 'K' and resid 69 through 75 removed outlier: 4.640A pdb=" N GLU K 73 " --> pdb=" O TYR K 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR K 57 " --> pdb=" O GLU K 73 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'K' and resid 120 through 124 Processing sheet with id=13, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=14, first strand: chain 'L' and resid 1005 through 1007 Processing sheet with id=15, first strand: chain 'L' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE L1088 " --> pdb=" O PHE L1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA L1055 " --> pdb=" O GLN L1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN L1086 " --> pdb=" O ALA L1055 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'L' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE L1063 " --> pdb=" O TYR L1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR L1078 " --> pdb=" O ILE L1063 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'P' and resid 47 through 50 Processing sheet with id=18, first strand: chain 'Q' and resid 25 through 27 Processing sheet with id=19, first strand: chain 'Q' and resid 69 through 75 removed outlier: 4.640A pdb=" N GLU Q 73 " --> pdb=" O TYR Q 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR Q 57 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'Q' and resid 120 through 124 Processing sheet with id=21, first strand: chain 'R' and resid 47 through 48 Processing sheet with id=22, first strand: chain 'R' and resid 1005 through 1007 Processing sheet with id=23, first strand: chain 'R' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE R1088 " --> pdb=" O PHE R1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA R1055 " --> pdb=" O GLN R1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN R1086 " --> pdb=" O ALA R1055 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'R' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE R1063 " --> pdb=" O TYR R1078 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR R1078 " --> pdb=" O ILE R1063 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'V' and resid 47 through 50 Processing sheet with id=26, first strand: chain 'W' and resid 25 through 27 Processing sheet with id=27, first strand: chain 'W' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU W 73 " --> pdb=" O TYR W 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR W 57 " --> pdb=" O GLU W 73 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'W' and resid 120 through 124 Processing sheet with id=29, first strand: chain 'X' and resid 47 through 48 Processing sheet with id=30, first strand: chain 'X' and resid 1005 through 1007 Processing sheet with id=31, first strand: chain 'X' and resid 1051 through 1056 removed outlier: 7.232A pdb=" N ILE X1088 " --> pdb=" O PHE X1053 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA X1055 " --> pdb=" O GLN X1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN X1086 " --> pdb=" O ALA X1055 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'X' and resid 1062 through 1069 removed outlier: 4.960A pdb=" N ILE X1063 " --> pdb=" O TYR X1078 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR X1078 " --> pdb=" O ILE X1063 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain '1' and resid 47 through 50 Processing sheet with id=34, first strand: chain '2' and resid 25 through 27 Processing sheet with id=35, first strand: chain '2' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU 2 73 " --> pdb=" O TYR 2 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR 2 57 " --> pdb=" O GLU 2 73 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain '2' and resid 120 through 124 Processing sheet with id=37, first strand: chain '3' and resid 47 through 48 Processing sheet with id=38, first strand: chain '3' and resid 1005 through 1007 Processing sheet with id=39, first strand: chain '3' and resid 1051 through 1056 removed outlier: 7.230A pdb=" N ILE 31088 " --> pdb=" O PHE 31053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA 31055 " --> pdb=" O GLN 31086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 31086 " --> pdb=" O ALA 31055 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain '3' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE 31063 " --> pdb=" O TYR 31078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR 31078 " --> pdb=" O ILE 31063 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain '7' and resid 47 through 50 Processing sheet with id=42, first strand: chain '8' and resid 25 through 27 Processing sheet with id=43, first strand: chain '8' and resid 69 through 75 removed outlier: 4.641A pdb=" N GLU 8 73 " --> pdb=" O TYR 8 57 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N TYR 8 57 " --> pdb=" O GLU 8 73 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain '8' and resid 120 through 124 Processing sheet with id=45, first strand: chain '9' and resid 47 through 48 Processing sheet with id=46, first strand: chain '9' and resid 1005 through 1007 Processing sheet with id=47, first strand: chain '9' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE 91088 " --> pdb=" O PHE 91053 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ALA 91055 " --> pdb=" O GLN 91086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN 91086 " --> pdb=" O ALA 91055 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain '9' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE 91063 " --> pdb=" O TYR 91078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR 91078 " --> pdb=" O ILE 91063 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'd' and resid 47 through 50 Processing sheet with id=50, first strand: chain 'e' and resid 25 through 27 Processing sheet with id=51, first strand: chain 'e' and resid 69 through 75 removed outlier: 4.642A pdb=" N GLU e 73 " --> pdb=" O TYR e 57 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR e 57 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'e' and resid 120 through 124 Processing sheet with id=53, first strand: chain 'f' and resid 47 through 48 Processing sheet with id=54, first strand: chain 'f' and resid 1005 through 1007 Processing sheet with id=55, first strand: chain 'f' and resid 1051 through 1056 removed outlier: 7.231A pdb=" N ILE f1088 " --> pdb=" O PHE f1053 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA f1055 " --> pdb=" O GLN f1086 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLN f1086 " --> pdb=" O ALA f1055 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'f' and resid 1062 through 1069 removed outlier: 4.959A pdb=" N ILE f1063 " --> pdb=" O TYR f1078 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR f1078 " --> pdb=" O ILE f1063 " (cutoff:3.500A) 3570 hydrogen bonds defined for protein. 10542 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: 17.06 Time building geometry restraints manager: 12.29 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: 15923 1.34 - 1.46: 13484 1.46 - 1.58: 25410 1.58 - 1.70: 0 1.70 - 1.81: 336 Bond restraints: 55153 Sorted by residual: bond pdb=" CB PRO K 49 " pdb=" CG PRO K 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.76e+00 bond pdb=" CB PRO Q 49 " pdb=" CG PRO Q 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO 8 49 " pdb=" CG PRO 8 49 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO E 49 " pdb=" CG PRO E 49 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.72e+00 bond pdb=" CB PRO 2 49 " pdb=" CG PRO 2 49 " ideal model delta sigma weight residual 1.492 1.574 -0.082 5.00e-02 4.00e+02 2.70e+00 ... (remaining 55148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 74517 2.51 - 5.02: 995 5.02 - 7.53: 109 7.53 - 10.04: 56 10.04 - 12.55: 14 Bond angle restraints: 75691 Sorted by residual: angle pdb=" C VAL e 101 " pdb=" N ASN e 102 " pdb=" CA ASN e 102 " ideal model delta sigma weight residual 121.54 129.69 -8.15 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL K 101 " pdb=" N ASN K 102 " pdb=" CA ASN K 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL W 101 " pdb=" N ASN W 102 " pdb=" CA ASN W 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL 2 101 " pdb=" N ASN 2 102 " pdb=" CA ASN 2 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 angle pdb=" C VAL E 101 " pdb=" N ASN E 102 " pdb=" CA ASN E 102 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.81e+01 ... (remaining 75686 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 27152 17.99 - 35.98: 3445 35.98 - 53.97: 882 53.97 - 71.96: 91 71.96 - 89.95: 42 Dihedral angle restraints: 31612 sinusoidal: 11641 harmonic: 19971 Sorted by residual: dihedral pdb=" CA PRO 2 49 " pdb=" C PRO 2 49 " pdb=" N THR 2 50 " pdb=" CA THR 2 50 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO e 49 " pdb=" C PRO e 49 " pdb=" N THR e 50 " pdb=" CA THR e 50 " ideal model delta harmonic sigma weight residual 180.00 157.57 22.43 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PRO E 49 " pdb=" C PRO E 49 " pdb=" N THR E 50 " pdb=" CA THR E 50 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 ... (remaining 31609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 7256 0.054 - 0.107: 1555 0.107 - 0.161: 190 0.161 - 0.215: 22 0.215 - 0.269: 7 Chirality restraints: 9030 Sorted by residual: chirality pdb=" CG LEU S 59 " pdb=" CB LEU S 59 " pdb=" CD1 LEU S 59 " pdb=" CD2 LEU S 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CG LEU A 59 " pdb=" CB LEU A 59 " pdb=" CD1 LEU A 59 " pdb=" CD2 LEU A 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU G 59 " pdb=" CB LEU G 59 " pdb=" CD1 LEU G 59 " pdb=" CD2 LEU G 59 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 9027 not shown) Planarity restraints: 9247 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 48 " -0.077 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO Q 49 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO Q 49 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO Q 49 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 8 48 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO 8 49 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO 8 49 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO 8 49 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU K 48 " -0.076 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO K 49 " 0.199 5.00e-02 4.00e+02 pdb=" CA PRO K 49 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO K 49 " -0.062 5.00e-02 4.00e+02 ... (remaining 9244 not shown) Histogram of nonbonded interaction distances: 0.14 - 1.09: 98 1.09 - 2.04: 392 2.04 - 2.99: 31344 2.99 - 3.95: 148310 3.95 - 4.90: 260983 Warning: very small nonbonded interaction distances. Nonbonded interactions: 441127 Sorted by model distance: nonbonded pdb=" CE MET X1214 " pdb=" CG PHE 2 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET 91214 " pdb=" CG PHE e 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET 31214 " pdb=" CG PHE 8 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET R1214 " pdb=" CG PHE W 173 " model vdw 0.137 3.680 nonbonded pdb=" CE MET F1214 " pdb=" CG PHE K 173 " model vdw 0.137 3.680 ... (remaining 441122 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '0' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain '1' selection = chain '7' selection = chain 'D' selection = chain 'J' selection = chain 'P' selection = chain 'V' selection = chain 'd' } ncs_group { reference = chain '2' selection = chain '8' selection = chain 'E' selection = chain 'K' selection = chain 'Q' selection = chain 'W' selection = chain 'e' } ncs_group { reference = chain '3' selection = chain '9' selection = chain 'F' selection = chain 'L' selection = chain 'R' selection = chain 'X' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.490 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 78.500 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 0.083 55153 Z= 0.220 Angle : 0.711 12.554 75691 Z= 0.351 Chirality : 0.043 0.269 9030 Planarity : 0.006 0.115 9247 Dihedral : 16.854 89.946 18788 Min Nonbonded Distance : 0.137 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.73 % Favored : 94.64 % Rotamer: Outliers : 0.56 % Allowed : 34.17 % Favored : 65.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.10), residues: 6664 helix: 1.50 (0.08), residues: 4116 sheet: -0.23 (0.20), residues: 609 loop : -2.21 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 82 HIS 0.002 0.001 HIS X1111 PHE 0.013 0.001 PHE f 647 TYR 0.021 0.001 TYR R 667 ARG 0.003 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1491 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1458 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LEU cc_start: 0.9231 (mp) cc_final: 0.8871 (pt) REVERT: F 977 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8331 (mmtt) REVERT: H 81 MET cc_start: 0.7876 (ptt) cc_final: 0.7580 (ptt) REVERT: J 39 GLN cc_start: 0.8724 (tt0) cc_final: 0.8497 (tt0) REVERT: J 46 ILE cc_start: 0.9050 (pt) cc_final: 0.8791 (mm) REVERT: K 46 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8431 (tm-30) REVERT: K 148 MET cc_start: 0.8952 (tpp) cc_final: 0.8680 (tpp) REVERT: L 649 MET cc_start: 0.8491 (tpp) cc_final: 0.8156 (mmm) REVERT: L 914 MET cc_start: 0.7895 (mmm) cc_final: 0.7501 (mmm) REVERT: L 977 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8326 (mmtp) REVERT: M 32 LEU cc_start: 0.9096 (mp) cc_final: 0.8747 (pt) REVERT: M 82 TYR cc_start: 0.5786 (m-80) cc_final: 0.5512 (m-80) REVERT: N 82 TYR cc_start: 0.7169 (m-80) cc_final: 0.6873 (m-80) REVERT: P 39 GLN cc_start: 0.8745 (tt0) cc_final: 0.8542 (tt0) REVERT: P 107 MET cc_start: 0.7564 (mtt) cc_final: 0.7128 (mtt) REVERT: Q 90 ASN cc_start: 0.8606 (t0) cc_final: 0.8357 (t0) REVERT: R 649 MET cc_start: 0.8457 (tpp) cc_final: 0.7950 (tpp) REVERT: R 914 MET cc_start: 0.8112 (mmm) cc_final: 0.7894 (mmm) REVERT: R 917 TYR cc_start: 0.8493 (t80) cc_final: 0.7750 (t80) REVERT: R 977 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8433 (mmtp) REVERT: R 1187 SER cc_start: 0.8363 (m) cc_final: 0.7815 (p) REVERT: R 1205 TYR cc_start: 0.8942 (t80) cc_final: 0.8571 (t80) REVERT: S 32 LEU cc_start: 0.9104 (mp) cc_final: 0.8652 (pt) REVERT: S 77 LEU cc_start: 0.8204 (tt) cc_final: 0.7954 (mm) REVERT: T 82 TYR cc_start: 0.7255 (m-80) cc_final: 0.6938 (m-80) REVERT: W 44 GLU cc_start: 0.8120 (tp30) cc_final: 0.7188 (tp30) REVERT: W 46 GLN cc_start: 0.8984 (tm-30) cc_final: 0.8358 (tm-30) REVERT: W 104 ASN cc_start: 0.8720 (t0) cc_final: 0.8403 (t0) REVERT: X 649 MET cc_start: 0.8645 (tpp) cc_final: 0.8197 (tpp) REVERT: X 917 TYR cc_start: 0.8451 (t80) cc_final: 0.8182 (t80) REVERT: X 933 MET cc_start: 0.5897 (ttt) cc_final: 0.5570 (ttt) REVERT: X 977 LYS cc_start: 0.8970 (mmtt) cc_final: 0.8584 (mmtt) REVERT: X 1043 ASN cc_start: 0.7940 (m-40) cc_final: 0.7673 (m110) REVERT: X 1099 LEU cc_start: 0.8681 (mt) cc_final: 0.8475 (mt) REVERT: Y 32 LEU cc_start: 0.9150 (mp) cc_final: 0.8929 (pt) REVERT: Z 82 TYR cc_start: 0.7040 (m-80) cc_final: 0.6697 (m-80) REVERT: 2 90 ASN cc_start: 0.8749 (t0) cc_final: 0.8419 (t0) REVERT: 2 192 ILE cc_start: 0.9251 (mm) cc_final: 0.9030 (mm) REVERT: 3 45 LEU cc_start: 0.8868 (tp) cc_final: 0.8651 (mt) REVERT: 3 601 GLU cc_start: 0.8649 (tp30) cc_final: 0.8368 (tp30) REVERT: 3 649 MET cc_start: 0.8534 (tpp) cc_final: 0.8196 (mmm) REVERT: 3 977 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8572 (mmtt) REVERT: 4 32 LEU cc_start: 0.9170 (mp) cc_final: 0.8767 (pt) REVERT: 5 22 LEU cc_start: 0.8524 (mp) cc_final: 0.7113 (mp) REVERT: 5 77 LEU cc_start: 0.8482 (mt) cc_final: 0.8279 (pp) REVERT: 5 82 TYR cc_start: 0.7210 (m-80) cc_final: 0.6905 (m-80) REVERT: 6 39 GLU cc_start: 0.8419 (tt0) cc_final: 0.8070 (tt0) REVERT: 7 39 GLN cc_start: 0.8713 (tt0) cc_final: 0.8337 (tt0) REVERT: 8 90 ASN cc_start: 0.8769 (t0) cc_final: 0.8515 (t0) REVERT: 9 58 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7447 (tm-30) REVERT: 9 108 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7092 (ttp-110) REVERT: 9 1099 LEU cc_start: 0.8669 (mt) cc_final: 0.8303 (mt) REVERT: 9 1205 TYR cc_start: 0.8907 (t80) cc_final: 0.8610 (t80) REVERT: b 82 TYR cc_start: 0.7033 (m-80) cc_final: 0.6723 (m-80) REVERT: d 39 GLN cc_start: 0.8719 (tt0) cc_final: 0.8384 (tt0) REVERT: e 148 MET cc_start: 0.8801 (tpp) cc_final: 0.8596 (tpp) REVERT: f 58 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7485 (tm-30) REVERT: f 917 TYR cc_start: 0.8445 (t80) cc_final: 0.8164 (t80) REVERT: f 1082 GLN cc_start: 0.7638 (pp30) cc_final: 0.7355 (pp30) REVERT: f 1099 LEU cc_start: 0.8406 (mt) cc_final: 0.8014 (mt) REVERT: f 1169 MET cc_start: 0.7889 (mtm) cc_final: 0.7605 (mtm) REVERT: f 1205 TYR cc_start: 0.8837 (t80) cc_final: 0.8319 (t80) outliers start: 33 outliers final: 15 residues processed: 1473 average time/residue: 0.4626 time to fit residues: 1195.5235 Evaluate side-chains 1346 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1331 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain K residue 166 ILE Chi-restraints excluded: chain L residue 1113 ILE Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain R residue 599 GLU Chi-restraints excluded: chain R residue 1113 ILE Chi-restraints excluded: chain V residue 33 ASN Chi-restraints excluded: chain X residue 599 GLU Chi-restraints excluded: chain 1 residue 33 ASN Chi-restraints excluded: chain 3 residue 1113 ILE Chi-restraints excluded: chain 7 residue 33 ASN Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain f residue 1113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 549 optimal weight: 0.0570 chunk 493 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 168 optimal weight: 0.9980 chunk 332 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 510 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 310 optimal weight: 2.9990 chunk 379 optimal weight: 4.9990 chunk 591 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 39 GLN D 43 GLN E 113 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1166 ASN L 97 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1166 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN R 57 HIS R 97 GLN ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1166 ASN X 57 HIS X 97 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X1166 ASN 3 97 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31043 ASN ** 31136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 31166 ASN 8 34 ASN 9 64 ASN 9 97 GLN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 91166 ASN ** a 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 43 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 97 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f1166 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 55153 Z= 0.269 Angle : 0.732 11.263 75691 Z= 0.373 Chirality : 0.046 0.436 9030 Planarity : 0.006 0.115 9247 Dihedral : 4.915 30.528 7276 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.31 % Favored : 94.06 % Rotamer: Outliers : 5.13 % Allowed : 30.12 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 6664 helix: 1.44 (0.08), residues: 4137 sheet: -0.31 (0.20), residues: 609 loop : -2.33 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 7 59 HIS 0.003 0.001 HIS 9 57 PHE 0.044 0.002 PHE K 177 TYR 0.031 0.001 TYR V 65 ARG 0.006 0.001 ARG d 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1430 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 ILE cc_start: 0.9071 (tt) cc_final: 0.8587 (pt) REVERT: F 58 GLU cc_start: 0.8297 (tm-30) cc_final: 0.7958 (tm-30) REVERT: F 673 TRP cc_start: 0.8139 (m-10) cc_final: 0.7905 (m-10) REVERT: F 977 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8417 (mmtp) REVERT: F 980 LEU cc_start: 0.8881 (mp) cc_final: 0.8645 (mp) REVERT: H 81 MET cc_start: 0.7771 (ptt) cc_final: 0.7434 (ptt) REVERT: I 77 LEU cc_start: 0.7264 (tt) cc_final: 0.6978 (tt) REVERT: J 39 GLN cc_start: 0.8637 (tt0) cc_final: 0.8398 (tt0) REVERT: K 46 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8103 (tm-30) REVERT: K 52 ASN cc_start: 0.8791 (m-40) cc_final: 0.8416 (m-40) REVERT: K 83 TYR cc_start: 0.7183 (m-80) cc_final: 0.6877 (m-80) REVERT: K 148 MET cc_start: 0.9006 (tpp) cc_final: 0.8662 (tpp) REVERT: K 149 LEU cc_start: 0.8722 (tp) cc_final: 0.8491 (tp) REVERT: K 176 MET cc_start: 0.7879 (OUTLIER) cc_final: 0.7563 (ttm) REVERT: L 73 LYS cc_start: 0.8647 (mttp) cc_final: 0.7787 (mmtp) REVERT: L 914 MET cc_start: 0.8003 (mmm) cc_final: 0.7694 (mmm) REVERT: L 933 MET cc_start: 0.6953 (ttt) cc_final: 0.6691 (ttt) REVERT: L 1114 MET cc_start: 0.8280 (ppp) cc_final: 0.7962 (tmm) REVERT: M 60 ASN cc_start: 0.8295 (m110) cc_final: 0.7906 (m110) REVERT: M 82 TYR cc_start: 0.5893 (m-80) cc_final: 0.5551 (m-80) REVERT: N 23 PHE cc_start: 0.6804 (m-80) cc_final: 0.6306 (m-80) REVERT: N 82 TYR cc_start: 0.7058 (m-80) cc_final: 0.6726 (m-80) REVERT: P 5 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8852 (mm) REVERT: P 43 GLN cc_start: 0.8341 (mt0) cc_final: 0.8124 (mt0) REVERT: Q 149 LEU cc_start: 0.8771 (tp) cc_final: 0.8448 (tp) REVERT: R 35 GLU cc_start: 0.8387 (tt0) cc_final: 0.7847 (tt0) REVERT: R 73 LYS cc_start: 0.8618 (mttp) cc_final: 0.7414 (mmtp) REVERT: R 597 TYR cc_start: 0.7952 (OUTLIER) cc_final: 0.6849 (m-80) REVERT: R 917 TYR cc_start: 0.8638 (t80) cc_final: 0.8113 (t80) REVERT: R 977 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8611 (mmtp) REVERT: R 979 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8567 (mt-10) REVERT: R 980 LEU cc_start: 0.9027 (mp) cc_final: 0.8715 (mp) REVERT: R 1187 SER cc_start: 0.8467 (m) cc_final: 0.7831 (p) REVERT: R 1188 ARG cc_start: 0.8475 (mmt180) cc_final: 0.8182 (mpt180) REVERT: R 1205 TYR cc_start: 0.8947 (t80) cc_final: 0.8583 (t80) REVERT: S 77 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8004 (mm) REVERT: T 82 TYR cc_start: 0.6914 (m-80) cc_final: 0.6565 (m-80) REVERT: V 70 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9012 (mp) REVERT: W 46 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8658 (tm-30) REVERT: X 80 PRO cc_start: 0.9454 (Cg_exo) cc_final: 0.9252 (Cg_endo) REVERT: X 601 GLU cc_start: 0.8654 (tp30) cc_final: 0.7471 (tp30) REVERT: X 933 MET cc_start: 0.6286 (ttt) cc_final: 0.5819 (ttt) REVERT: X 977 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8403 (mmtt) REVERT: X 1004 ARG cc_start: 0.7479 (ptp90) cc_final: 0.7028 (ptt-90) REVERT: X 1025 GLN cc_start: 0.7782 (mt0) cc_final: 0.7582 (pt0) REVERT: X 1045 TRP cc_start: 0.8418 (m100) cc_final: 0.8143 (m100) REVERT: Y 64 LEU cc_start: 0.7424 (tt) cc_final: 0.7217 (tt) REVERT: Z 23 PHE cc_start: 0.7070 (m-80) cc_final: 0.6620 (m-80) REVERT: Z 82 TYR cc_start: 0.7176 (m-80) cc_final: 0.6949 (m-80) REVERT: 0 33 LEU cc_start: 0.7879 (pp) cc_final: 0.7679 (pp) REVERT: 1 5 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8629 (mm) REVERT: 2 90 ASN cc_start: 0.8804 (t0) cc_final: 0.8400 (t0) REVERT: 2 199 ARG cc_start: 0.6987 (ttt180) cc_final: 0.6772 (ttt180) REVERT: 3 108 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7127 (ttm110) REVERT: 3 606 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8214 (mm) REVERT: 3 977 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8554 (mmtt) REVERT: 3 1003 GLN cc_start: 0.8522 (mt0) cc_final: 0.8029 (mt0) REVERT: 3 1114 MET cc_start: 0.8455 (ppp) cc_final: 0.8202 (ppp) REVERT: 5 23 PHE cc_start: 0.7175 (m-80) cc_final: 0.6729 (m-80) REVERT: 5 82 TYR cc_start: 0.7005 (m-80) cc_final: 0.6721 (m-80) REVERT: 6 39 GLU cc_start: 0.8395 (tt0) cc_final: 0.8024 (tt0) REVERT: 7 39 GLN cc_start: 0.8694 (tt0) cc_final: 0.8459 (tt0) REVERT: 7 70 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8931 (mp) REVERT: 7 117 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8473 (tp) REVERT: 8 52 ASN cc_start: 0.8815 (m-40) cc_final: 0.8562 (m-40) REVERT: 8 55 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7955 (mm110) REVERT: 8 90 ASN cc_start: 0.8836 (t0) cc_final: 0.8561 (t0) REVERT: 8 199 ARG cc_start: 0.7321 (ttt180) cc_final: 0.7103 (ttt180) REVERT: 9 58 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7434 (tm-30) REVERT: 9 108 ARG cc_start: 0.7646 (mtm-85) cc_final: 0.7191 (ttp-110) REVERT: 9 606 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8346 (mm) REVERT: 9 673 TRP cc_start: 0.8247 (m-10) cc_final: 0.7800 (m-10) REVERT: 9 933 MET cc_start: 0.6210 (ttt) cc_final: 0.5889 (ttt) REVERT: 9 979 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8497 (mt-10) REVERT: 9 980 LEU cc_start: 0.8983 (mp) cc_final: 0.8679 (mp) REVERT: 9 990 ASN cc_start: 0.7681 (t0) cc_final: 0.7230 (t0) REVERT: 9 1026 MET cc_start: 0.8667 (ttp) cc_final: 0.8140 (ttt) REVERT: 9 1045 TRP cc_start: 0.8482 (m100) cc_final: 0.8241 (m100) REVERT: 9 1099 LEU cc_start: 0.8617 (mt) cc_final: 0.8170 (mt) REVERT: 9 1175 ILE cc_start: 0.9118 (mt) cc_final: 0.8875 (mt) REVERT: 9 1205 TYR cc_start: 0.8947 (t80) cc_final: 0.8625 (t80) REVERT: b 22 LEU cc_start: 0.8574 (mp) cc_final: 0.7577 (mp) REVERT: b 77 LEU cc_start: 0.8340 (mt) cc_final: 0.7964 (pp) REVERT: b 82 TYR cc_start: 0.6959 (m-80) cc_final: 0.6632 (m-80) REVERT: d 71 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8472 (pt) REVERT: f 58 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7326 (tm-30) REVERT: f 108 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7123 (ttp-170) REVERT: f 606 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8023 (mm) REVERT: f 620 MET cc_start: 0.8444 (tpp) cc_final: 0.8235 (mtt) REVERT: f 980 LEU cc_start: 0.9121 (mp) cc_final: 0.8869 (mp) REVERT: f 992 THR cc_start: 0.9031 (m) cc_final: 0.8773 (p) REVERT: f 1082 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7334 (pp30) REVERT: f 1099 LEU cc_start: 0.8310 (mt) cc_final: 0.8012 (mt) outliers start: 301 outliers final: 174 residues processed: 1589 average time/residue: 0.4637 time to fit residues: 1286.0219 Evaluate side-chains 1528 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1341 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 33 ASN Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 982 SER Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 598 TYR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 924 THR Chi-restraints excluded: chain R residue 1033 TRP Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 33 ASN Chi-restraints excluded: chain V residue 70 LEU Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 33 ASN Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 152 MET Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 110 GLU Chi-restraints excluded: chain 3 residue 598 TYR Chi-restraints excluded: chain 3 residue 606 LEU Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 914 MET Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 3 residue 1225 MET Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 81 MET Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 33 ASN Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 98 VAL Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 117 ILE Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 924 THR Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 53 THR Chi-restraints excluded: chain e residue 61 VAL Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 154 VAL Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 658 THR Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 328 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 492 optimal weight: 1.9990 chunk 402 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 592 optimal weight: 1.9990 chunk 639 optimal weight: 5.9990 chunk 527 optimal weight: 4.9990 chunk 587 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 475 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 33 ASN D 39 GLN ** E 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 43 GLN L 64 ASN L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 98 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 64 ASN 91135 ASN ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 43 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 55153 Z= 0.340 Angle : 0.717 9.226 75691 Z= 0.366 Chirality : 0.046 0.372 9030 Planarity : 0.006 0.116 9247 Dihedral : 4.909 28.478 7257 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.63 % Allowed : 4.94 % Favored : 94.43 % Rotamer: Outliers : 7.49 % Allowed : 28.20 % Favored : 64.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 6664 helix: 1.57 (0.08), residues: 4102 sheet: -0.43 (0.19), residues: 672 loop : -2.26 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L1045 HIS 0.007 0.002 HIS R 57 PHE 0.031 0.002 PHE Q 177 TYR 0.030 0.002 TYR V 65 ARG 0.006 0.001 ARG V 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 440 poor density : 1398 time to evaluate : 4.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8345 (t) cc_final: 0.8144 (t) REVERT: B 23 PHE cc_start: 0.7360 (m-80) cc_final: 0.6896 (m-80) REVERT: B 82 TYR cc_start: 0.6846 (m-80) cc_final: 0.6542 (m-80) REVERT: E 203 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7769 (mttt) REVERT: F 588 TRP cc_start: 0.7247 (OUTLIER) cc_final: 0.4908 (m100) REVERT: F 619 GLN cc_start: 0.8479 (mt0) cc_final: 0.8218 (mt0) REVERT: F 977 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8440 (mmtp) REVERT: H 77 LEU cc_start: 0.8571 (mt) cc_final: 0.8173 (tt) REVERT: H 81 MET cc_start: 0.7803 (ptt) cc_final: 0.7317 (ptt) REVERT: H 82 TYR cc_start: 0.7090 (m-80) cc_final: 0.6872 (m-80) REVERT: I 77 LEU cc_start: 0.7252 (tt) cc_final: 0.6924 (tt) REVERT: K 46 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8689 (tm-30) REVERT: K 176 MET cc_start: 0.7905 (mtp) cc_final: 0.7547 (ttm) REVERT: K 203 LYS cc_start: 0.8306 (mtpt) cc_final: 0.8083 (ttmt) REVERT: L 649 MET cc_start: 0.8531 (tpp) cc_final: 0.8134 (mmm) REVERT: L 914 MET cc_start: 0.8030 (mmm) cc_final: 0.7664 (mmm) REVERT: L 933 MET cc_start: 0.7054 (ttt) cc_final: 0.6840 (ttt) REVERT: L 1020 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.4071 (m-80) REVERT: L 1114 MET cc_start: 0.8374 (ppp) cc_final: 0.8048 (tmm) REVERT: L 1203 ILE cc_start: 0.9070 (mt) cc_final: 0.8861 (mt) REVERT: M 60 ASN cc_start: 0.8161 (m110) cc_final: 0.7942 (m110) REVERT: N 23 PHE cc_start: 0.6946 (m-80) cc_final: 0.6297 (m-80) REVERT: N 82 TYR cc_start: 0.7202 (m-80) cc_final: 0.6934 (m-80) REVERT: P 43 GLN cc_start: 0.8288 (mt0) cc_final: 0.8073 (mt0) REVERT: R 35 GLU cc_start: 0.8514 (tt0) cc_final: 0.7942 (tt0) REVERT: R 73 LYS cc_start: 0.8661 (mttp) cc_final: 0.7357 (mmtp) REVERT: R 597 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: R 649 MET cc_start: 0.8320 (mmm) cc_final: 0.8113 (mmm) REVERT: R 914 MET cc_start: 0.8275 (mmm) cc_final: 0.8053 (mmm) REVERT: R 933 MET cc_start: 0.7367 (ttt) cc_final: 0.7074 (ttt) REVERT: R 977 LYS cc_start: 0.8815 (mmtt) cc_final: 0.8442 (mmtp) REVERT: R 979 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8525 (mt-10) REVERT: R 980 LEU cc_start: 0.9199 (mp) cc_final: 0.8913 (mp) REVERT: R 1187 SER cc_start: 0.8451 (m) cc_final: 0.7896 (p) REVERT: R 1205 TYR cc_start: 0.9018 (t80) cc_final: 0.8587 (t80) REVERT: S 81 MET cc_start: 0.8017 (mmp) cc_final: 0.7585 (mmm) REVERT: T 23 PHE cc_start: 0.6981 (m-80) cc_final: 0.6479 (m-80) REVERT: T 82 TYR cc_start: 0.7002 (m-80) cc_final: 0.6761 (m-80) REVERT: W 44 GLU cc_start: 0.8278 (tp30) cc_final: 0.7954 (tp30) REVERT: W 83 TYR cc_start: 0.7584 (m-80) cc_final: 0.6851 (m-80) REVERT: X 80 PRO cc_start: 0.9480 (Cg_exo) cc_final: 0.9264 (Cg_endo) REVERT: X 601 GLU cc_start: 0.8738 (tp30) cc_final: 0.7530 (tp30) REVERT: X 649 MET cc_start: 0.8502 (tpp) cc_final: 0.8263 (tpp) REVERT: X 933 MET cc_start: 0.6801 (ttt) cc_final: 0.6244 (ttt) REVERT: X 977 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8438 (mmtt) REVERT: X 1045 TRP cc_start: 0.8441 (m100) cc_final: 0.8185 (m100) REVERT: Z 23 PHE cc_start: 0.7262 (m-80) cc_final: 0.6752 (m-80) REVERT: Z 77 LEU cc_start: 0.8570 (mt) cc_final: 0.8076 (pp) REVERT: Z 82 TYR cc_start: 0.7371 (m-80) cc_final: 0.7125 (m-80) REVERT: 1 92 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8533 (mt) REVERT: 2 186 MET cc_start: 0.8462 (ttp) cc_final: 0.8233 (ttp) REVERT: 2 199 ARG cc_start: 0.6950 (ttt180) cc_final: 0.6730 (ttt180) REVERT: 3 606 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8299 (mm) REVERT: 3 977 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8589 (mmtt) REVERT: 3 983 GLU cc_start: 0.7575 (tp30) cc_final: 0.7187 (tp30) REVERT: 3 1003 GLN cc_start: 0.8716 (mt0) cc_final: 0.8329 (mt0) REVERT: 3 1020 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.3508 (m-80) REVERT: 3 1045 TRP cc_start: 0.8391 (m100) cc_final: 0.8021 (m100) REVERT: 3 1114 MET cc_start: 0.8533 (ppp) cc_final: 0.8251 (ppp) REVERT: 3 1170 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8763 (tp) REVERT: 5 23 PHE cc_start: 0.7248 (m-80) cc_final: 0.6624 (m-80) REVERT: 5 77 LEU cc_start: 0.8498 (mt) cc_final: 0.7965 (pp) REVERT: 5 82 TYR cc_start: 0.7300 (m-80) cc_final: 0.7077 (m-80) REVERT: 6 39 GLU cc_start: 0.8296 (tt0) cc_final: 0.7865 (tt0) REVERT: 7 39 GLN cc_start: 0.8667 (tt0) cc_final: 0.8419 (tt0) REVERT: 7 70 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9010 (mp) REVERT: 7 92 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8445 (mm) REVERT: 7 117 ILE cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (tp) REVERT: 8 52 ASN cc_start: 0.9053 (m-40) cc_final: 0.8816 (m-40) REVERT: 8 90 ASN cc_start: 0.8767 (t0) cc_final: 0.8474 (t0) REVERT: 9 58 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7565 (tm-30) REVERT: 9 80 PRO cc_start: 0.9586 (Cg_exo) cc_final: 0.9305 (Cg_endo) REVERT: 9 606 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8402 (mm) REVERT: 9 673 TRP cc_start: 0.8248 (m-10) cc_final: 0.7763 (m-10) REVERT: 9 933 MET cc_start: 0.6488 (ttt) cc_final: 0.6231 (ttp) REVERT: 9 979 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8496 (mt-10) REVERT: 9 980 LEU cc_start: 0.9210 (mp) cc_final: 0.8973 (mp) REVERT: 9 1020 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.3485 (m-80) REVERT: 9 1026 MET cc_start: 0.8687 (ttp) cc_final: 0.8158 (ttt) REVERT: 9 1099 LEU cc_start: 0.8594 (mt) cc_final: 0.8154 (mt) REVERT: 9 1125 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7576 (p0) REVERT: 9 1205 TYR cc_start: 0.9005 (t80) cc_final: 0.8650 (t80) REVERT: b 22 LEU cc_start: 0.8578 (mp) cc_final: 0.8307 (mp) REVERT: b 77 LEU cc_start: 0.8435 (mt) cc_final: 0.7943 (tt) REVERT: b 82 TYR cc_start: 0.6960 (m-80) cc_final: 0.6722 (m-80) REVERT: c 77 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6738 (tt) REVERT: d 71 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8536 (pt) REVERT: d 107 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7391 (mtt) REVERT: e 44 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: e 83 TYR cc_start: 0.7433 (m-80) cc_final: 0.6506 (m-80) REVERT: f 58 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7438 (tm-30) REVERT: f 588 TRP cc_start: 0.6950 (OUTLIER) cc_final: 0.5828 (m100) REVERT: f 606 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8346 (mm) REVERT: f 1003 GLN cc_start: 0.8671 (mt0) cc_final: 0.8468 (mt0) REVERT: f 1099 LEU cc_start: 0.8279 (mt) cc_final: 0.7566 (mt) outliers start: 440 outliers final: 294 residues processed: 1623 average time/residue: 0.5101 time to fit residues: 1461.0577 Evaluate side-chains 1653 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 313 poor density : 1340 time to evaluate : 4.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 632 LEU Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 982 SER Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1030 THR Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1098 VAL Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1212 THR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 80 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 78 SER Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain L residue 111 TYR Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 657 ILE Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1091 THR Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1212 THR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain O residue 57 THR Chi-restraints excluded: chain P residue 22 SER Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 54 SER Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 83 TYR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 596 ASN Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 657 ILE Chi-restraints excluded: chain R residue 924 THR Chi-restraints excluded: chain R residue 1033 TRP Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1085 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 33 ASN Chi-restraints excluded: chain V residue 54 SER Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 98 GLN Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 657 ILE Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1046 SER Chi-restraints excluded: chain X residue 1085 VAL Chi-restraints excluded: chain X residue 1098 VAL Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1212 THR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain X residue 1225 MET Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Z residue 72 ILE Chi-restraints excluded: chain 0 residue 18 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 22 SER Chi-restraints excluded: chain 1 residue 54 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 119 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 174 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 98 GLN Chi-restraints excluded: chain 3 residue 110 GLU Chi-restraints excluded: chain 3 residue 111 TYR Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 606 LEU Chi-restraints excluded: chain 3 residue 644 LEU Chi-restraints excluded: chain 3 residue 657 ILE Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1091 THR Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1170 LEU Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 35 VAL Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 6 residue 57 THR Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 64 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 33 ASN Chi-restraints excluded: chain 7 residue 54 SER Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 117 ILE Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 78 SER Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 8 residue 174 ILE Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 78 ILE Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 84 SER Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 657 ILE Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1091 THR Chi-restraints excluded: chain 9 residue 1098 VAL Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1181 MET Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1212 THR Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 31 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 58 LEU Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 107 MET Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 61 VAL Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 78 SER Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 657 ILE Chi-restraints excluded: chain f residue 658 THR Chi-restraints excluded: chain f residue 999 SER Chi-restraints excluded: chain f residue 1033 TRP Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1162 THR Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 585 optimal weight: 0.0770 chunk 445 optimal weight: 1.9990 chunk 307 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 chunk 282 optimal weight: 50.0000 chunk 397 optimal weight: 0.7980 chunk 594 optimal weight: 1.9990 chunk 629 optimal weight: 0.9990 chunk 310 optimal weight: 0.2980 chunk 563 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN K 55 GLN L 64 ASN L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 ASN Q 55 GLN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 616 GLN ** X1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 31136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 55 GLN 9 64 ASN 91135 ASN d 39 GLN e 55 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 55153 Z= 0.227 Angle : 0.678 12.536 75691 Z= 0.343 Chirality : 0.044 0.418 9030 Planarity : 0.006 0.113 9247 Dihedral : 4.857 27.760 7255 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.65 % Allowed : 4.92 % Favored : 94.43 % Rotamer: Outliers : 7.13 % Allowed : 29.07 % Favored : 63.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.10), residues: 6664 helix: 1.69 (0.08), residues: 4095 sheet: -0.49 (0.19), residues: 672 loop : -2.25 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 48 HIS 0.006 0.001 HIS R 57 PHE 0.030 0.002 PHE K 173 TYR 0.023 0.001 TYR f 667 ARG 0.005 0.000 ARG R1233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1816 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 419 poor density : 1397 time to evaluate : 4.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7981 (mm) REVERT: A 62 VAL cc_start: 0.8367 (t) cc_final: 0.8161 (t) REVERT: B 82 TYR cc_start: 0.6838 (m-80) cc_final: 0.6606 (m-80) REVERT: D 108 PHE cc_start: 0.7639 (m-10) cc_final: 0.6932 (m-10) REVERT: E 148 MET cc_start: 0.8758 (tpp) cc_final: 0.8517 (mmm) REVERT: E 172 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8253 (tt) REVERT: E 203 LYS cc_start: 0.7914 (mtpt) cc_final: 0.7554 (ttmt) REVERT: F 35 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8246 (tt0) REVERT: F 588 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.4759 (m100) REVERT: F 977 LYS cc_start: 0.8791 (mmtt) cc_final: 0.8501 (mmtp) REVERT: F 980 LEU cc_start: 0.8973 (mp) cc_final: 0.8731 (mp) REVERT: F 1181 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7795 (mmt) REVERT: F 1205 TYR cc_start: 0.8925 (t80) cc_final: 0.8544 (t80) REVERT: F 1225 MET cc_start: 0.9343 (mmp) cc_final: 0.8998 (mmp) REVERT: H 23 PHE cc_start: 0.7458 (m-80) cc_final: 0.7058 (m-80) REVERT: H 77 LEU cc_start: 0.8537 (mt) cc_final: 0.8159 (tt) REVERT: H 81 MET cc_start: 0.7884 (ptt) cc_final: 0.7416 (ptt) REVERT: I 77 LEU cc_start: 0.7168 (tt) cc_final: 0.6875 (tt) REVERT: K 46 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8638 (tm-30) REVERT: K 149 LEU cc_start: 0.8796 (tp) cc_final: 0.8595 (tp) REVERT: K 172 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8748 (tt) REVERT: K 176 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.7523 (ttm) REVERT: L 649 MET cc_start: 0.8499 (tpp) cc_final: 0.8102 (mmm) REVERT: L 914 MET cc_start: 0.7983 (mmm) cc_final: 0.7661 (mmm) REVERT: L 917 TYR cc_start: 0.8458 (t80) cc_final: 0.8032 (t80) REVERT: L 933 MET cc_start: 0.7463 (ttt) cc_final: 0.7221 (ttt) REVERT: L 983 GLU cc_start: 0.8080 (tp30) cc_final: 0.7787 (tp30) REVERT: L 1000 ARG cc_start: 0.8746 (mmm160) cc_final: 0.8540 (mmm160) REVERT: L 1045 TRP cc_start: 0.8641 (m100) cc_final: 0.8283 (m100) REVERT: L 1114 MET cc_start: 0.8282 (ppp) cc_final: 0.8018 (tmm) REVERT: L 1203 ILE cc_start: 0.9020 (mt) cc_final: 0.8810 (mt) REVERT: N 23 PHE cc_start: 0.6817 (m-80) cc_final: 0.6299 (m-80) REVERT: N 82 TYR cc_start: 0.7119 (m-80) cc_final: 0.6851 (m-80) REVERT: P 43 GLN cc_start: 0.8146 (mt0) cc_final: 0.7939 (mt0) REVERT: Q 44 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7869 (mm-30) REVERT: Q 52 ASN cc_start: 0.9126 (m-40) cc_final: 0.8504 (m-40) REVERT: R 35 GLU cc_start: 0.8531 (tt0) cc_final: 0.7947 (tt0) REVERT: R 47 SER cc_start: 0.8851 (t) cc_final: 0.8140 (m) REVERT: R 73 LYS cc_start: 0.8694 (mttp) cc_final: 0.7427 (mmtp) REVERT: R 597 TYR cc_start: 0.8242 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: R 914 MET cc_start: 0.8225 (mmm) cc_final: 0.7960 (mmm) REVERT: R 977 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8388 (mmtp) REVERT: R 980 LEU cc_start: 0.9203 (mp) cc_final: 0.9003 (mt) REVERT: R 983 GLU cc_start: 0.7903 (tp30) cc_final: 0.7420 (tp30) REVERT: R 1187 SER cc_start: 0.8323 (m) cc_final: 0.7808 (p) REVERT: R 1205 TYR cc_start: 0.9010 (t80) cc_final: 0.8605 (t80) REVERT: T 82 TYR cc_start: 0.7067 (m-80) cc_final: 0.6800 (m-80) REVERT: W 83 TYR cc_start: 0.7577 (m-80) cc_final: 0.7069 (m-80) REVERT: W 172 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8630 (tt) REVERT: X 47 SER cc_start: 0.8518 (t) cc_final: 0.7805 (m) REVERT: X 51 THR cc_start: 0.6033 (OUTLIER) cc_final: 0.4359 (m) REVERT: X 601 GLU cc_start: 0.8544 (tp30) cc_final: 0.7271 (tp30) REVERT: X 933 MET cc_start: 0.6933 (ttt) cc_final: 0.6421 (ttt) REVERT: X 977 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8334 (mmtt) REVERT: X 995 SER cc_start: 0.8852 (m) cc_final: 0.8552 (m) REVERT: X 1078 TYR cc_start: 0.8299 (t80) cc_final: 0.7972 (t80) REVERT: Y 81 MET cc_start: 0.7838 (mmp) cc_final: 0.7565 (mmm) REVERT: Z 23 PHE cc_start: 0.6726 (m-80) cc_final: 0.6212 (m-80) REVERT: 1 20 MET cc_start: 0.9262 (mmt) cc_final: 0.9059 (mmm) REVERT: 1 92 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8092 (mm) REVERT: 2 44 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8222 (mm-30) REVERT: 2 52 ASN cc_start: 0.9024 (m-40) cc_final: 0.8605 (m-40) REVERT: 2 83 TYR cc_start: 0.7407 (m-80) cc_final: 0.6769 (m-80) REVERT: 2 90 ASN cc_start: 0.8744 (t0) cc_final: 0.8346 (t0) REVERT: 2 172 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8307 (tt) REVERT: 2 186 MET cc_start: 0.8281 (ttp) cc_final: 0.8019 (ttp) REVERT: 2 199 ARG cc_start: 0.6885 (ttt180) cc_final: 0.6684 (ttt180) REVERT: 3 51 THR cc_start: 0.4868 (OUTLIER) cc_final: 0.3541 (m) REVERT: 3 606 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8205 (mm) REVERT: 3 976 TYR cc_start: 0.8614 (p90) cc_final: 0.8291 (p90) REVERT: 3 977 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8516 (mmtt) REVERT: 3 983 GLU cc_start: 0.7567 (tp30) cc_final: 0.7218 (tp30) REVERT: 3 1000 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.7626 (mmm160) REVERT: 3 1003 GLN cc_start: 0.8676 (mt0) cc_final: 0.8285 (mt0) REVERT: 3 1192 ILE cc_start: 0.9311 (OUTLIER) cc_final: 0.9050 (mm) REVERT: 5 23 PHE cc_start: 0.7298 (m-80) cc_final: 0.6711 (m-80) REVERT: 5 82 TYR cc_start: 0.7252 (m-80) cc_final: 0.7045 (m-80) REVERT: 6 39 GLU cc_start: 0.8383 (tt0) cc_final: 0.7960 (tt0) REVERT: 7 39 GLN cc_start: 0.8627 (tt0) cc_final: 0.8409 (tt0) REVERT: 7 70 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8975 (mp) REVERT: 7 92 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8216 (mm) REVERT: 7 117 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8718 (tp) REVERT: 8 44 GLU cc_start: 0.8228 (tp30) cc_final: 0.7875 (tp30) REVERT: 8 52 ASN cc_start: 0.9004 (m-40) cc_final: 0.8698 (m-40) REVERT: 8 83 TYR cc_start: 0.7272 (m-80) cc_final: 0.6842 (m-80) REVERT: 8 90 ASN cc_start: 0.8834 (t0) cc_final: 0.8561 (t0) REVERT: 9 58 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7427 (tm-30) REVERT: 9 80 PRO cc_start: 0.9577 (Cg_exo) cc_final: 0.9311 (Cg_endo) REVERT: 9 108 ARG cc_start: 0.7439 (mtm-85) cc_final: 0.7141 (ttp-110) REVERT: 9 601 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: 9 606 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8389 (mm) REVERT: 9 673 TRP cc_start: 0.8313 (m-10) cc_final: 0.7771 (m-10) REVERT: 9 979 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8507 (mt-10) REVERT: 9 980 LEU cc_start: 0.9202 (mp) cc_final: 0.8963 (mp) REVERT: 9 1026 MET cc_start: 0.8581 (ttp) cc_final: 0.8119 (ttt) REVERT: 9 1099 LEU cc_start: 0.8585 (mt) cc_final: 0.8153 (mt) REVERT: 9 1125 ASN cc_start: 0.8193 (OUTLIER) cc_final: 0.7595 (p0) REVERT: 9 1175 ILE cc_start: 0.9163 (mt) cc_final: 0.8902 (mt) REVERT: 9 1205 TYR cc_start: 0.9021 (t80) cc_final: 0.8646 (t80) REVERT: b 22 LEU cc_start: 0.8507 (mp) cc_final: 0.8247 (mp) REVERT: b 77 LEU cc_start: 0.8374 (mt) cc_final: 0.7858 (tt) REVERT: d 71 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8413 (pt) REVERT: e 83 TYR cc_start: 0.7382 (m-80) cc_final: 0.6835 (m-80) REVERT: e 90 ASN cc_start: 0.8752 (t0) cc_final: 0.8529 (t0) REVERT: f 58 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7282 (tm-30) REVERT: f 108 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7125 (ttp-170) REVERT: f 588 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.5831 (m100) REVERT: f 601 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: f 606 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8288 (mm) REVERT: f 992 THR cc_start: 0.9055 (m) cc_final: 0.8827 (p) REVERT: f 1099 LEU cc_start: 0.8291 (mt) cc_final: 0.7575 (mt) REVERT: f 1205 TYR cc_start: 0.8702 (t80) cc_final: 0.8455 (t80) outliers start: 419 outliers final: 250 residues processed: 1631 average time/residue: 0.4627 time to fit residues: 1318.9125 Evaluate side-chains 1595 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1318 time to evaluate : 4.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 982 SER Chi-restraints excluded: chain F residue 998 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1181 MET Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 33 ASN Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain L residue 78 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 632 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 33 ASN Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 44 GLU Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 83 TYR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 657 ILE Chi-restraints excluded: chain R residue 1033 TRP Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 33 ASN Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 98 VAL Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain W residue 183 SER Chi-restraints excluded: chain W residue 190 LEU Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1024 LEU Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain X residue 1230 ILE Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 18 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 44 GLU Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 119 THR Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 606 LEU Chi-restraints excluded: chain 3 residue 644 LEU Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1192 ILE Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 33 ASN Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 98 VAL Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 117 ILE Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 84 SER Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 106 ILE Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 598 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 657 ILE Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 667 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 71 ILE Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 61 VAL Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 78 SER Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 658 THR Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 524 optimal weight: 2.9990 chunk 357 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 468 optimal weight: 50.0000 chunk 259 optimal weight: 0.8980 chunk 536 optimal weight: 6.9990 chunk 434 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 321 optimal weight: 0.8980 chunk 564 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN D 49 ASN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 43 GLN L 64 ASN L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 596 ASN ** R 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R1139 GLN V 49 ASN W 34 ASN X 98 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 616 GLN X1043 ASN 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 31136 GLN 7 49 ASN 9 64 ASN 91135 ASN ** 91136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN d 43 GLN e 113 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 97 GLN f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 55153 Z= 0.320 Angle : 0.716 12.959 75691 Z= 0.360 Chirality : 0.044 0.382 9030 Planarity : 0.006 0.115 9247 Dihedral : 4.855 26.474 7255 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.22 % Favored : 94.15 % Rotamer: Outliers : 8.12 % Allowed : 28.62 % Favored : 63.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.10), residues: 6664 helix: 1.65 (0.08), residues: 4081 sheet: -0.12 (0.21), residues: 588 loop : -2.31 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP 31045 HIS 0.006 0.001 HIS R 57 PHE 0.027 0.002 PHE K 158 TYR 0.025 0.001 TYR L 667 ARG 0.006 0.000 ARG 6 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1854 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 477 poor density : 1377 time to evaluate : 4.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8112 (mm) REVERT: A 77 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7627 (mt) REVERT: B 23 PHE cc_start: 0.7418 (m-80) cc_final: 0.6925 (m-80) REVERT: B 77 LEU cc_start: 0.8560 (mp) cc_final: 0.7935 (pp) REVERT: B 82 TYR cc_start: 0.6959 (m-80) cc_final: 0.6756 (m-80) REVERT: D 108 PHE cc_start: 0.7745 (m-10) cc_final: 0.7016 (m-10) REVERT: E 148 MET cc_start: 0.8707 (tpp) cc_final: 0.8296 (mmt) REVERT: E 172 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8574 (tt) REVERT: E 203 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7719 (ttmt) REVERT: F 35 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7907 (tt0) REVERT: F 45 LEU cc_start: 0.8744 (tp) cc_final: 0.8517 (tp) REVERT: F 588 TRP cc_start: 0.7111 (OUTLIER) cc_final: 0.4606 (m100) REVERT: F 601 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.6989 (tp30) REVERT: F 619 GLN cc_start: 0.8740 (mt0) cc_final: 0.7845 (mt0) REVERT: F 977 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8560 (mmtp) REVERT: F 1121 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7254 (mt-10) REVERT: F 1205 TYR cc_start: 0.8966 (t80) cc_final: 0.8569 (t80) REVERT: H 23 PHE cc_start: 0.7420 (m-80) cc_final: 0.7030 (m-80) REVERT: H 77 LEU cc_start: 0.8521 (mt) cc_final: 0.8215 (tt) REVERT: H 81 MET cc_start: 0.7781 (ptt) cc_final: 0.7399 (ptt) REVERT: I 77 LEU cc_start: 0.7175 (tt) cc_final: 0.6838 (tt) REVERT: K 46 GLN cc_start: 0.9118 (tm-30) cc_final: 0.7727 (tm-30) REVERT: L 73 LYS cc_start: 0.8667 (mttt) cc_final: 0.8418 (mttp) REVERT: L 649 MET cc_start: 0.8576 (tpp) cc_final: 0.8151 (mmm) REVERT: L 914 MET cc_start: 0.8031 (mmm) cc_final: 0.7668 (mmm) REVERT: L 998 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8544 (tp) REVERT: L 1020 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.3744 (m-80) REVERT: L 1045 TRP cc_start: 0.8771 (m100) cc_final: 0.8308 (m100) REVERT: L 1203 ILE cc_start: 0.9085 (mt) cc_final: 0.8870 (mt) REVERT: N 23 PHE cc_start: 0.6975 (m-80) cc_final: 0.6452 (m-80) REVERT: N 77 LEU cc_start: 0.8482 (mp) cc_final: 0.7926 (pp) REVERT: N 82 TYR cc_start: 0.7095 (m-80) cc_final: 0.6849 (m-80) REVERT: Q 52 ASN cc_start: 0.9155 (m-40) cc_final: 0.8580 (m-40) REVERT: R 35 GLU cc_start: 0.8562 (tt0) cc_final: 0.8011 (tt0) REVERT: R 47 SER cc_start: 0.8864 (t) cc_final: 0.8139 (m) REVERT: R 73 LYS cc_start: 0.8654 (mttp) cc_final: 0.7335 (mmtp) REVERT: R 597 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: R 976 TYR cc_start: 0.8697 (p90) cc_final: 0.8219 (p90) REVERT: R 977 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8382 (mmtp) REVERT: R 980 LEU cc_start: 0.9203 (mp) cc_final: 0.8964 (mp) REVERT: R 983 GLU cc_start: 0.8008 (tp30) cc_final: 0.7535 (tp30) REVERT: R 1187 SER cc_start: 0.8413 (m) cc_final: 0.7912 (p) REVERT: R 1214 MET cc_start: 0.8486 (ttp) cc_final: 0.8218 (ttm) REVERT: S 81 MET cc_start: 0.8153 (mmp) cc_final: 0.7697 (mmm) REVERT: T 23 PHE cc_start: 0.6996 (m-80) cc_final: 0.6514 (m-80) REVERT: T 77 LEU cc_start: 0.8579 (mt) cc_final: 0.8325 (mt) REVERT: T 82 TYR cc_start: 0.7017 (m-80) cc_final: 0.6771 (m-80) REVERT: W 44 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8284 (tp30) REVERT: W 83 TYR cc_start: 0.7562 (m-80) cc_final: 0.7062 (m-80) REVERT: W 172 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8682 (tt) REVERT: X 47 SER cc_start: 0.8527 (t) cc_final: 0.7786 (m) REVERT: X 51 THR cc_start: 0.6050 (OUTLIER) cc_final: 0.4759 (m) REVERT: X 601 GLU cc_start: 0.8590 (tp30) cc_final: 0.7251 (tp30) REVERT: X 933 MET cc_start: 0.7078 (ttt) cc_final: 0.6621 (ttt) REVERT: X 977 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8368 (mmtt) REVERT: X 983 GLU cc_start: 0.8300 (tp30) cc_final: 0.7882 (tp30) REVERT: Z 23 PHE cc_start: 0.6843 (m-80) cc_final: 0.6620 (m-80) REVERT: 1 20 MET cc_start: 0.9257 (mmt) cc_final: 0.9018 (mmm) REVERT: 1 92 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8440 (mt) REVERT: 2 52 ASN cc_start: 0.9129 (m-40) cc_final: 0.8874 (m-40) REVERT: 2 90 ASN cc_start: 0.8798 (t0) cc_final: 0.8445 (t0) REVERT: 2 172 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8328 (tt) REVERT: 2 176 MET cc_start: 0.8316 (mtp) cc_final: 0.8088 (mtm) REVERT: 2 186 MET cc_start: 0.8370 (ttp) cc_final: 0.8148 (ttp) REVERT: 2 199 ARG cc_start: 0.6917 (ttt180) cc_final: 0.6695 (ttt180) REVERT: 3 51 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.4686 (m) REVERT: 3 78 ILE cc_start: 0.9359 (tp) cc_final: 0.9098 (tp) REVERT: 3 108 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7153 (ttm110) REVERT: 3 601 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7299 (tp30) REVERT: 3 606 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8237 (mm) REVERT: 3 976 TYR cc_start: 0.8628 (p90) cc_final: 0.8301 (p90) REVERT: 3 983 GLU cc_start: 0.7618 (tp30) cc_final: 0.7253 (tp30) REVERT: 3 991 ASN cc_start: 0.8039 (m-40) cc_final: 0.7191 (m-40) REVERT: 3 1003 GLN cc_start: 0.8718 (mt0) cc_final: 0.8366 (mt0) REVERT: 3 1020 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.3628 (m-80) REVERT: 3 1045 TRP cc_start: 0.8298 (m100) cc_final: 0.7819 (m100) REVERT: 3 1170 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8873 (mp) REVERT: 3 1192 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9041 (mm) REVERT: 3 1205 TYR cc_start: 0.9097 (t80) cc_final: 0.8621 (t80) REVERT: 6 39 GLU cc_start: 0.8369 (tt0) cc_final: 0.7965 (tt0) REVERT: 6 77 LEU cc_start: 0.7385 (tt) cc_final: 0.7144 (tt) REVERT: 7 39 GLN cc_start: 0.8655 (tt0) cc_final: 0.8425 (tt0) REVERT: 7 70 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.8978 (mp) REVERT: 7 117 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8832 (tp) REVERT: 8 44 GLU cc_start: 0.8385 (tp30) cc_final: 0.7821 (tp30) REVERT: 8 52 ASN cc_start: 0.9097 (m-40) cc_final: 0.8870 (m-40) REVERT: 8 83 TYR cc_start: 0.7440 (m-80) cc_final: 0.7000 (m-80) REVERT: 8 90 ASN cc_start: 0.8788 (t0) cc_final: 0.8503 (t0) REVERT: 9 35 GLU cc_start: 0.8332 (tt0) cc_final: 0.8116 (tt0) REVERT: 9 58 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7217 (tm-30) REVERT: 9 80 PRO cc_start: 0.9594 (Cg_exo) cc_final: 0.9311 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.7129 (tp30) REVERT: 9 606 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8436 (mm) REVERT: 9 673 TRP cc_start: 0.8300 (m-10) cc_final: 0.7720 (m-10) REVERT: 9 980 LEU cc_start: 0.9244 (mp) cc_final: 0.8994 (mp) REVERT: 9 1020 TYR cc_start: 0.7057 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: 9 1027 ASN cc_start: 0.8928 (t0) cc_final: 0.8703 (t0) REVERT: 9 1099 LEU cc_start: 0.8600 (mt) cc_final: 0.8138 (mt) REVERT: 9 1125 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7675 (p0) REVERT: 9 1205 TYR cc_start: 0.9024 (t80) cc_final: 0.8647 (t80) REVERT: b 22 LEU cc_start: 0.8537 (mp) cc_final: 0.8251 (mp) REVERT: b 77 LEU cc_start: 0.8419 (mt) cc_final: 0.7854 (tt) REVERT: c 77 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7008 (tt) REVERT: e 44 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8383 (tp30) REVERT: e 83 TYR cc_start: 0.7558 (m-80) cc_final: 0.7051 (m-80) REVERT: f 58 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7271 (tm-30) REVERT: f 108 ARG cc_start: 0.7563 (mtm-85) cc_final: 0.7084 (ttp-110) REVERT: f 588 TRP cc_start: 0.7098 (OUTLIER) cc_final: 0.5887 (m100) REVERT: f 601 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: f 606 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8368 (mm) REVERT: f 615 SER cc_start: 0.8180 (p) cc_final: 0.7857 (m) REVERT: f 1099 LEU cc_start: 0.8357 (mt) cc_final: 0.7662 (mt) REVERT: f 1205 TYR cc_start: 0.8891 (t80) cc_final: 0.8627 (t80) outliers start: 477 outliers final: 332 residues processed: 1655 average time/residue: 0.4697 time to fit residues: 1361.3493 Evaluate side-chains 1688 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1325 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 606 LEU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 982 SER Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 998 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1085 VAL Chi-restraints excluded: chain F residue 1098 VAL Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1212 THR Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 111 TYR Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 620 MET Chi-restraints excluded: chain L residue 632 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 998 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1024 LEU Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1091 THR Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 72 ILE Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 110 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 83 TYR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 152 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 596 ASN Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 657 ILE Chi-restraints excluded: chain R residue 988 ILE Chi-restraints excluded: chain R residue 1033 TRP Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1091 THR Chi-restraints excluded: chain R residue 1170 LEU Chi-restraints excluded: chain R residue 1212 THR Chi-restraints excluded: chain R residue 1213 TYR Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 77 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 98 GLN Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 111 TYR Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1004 ARG Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1098 VAL Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain X residue 1225 MET Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 18 LEU Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 119 THR Chi-restraints excluded: chain 2 residue 120 THR Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 98 GLN Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 606 LEU Chi-restraints excluded: chain 3 residue 644 LEU Chi-restraints excluded: chain 3 residue 657 ILE Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1170 LEU Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1192 ILE Chi-restraints excluded: chain 3 residue 1212 THR Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 72 ILE Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 33 LEU Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 7 residue 80 VAL Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 106 LEU Chi-restraints excluded: chain 7 residue 117 ILE Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 78 SER Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 88 VAL Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 120 THR Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 84 SER Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 641 THR Chi-restraints excluded: chain 9 residue 657 ILE Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1085 VAL Chi-restraints excluded: chain 9 residue 1091 THR Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 44 GLU Chi-restraints excluded: chain e residue 61 VAL Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 78 SER Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 111 TYR Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 657 ILE Chi-restraints excluded: chain f residue 658 THR Chi-restraints excluded: chain f residue 998 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1033 TRP Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1162 THR Chi-restraints excluded: chain f residue 1192 ILE Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 211 optimal weight: 0.6980 chunk 566 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 369 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 629 optimal weight: 3.9990 chunk 522 optimal weight: 4.9990 chunk 291 optimal weight: 0.3980 chunk 52 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 chunk 330 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN E 55 GLN ** E 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 43 GLN K 51 ASN L 64 ASN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN P 113 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 GLN R 596 ASN ** R 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 113 ASN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 616 GLN 7 49 ASN 9 64 ASN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN d 113 ASN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 55153 Z= 0.231 Angle : 0.701 14.046 75691 Z= 0.347 Chirality : 0.044 0.311 9030 Planarity : 0.006 0.112 9247 Dihedral : 4.795 24.377 7245 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.10 % Favored : 94.24 % Rotamer: Outliers : 7.10 % Allowed : 30.12 % Favored : 62.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 6664 helix: 1.71 (0.08), residues: 4081 sheet: 0.08 (0.22), residues: 532 loop : -2.28 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 48 HIS 0.006 0.001 HIS R 57 PHE 0.018 0.002 PHE Q 177 TYR 0.024 0.001 TYR 31228 ARG 0.005 0.000 ARG 6 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1793 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 417 poor density : 1376 time to evaluate : 4.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 23 PHE cc_start: 0.7353 (m-80) cc_final: 0.6929 (m-80) REVERT: B 82 TYR cc_start: 0.7095 (m-80) cc_final: 0.6848 (m-80) REVERT: D 108 PHE cc_start: 0.7684 (m-10) cc_final: 0.6932 (m-10) REVERT: E 172 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8407 (tt) REVERT: E 203 LYS cc_start: 0.8025 (mtpt) cc_final: 0.7730 (ttmt) REVERT: F 35 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8290 (tt0) REVERT: F 45 LEU cc_start: 0.8762 (tp) cc_final: 0.8515 (tp) REVERT: F 588 TRP cc_start: 0.7108 (OUTLIER) cc_final: 0.4506 (m100) REVERT: F 601 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.6984 (tp30) REVERT: F 619 GLN cc_start: 0.8685 (mt0) cc_final: 0.7760 (mt0) REVERT: F 1121 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7268 (mt-10) REVERT: F 1189 ASN cc_start: 0.8370 (t0) cc_final: 0.8169 (t0) REVERT: F 1205 TYR cc_start: 0.8941 (t80) cc_final: 0.8548 (t80) REVERT: H 77 LEU cc_start: 0.8578 (mt) cc_final: 0.8258 (tt) REVERT: H 81 MET cc_start: 0.7833 (ptt) cc_final: 0.7399 (ptt) REVERT: I 77 LEU cc_start: 0.7167 (tt) cc_final: 0.6831 (tt) REVERT: K 46 GLN cc_start: 0.9117 (tm-30) cc_final: 0.7659 (tm-30) REVERT: K 148 MET cc_start: 0.8736 (tpp) cc_final: 0.8535 (mmm) REVERT: K 149 LEU cc_start: 0.8760 (tp) cc_final: 0.8518 (tp) REVERT: K 172 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8785 (tt) REVERT: L 649 MET cc_start: 0.8537 (tpp) cc_final: 0.8110 (mmm) REVERT: L 914 MET cc_start: 0.7987 (mmm) cc_final: 0.7639 (mmm) REVERT: L 983 GLU cc_start: 0.8087 (tp30) cc_final: 0.7815 (tp30) REVERT: L 1020 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.3580 (m-80) REVERT: L 1045 TRP cc_start: 0.8722 (m100) cc_final: 0.8281 (m100) REVERT: L 1114 MET cc_start: 0.8341 (ppp) cc_final: 0.8099 (tmm) REVERT: L 1203 ILE cc_start: 0.9049 (mt) cc_final: 0.8830 (mt) REVERT: N 23 PHE cc_start: 0.6824 (m-80) cc_final: 0.6282 (m-80) REVERT: N 77 LEU cc_start: 0.8433 (mp) cc_final: 0.7870 (pp) REVERT: N 82 TYR cc_start: 0.7071 (m-80) cc_final: 0.6814 (m-80) REVERT: Q 52 ASN cc_start: 0.9174 (m-40) cc_final: 0.8628 (m-40) REVERT: R 35 GLU cc_start: 0.8565 (tt0) cc_final: 0.8006 (tt0) REVERT: R 47 SER cc_start: 0.8813 (t) cc_final: 0.8082 (m) REVERT: R 590 GLU cc_start: 0.8237 (pm20) cc_final: 0.7841 (pm20) REVERT: R 620 MET cc_start: 0.8015 (mtt) cc_final: 0.7696 (mtt) REVERT: R 976 TYR cc_start: 0.8687 (p90) cc_final: 0.8221 (p90) REVERT: R 977 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8256 (mmtp) REVERT: R 980 LEU cc_start: 0.9189 (mp) cc_final: 0.8947 (mp) REVERT: R 983 GLU cc_start: 0.7963 (tp30) cc_final: 0.7521 (tp30) REVERT: R 1120 LEU cc_start: 0.8246 (mp) cc_final: 0.7963 (tp) REVERT: R 1187 SER cc_start: 0.8358 (m) cc_final: 0.7790 (p) REVERT: S 81 MET cc_start: 0.8039 (mmp) cc_final: 0.7613 (mmm) REVERT: T 23 PHE cc_start: 0.6984 (m-80) cc_final: 0.6493 (m-80) REVERT: T 77 LEU cc_start: 0.8573 (mt) cc_final: 0.8343 (mt) REVERT: T 82 TYR cc_start: 0.7109 (m-80) cc_final: 0.6888 (m-80) REVERT: W 44 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8253 (tp30) REVERT: W 83 TYR cc_start: 0.7519 (m-80) cc_final: 0.6993 (m-80) REVERT: W 172 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8623 (tt) REVERT: W 176 MET cc_start: 0.8253 (mtp) cc_final: 0.8039 (ttt) REVERT: X 47 SER cc_start: 0.8468 (t) cc_final: 0.7721 (m) REVERT: X 51 THR cc_start: 0.5930 (OUTLIER) cc_final: 0.4568 (m) REVERT: X 601 GLU cc_start: 0.8438 (tp30) cc_final: 0.7087 (tp30) REVERT: X 933 MET cc_start: 0.7069 (ttt) cc_final: 0.6661 (ttt) REVERT: X 976 TYR cc_start: 0.8537 (p90) cc_final: 0.8216 (p90) REVERT: X 977 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8283 (mmtt) REVERT: X 995 SER cc_start: 0.8810 (m) cc_final: 0.8546 (m) REVERT: X 1000 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8015 (mmm160) REVERT: X 1045 TRP cc_start: 0.8182 (m100) cc_final: 0.7771 (m100) REVERT: Y 58 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7778 (mm) REVERT: Z 23 PHE cc_start: 0.6858 (m-80) cc_final: 0.6633 (m-80) REVERT: 1 20 MET cc_start: 0.9292 (mmt) cc_final: 0.9017 (mmm) REVERT: 1 92 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8287 (mt) REVERT: 2 44 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7210 (mm-30) REVERT: 2 90 ASN cc_start: 0.8776 (t0) cc_final: 0.8386 (t0) REVERT: 2 172 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8247 (tt) REVERT: 2 186 MET cc_start: 0.8248 (ttp) cc_final: 0.8031 (ttp) REVERT: 2 199 ARG cc_start: 0.6796 (ttt180) cc_final: 0.6559 (ttt180) REVERT: 3 51 THR cc_start: 0.4817 (OUTLIER) cc_final: 0.3430 (m) REVERT: 3 78 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9032 (tp) REVERT: 3 601 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: 3 620 MET cc_start: 0.8841 (tpp) cc_final: 0.8446 (mtp) REVERT: 3 976 TYR cc_start: 0.8550 (p90) cc_final: 0.8334 (p90) REVERT: 3 1000 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7702 (mmm-85) REVERT: 3 1003 GLN cc_start: 0.8706 (mt0) cc_final: 0.8237 (mt0) REVERT: 3 1020 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.3765 (m-80) REVERT: 3 1045 TRP cc_start: 0.8268 (m100) cc_final: 0.7925 (m100) REVERT: 3 1170 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8773 (mp) REVERT: 3 1205 TYR cc_start: 0.9100 (t80) cc_final: 0.8612 (t80) REVERT: 5 59 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7150 (tp) REVERT: 6 39 GLU cc_start: 0.8446 (tt0) cc_final: 0.8044 (tt0) REVERT: 6 77 LEU cc_start: 0.7381 (tt) cc_final: 0.7142 (tt) REVERT: 7 39 GLN cc_start: 0.8622 (tt0) cc_final: 0.8404 (tt0) REVERT: 7 70 LEU cc_start: 0.9356 (OUTLIER) cc_final: 0.8962 (mp) REVERT: 8 52 ASN cc_start: 0.9166 (m-40) cc_final: 0.8934 (m-40) REVERT: 8 90 ASN cc_start: 0.8844 (t0) cc_final: 0.8619 (t0) REVERT: 9 35 GLU cc_start: 0.8329 (tt0) cc_final: 0.8075 (tt0) REVERT: 9 58 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7847 (tm-30) REVERT: 9 80 PRO cc_start: 0.9598 (Cg_exo) cc_final: 0.9329 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: 9 606 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8439 (mm) REVERT: 9 673 TRP cc_start: 0.8262 (m-10) cc_final: 0.7632 (m-10) REVERT: 9 1020 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.3600 (m-80) REVERT: 9 1099 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8095 (mt) REVERT: 9 1125 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7742 (p0) REVERT: 9 1175 ILE cc_start: 0.9205 (mt) cc_final: 0.8978 (mt) REVERT: 9 1205 TYR cc_start: 0.8990 (t80) cc_final: 0.8635 (t80) REVERT: 9 1232 ARG cc_start: 0.5438 (mtt90) cc_final: 0.5141 (mtt-85) REVERT: b 22 LEU cc_start: 0.8554 (mp) cc_final: 0.8265 (mp) REVERT: b 77 LEU cc_start: 0.8430 (mt) cc_final: 0.7855 (tt) REVERT: c 60 ASN cc_start: 0.8543 (t0) cc_final: 0.8257 (t0) REVERT: c 77 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.7042 (tt) REVERT: e 90 ASN cc_start: 0.8808 (t0) cc_final: 0.8585 (t0) REVERT: f 58 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7240 (tm-30) REVERT: f 108 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.7104 (ttp-110) REVERT: f 588 TRP cc_start: 0.7141 (OUTLIER) cc_final: 0.5974 (m100) REVERT: f 601 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: f 606 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8318 (mm) REVERT: f 615 SER cc_start: 0.8103 (p) cc_final: 0.7831 (m) REVERT: f 644 LEU cc_start: 0.8726 (tt) cc_final: 0.8361 (tt) REVERT: f 1099 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7650 (mt) REVERT: f 1205 TYR cc_start: 0.8874 (t80) cc_final: 0.8621 (t80) outliers start: 417 outliers final: 298 residues processed: 1631 average time/residue: 0.4678 time to fit residues: 1339.6512 Evaluate side-chains 1661 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1333 time to evaluate : 4.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 998 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1057 LEU Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 111 TYR Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 632 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 924 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1024 LEU Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1064 THR Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 64 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 172 LEU Chi-restraints excluded: chain W residue 174 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain X residue 1230 ILE Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 58 LEU Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 119 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 106 ILE Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 644 LEU Chi-restraints excluded: chain 3 residue 931 LEU Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 988 ILE Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1170 LEU Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 71 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 78 SER Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 88 VAL Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 8 residue 174 ILE Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 106 ILE Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 597 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 657 ILE Chi-restraints excluded: chain 9 residue 988 ILE Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1099 LEU Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 72 ILE Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 988 ILE Chi-restraints excluded: chain f residue 998 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1099 LEU Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1178 VAL Chi-restraints excluded: chain f residue 1192 ILE Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 607 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 358 optimal weight: 3.9990 chunk 459 optimal weight: 0.5980 chunk 356 optimal weight: 0.7980 chunk 530 optimal weight: 0.9990 chunk 351 optimal weight: 0.9990 chunk 627 optimal weight: 0.2980 chunk 392 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN ** G 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN J 43 GLN L 64 ASN L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN P 49 ASN P 113 ASN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1139 GLN V 43 GLN W 34 ASN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 9 64 ASN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN f 64 ASN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 55153 Z= 0.233 Angle : 0.706 14.769 75691 Z= 0.348 Chirality : 0.044 0.303 9030 Planarity : 0.005 0.112 9247 Dihedral : 4.761 24.437 7245 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.24 % Favored : 94.13 % Rotamer: Outliers : 7.34 % Allowed : 30.26 % Favored : 62.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.10), residues: 6664 helix: 1.73 (0.08), residues: 4081 sheet: 0.11 (0.21), residues: 532 loop : -2.29 (0.12), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 1 48 HIS 0.006 0.001 HIS R 57 PHE 0.019 0.002 PHE Q 177 TYR 0.035 0.001 TYR X 917 ARG 0.006 0.000 ARG c 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1808 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 431 poor density : 1377 time to evaluate : 4.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 59 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8177 (mm) REVERT: B 22 LEU cc_start: 0.8548 (mp) cc_final: 0.7876 (mp) REVERT: B 77 LEU cc_start: 0.8670 (mp) cc_final: 0.8022 (pp) REVERT: B 82 TYR cc_start: 0.7093 (m-80) cc_final: 0.6880 (m-80) REVERT: D 108 PHE cc_start: 0.7203 (m-10) cc_final: 0.6627 (m-10) REVERT: E 172 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8520 (tt) REVERT: E 203 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7665 (ttmt) REVERT: F 35 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8245 (tt0) REVERT: F 45 LEU cc_start: 0.8740 (tp) cc_final: 0.8471 (tp) REVERT: F 588 TRP cc_start: 0.7126 (OUTLIER) cc_final: 0.4405 (m100) REVERT: F 601 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.6959 (tp30) REVERT: F 619 GLN cc_start: 0.8749 (mt0) cc_final: 0.7934 (mt0) REVERT: F 673 TRP cc_start: 0.8423 (m-10) cc_final: 0.8010 (m-10) REVERT: F 933 MET cc_start: 0.7033 (ttt) cc_final: 0.6723 (ttt) REVERT: F 1121 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7275 (mt-10) REVERT: F 1175 ILE cc_start: 0.9027 (mt) cc_final: 0.8811 (mt) REVERT: F 1205 TYR cc_start: 0.8935 (t80) cc_final: 0.8522 (t80) REVERT: H 77 LEU cc_start: 0.8515 (mt) cc_final: 0.8174 (tt) REVERT: H 81 MET cc_start: 0.7831 (ptt) cc_final: 0.7381 (ptt) REVERT: I 77 LEU cc_start: 0.7168 (tt) cc_final: 0.6831 (tt) REVERT: K 46 GLN cc_start: 0.9090 (tm-30) cc_final: 0.7715 (tm-30) REVERT: K 149 LEU cc_start: 0.8755 (tp) cc_final: 0.8546 (tp) REVERT: K 172 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8914 (tt) REVERT: L 601 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: L 649 MET cc_start: 0.8512 (tpp) cc_final: 0.8079 (mmm) REVERT: L 914 MET cc_start: 0.7956 (mmm) cc_final: 0.7607 (mmm) REVERT: L 977 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8561 (mmtp) REVERT: L 983 GLU cc_start: 0.8121 (tp30) cc_final: 0.7793 (tp30) REVERT: L 998 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8529 (tp) REVERT: L 1020 TYR cc_start: 0.6990 (OUTLIER) cc_final: 0.3509 (m-80) REVERT: L 1026 MET cc_start: 0.8668 (ttm) cc_final: 0.8436 (ttt) REVERT: L 1045 TRP cc_start: 0.8737 (m100) cc_final: 0.8274 (m100) REVERT: L 1114 MET cc_start: 0.8380 (ppp) cc_final: 0.8101 (tmm) REVERT: L 1203 ILE cc_start: 0.9012 (mt) cc_final: 0.8797 (mt) REVERT: N 23 PHE cc_start: 0.6786 (m-80) cc_final: 0.6288 (m-80) REVERT: N 82 TYR cc_start: 0.7115 (m-80) cc_final: 0.6852 (m-80) REVERT: P 68 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.8349 (m-30) REVERT: Q 46 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8745 (tm-30) REVERT: Q 52 ASN cc_start: 0.9168 (m-40) cc_final: 0.8646 (m-40) REVERT: Q 126 ASN cc_start: 0.7593 (m-40) cc_final: 0.7300 (m-40) REVERT: R 35 GLU cc_start: 0.8562 (tt0) cc_final: 0.8022 (tt0) REVERT: R 47 SER cc_start: 0.8804 (t) cc_final: 0.8084 (m) REVERT: R 590 GLU cc_start: 0.8312 (pm20) cc_final: 0.8016 (pm20) REVERT: R 596 ASN cc_start: 0.7618 (t0) cc_final: 0.7184 (t0) REVERT: R 597 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: R 976 TYR cc_start: 0.8679 (p90) cc_final: 0.8017 (p90) REVERT: R 977 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8068 (mmtp) REVERT: R 980 LEU cc_start: 0.9198 (mp) cc_final: 0.8933 (mp) REVERT: R 983 GLU cc_start: 0.7945 (tp30) cc_final: 0.7532 (tp30) REVERT: R 1120 LEU cc_start: 0.8203 (mp) cc_final: 0.7931 (tp) REVERT: R 1205 TYR cc_start: 0.9050 (t80) cc_final: 0.8619 (t80) REVERT: T 23 PHE cc_start: 0.6962 (m-80) cc_final: 0.6512 (m-80) REVERT: T 77 LEU cc_start: 0.8583 (mt) cc_final: 0.8351 (mt) REVERT: W 44 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: W 83 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: X 47 SER cc_start: 0.8424 (t) cc_final: 0.7676 (m) REVERT: X 51 THR cc_start: 0.5995 (OUTLIER) cc_final: 0.4711 (m) REVERT: X 601 GLU cc_start: 0.8351 (tp30) cc_final: 0.6932 (tp30) REVERT: X 921 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7527 (mmtm) REVERT: X 933 MET cc_start: 0.7126 (ttt) cc_final: 0.6760 (ttt) REVERT: X 976 TYR cc_start: 0.8524 (p90) cc_final: 0.8137 (p90) REVERT: X 977 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8269 (mmtt) REVERT: X 1000 ARG cc_start: 0.8346 (mmm-85) cc_final: 0.8042 (mmm160) REVERT: X 1004 ARG cc_start: 0.8236 (ptt180) cc_final: 0.7971 (ptt180) REVERT: X 1045 TRP cc_start: 0.8231 (m100) cc_final: 0.7830 (m100) REVERT: Y 81 MET cc_start: 0.7834 (mmp) cc_final: 0.7556 (mmm) REVERT: Z 23 PHE cc_start: 0.6751 (m-80) cc_final: 0.6519 (m-80) REVERT: 1 20 MET cc_start: 0.9268 (mmt) cc_final: 0.8981 (mmm) REVERT: 1 92 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8141 (mm) REVERT: 2 52 ASN cc_start: 0.9027 (m-40) cc_final: 0.8676 (m-40) REVERT: 2 90 ASN cc_start: 0.8788 (t0) cc_final: 0.8395 (t0) REVERT: 2 104 ASN cc_start: 0.8663 (OUTLIER) cc_final: 0.8426 (t0) REVERT: 2 172 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8292 (tt) REVERT: 2 186 MET cc_start: 0.8251 (ttp) cc_final: 0.7994 (ttp) REVERT: 3 51 THR cc_start: 0.5581 (OUTLIER) cc_final: 0.4227 (m) REVERT: 3 78 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9049 (tp) REVERT: 3 108 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7198 (ttm110) REVERT: 3 601 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: 3 620 MET cc_start: 0.8651 (tpp) cc_final: 0.8212 (mtp) REVERT: 3 917 TYR cc_start: 0.8662 (t80) cc_final: 0.8462 (t80) REVERT: 3 983 GLU cc_start: 0.7760 (tp30) cc_final: 0.7369 (tp30) REVERT: 3 991 ASN cc_start: 0.7995 (m-40) cc_final: 0.7253 (m-40) REVERT: 3 1000 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.7592 (mmm-85) REVERT: 3 1003 GLN cc_start: 0.8752 (mt0) cc_final: 0.8284 (mt0) REVERT: 3 1020 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.3711 (m-80) REVERT: 3 1045 TRP cc_start: 0.8315 (m100) cc_final: 0.7708 (m100) REVERT: 3 1170 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8853 (mp) REVERT: 3 1205 TYR cc_start: 0.9106 (t80) cc_final: 0.8615 (t80) REVERT: 3 1214 MET cc_start: 0.8642 (ttp) cc_final: 0.8204 (ttm) REVERT: 4 58 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7504 (mm) REVERT: 5 23 PHE cc_start: 0.7213 (m-80) cc_final: 0.6526 (m-80) REVERT: 5 59 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7048 (tp) REVERT: 6 39 GLU cc_start: 0.8431 (tt0) cc_final: 0.8041 (tt0) REVERT: 6 77 LEU cc_start: 0.7396 (tt) cc_final: 0.7149 (tt) REVERT: 7 39 GLN cc_start: 0.8619 (tt0) cc_final: 0.8297 (tt0) REVERT: 7 70 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8967 (mp) REVERT: 8 44 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7503 (mm-30) REVERT: 8 52 ASN cc_start: 0.9095 (m-40) cc_final: 0.8851 (m-40) REVERT: 8 83 TYR cc_start: 0.7600 (m-80) cc_final: 0.7316 (m-80) REVERT: 8 90 ASN cc_start: 0.8917 (t0) cc_final: 0.8676 (t0) REVERT: 8 131 PHE cc_start: 0.7176 (t80) cc_final: 0.6930 (t80) REVERT: 9 35 GLU cc_start: 0.8327 (tt0) cc_final: 0.8018 (tt0) REVERT: 9 58 GLU cc_start: 0.8104 (tm-30) cc_final: 0.7674 (tm-30) REVERT: 9 76 GLU cc_start: 0.8301 (tt0) cc_final: 0.8037 (tt0) REVERT: 9 80 PRO cc_start: 0.9570 (Cg_exo) cc_final: 0.9321 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: 9 606 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8426 (mm) REVERT: 9 619 GLN cc_start: 0.8775 (mp10) cc_final: 0.7796 (mp10) REVERT: 9 673 TRP cc_start: 0.8294 (m-10) cc_final: 0.7613 (m-10) REVERT: 9 1000 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8626 (mmm160) REVERT: 9 1020 TYR cc_start: 0.7093 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: 9 1078 TYR cc_start: 0.8582 (t80) cc_final: 0.8191 (t80) REVERT: 9 1099 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8105 (mt) REVERT: 9 1114 MET cc_start: 0.8367 (tmm) cc_final: 0.8036 (tmm) REVERT: 9 1125 ASN cc_start: 0.8187 (OUTLIER) cc_final: 0.7841 (p0) REVERT: 9 1175 ILE cc_start: 0.9177 (mt) cc_final: 0.8954 (mt) REVERT: 9 1205 TYR cc_start: 0.8973 (t80) cc_final: 0.8605 (t80) REVERT: 9 1232 ARG cc_start: 0.5421 (mtt90) cc_final: 0.5138 (mtt-85) REVERT: b 22 LEU cc_start: 0.8550 (mp) cc_final: 0.8274 (mp) REVERT: b 77 LEU cc_start: 0.8396 (mt) cc_final: 0.7819 (tt) REVERT: c 77 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.7020 (tt) REVERT: e 44 GLU cc_start: 0.8343 (tp30) cc_final: 0.7262 (tp30) REVERT: e 83 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: e 90 ASN cc_start: 0.8819 (t0) cc_final: 0.8585 (t0) REVERT: f 58 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7170 (tm-30) REVERT: f 108 ARG cc_start: 0.7546 (mtm-85) cc_final: 0.7161 (ttp-110) REVERT: f 588 TRP cc_start: 0.7167 (OUTLIER) cc_final: 0.6002 (m100) REVERT: f 601 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7647 (tp30) REVERT: f 606 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8367 (mm) REVERT: f 615 SER cc_start: 0.8152 (p) cc_final: 0.7925 (m) REVERT: f 1099 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7608 (mt) REVERT: f 1205 TYR cc_start: 0.8939 (t80) cc_final: 0.8666 (t80) REVERT: f 1232 ARG cc_start: 0.5362 (mtt90) cc_final: 0.4796 (ttt90) outliers start: 431 outliers final: 323 residues processed: 1641 average time/residue: 0.4742 time to fit residues: 1361.1976 Evaluate side-chains 1683 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 360 poor density : 1323 time to evaluate : 4.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1057 LEU Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain F residue 1218 LEU Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 64 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 181 LEU Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 632 LEU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 924 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 998 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1064 THR Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 152 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 110 GLU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 924 THR Chi-restraints excluded: chain R residue 988 ILE Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1085 VAL Chi-restraints excluded: chain R residue 1139 GLN Chi-restraints excluded: chain R residue 1170 LEU Chi-restraints excluded: chain R residue 1213 TYR Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain S residue 20 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 33 LEU Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 83 TYR Chi-restraints excluded: chain W residue 104 ASN Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 78 ILE Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1085 VAL Chi-restraints excluded: chain X residue 1098 VAL Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 71 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 104 ASN Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 119 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 152 MET Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 98 GLN Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 106 ILE Chi-restraints excluded: chain 3 residue 110 GLU Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 988 ILE Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1170 LEU Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 LEU Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 71 VAL Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 98 VAL Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 88 VAL Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 106 ILE Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 597 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 988 ILE Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1082 GLN Chi-restraints excluded: chain 9 residue 1099 LEU Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1214 MET Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 98 VAL Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 83 TYR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 606 LEU Chi-restraints excluded: chain f residue 998 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1099 LEU Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1192 ILE Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 388 optimal weight: 7.9990 chunk 250 optimal weight: 2.9990 chunk 374 optimal weight: 5.9990 chunk 189 optimal weight: 5.9990 chunk 123 optimal weight: 0.0370 chunk 121 optimal weight: 2.9990 chunk 398 optimal weight: 2.9990 chunk 427 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 493 optimal weight: 0.8980 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN J 43 GLN L 64 ASN L 98 GLN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1043 ASN ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 43 GLN ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1139 GLN X 98 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 43 GLN 7 49 ASN 9 64 ASN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN d 43 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 55153 Z= 0.319 Angle : 0.737 22.696 75691 Z= 0.365 Chirality : 0.045 0.306 9030 Planarity : 0.006 0.190 9247 Dihedral : 4.827 34.207 7245 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.63 % Allowed : 5.31 % Favored : 94.06 % Rotamer: Outliers : 8.05 % Allowed : 29.93 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.10), residues: 6664 helix: 1.67 (0.08), residues: 4081 sheet: 0.07 (0.21), residues: 532 loop : -2.29 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 31045 HIS 0.005 0.001 HIS R 57 PHE 0.025 0.002 PHE Q 177 TYR 0.037 0.002 TYR f 917 ARG 0.009 0.000 ARG R1233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1828 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 473 poor density : 1355 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8890 (tt) REVERT: A 59 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8112 (mm) REVERT: B 22 LEU cc_start: 0.8527 (mp) cc_final: 0.7787 (mp) REVERT: B 23 PHE cc_start: 0.7401 (m-80) cc_final: 0.6958 (m-80) REVERT: B 77 LEU cc_start: 0.8646 (mp) cc_final: 0.7855 (pp) REVERT: B 82 TYR cc_start: 0.7148 (m-80) cc_final: 0.6920 (m-80) REVERT: D 106 LEU cc_start: 0.9427 (tp) cc_final: 0.9215 (tp) REVERT: D 108 PHE cc_start: 0.7387 (m-10) cc_final: 0.6782 (m-10) REVERT: E 172 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8468 (tt) REVERT: E 203 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7870 (ttmt) REVERT: F 35 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: F 45 LEU cc_start: 0.8821 (tp) cc_final: 0.8567 (tp) REVERT: F 588 TRP cc_start: 0.7252 (OUTLIER) cc_final: 0.4472 (m100) REVERT: F 601 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.6981 (tp30) REVERT: F 619 GLN cc_start: 0.8820 (mt0) cc_final: 0.8551 (mt0) REVERT: F 673 TRP cc_start: 0.8446 (m-10) cc_final: 0.8034 (m-10) REVERT: F 933 MET cc_start: 0.7217 (ttt) cc_final: 0.6954 (ttt) REVERT: F 977 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8622 (mmtp) REVERT: F 1000 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8486 (mmm160) REVERT: F 1121 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7272 (mt-10) REVERT: F 1205 TYR cc_start: 0.8950 (t80) cc_final: 0.8560 (t80) REVERT: H 59 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6810 (pt) REVERT: H 77 LEU cc_start: 0.8548 (mt) cc_final: 0.8237 (tt) REVERT: H 81 MET cc_start: 0.7797 (ptt) cc_final: 0.7372 (ptt) REVERT: K 46 GLN cc_start: 0.9136 (tm-30) cc_final: 0.7884 (tm-30) REVERT: K 172 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8949 (tt) REVERT: K 183 SER cc_start: 0.9186 (m) cc_final: 0.8847 (p) REVERT: L 649 MET cc_start: 0.8560 (tpp) cc_final: 0.8147 (mmm) REVERT: L 914 MET cc_start: 0.8048 (mmm) cc_final: 0.7674 (mmm) REVERT: L 977 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8569 (mmtp) REVERT: L 983 GLU cc_start: 0.8167 (tp30) cc_final: 0.7806 (tp30) REVERT: L 998 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8536 (tp) REVERT: L 1020 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.3556 (m-80) REVERT: L 1045 TRP cc_start: 0.8797 (m100) cc_final: 0.8270 (m100) REVERT: L 1203 ILE cc_start: 0.9082 (mt) cc_final: 0.8836 (mt) REVERT: N 23 PHE cc_start: 0.6844 (m-80) cc_final: 0.6385 (m-80) REVERT: N 77 LEU cc_start: 0.8472 (mp) cc_final: 0.8111 (pp) REVERT: N 82 TYR cc_start: 0.7133 (m-80) cc_final: 0.6919 (m-80) REVERT: P 43 GLN cc_start: 0.8306 (mt0) cc_final: 0.7929 (mt0) REVERT: P 68 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8444 (m-30) REVERT: Q 46 GLN cc_start: 0.9041 (tm-30) cc_final: 0.8705 (tm-30) REVERT: Q 52 ASN cc_start: 0.9220 (m-40) cc_final: 0.8731 (m-40) REVERT: Q 90 ASN cc_start: 0.8496 (t0) cc_final: 0.8159 (t0) REVERT: Q 126 ASN cc_start: 0.7597 (m-40) cc_final: 0.7327 (m-40) REVERT: R 35 GLU cc_start: 0.8595 (tt0) cc_final: 0.8033 (tt0) REVERT: R 47 SER cc_start: 0.8800 (t) cc_final: 0.8059 (m) REVERT: R 590 GLU cc_start: 0.8346 (pm20) cc_final: 0.8032 (pm20) REVERT: R 597 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: R 620 MET cc_start: 0.8591 (mtp) cc_final: 0.8194 (mtt) REVERT: R 976 TYR cc_start: 0.8599 (p90) cc_final: 0.7869 (p90) REVERT: R 977 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8060 (mmtp) REVERT: R 980 LEU cc_start: 0.9241 (mp) cc_final: 0.8987 (mp) REVERT: R 983 GLU cc_start: 0.7983 (tp30) cc_final: 0.7557 (tp30) REVERT: R 1120 LEU cc_start: 0.8274 (mp) cc_final: 0.7968 (tp) REVERT: R 1187 SER cc_start: 0.8377 (m) cc_final: 0.7821 (p) REVERT: T 23 PHE cc_start: 0.7097 (m-80) cc_final: 0.6648 (m-80) REVERT: V 25 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.8833 (p) REVERT: W 44 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8329 (mm-30) REVERT: X 47 SER cc_start: 0.8453 (t) cc_final: 0.7676 (m) REVERT: X 51 THR cc_start: 0.6222 (OUTLIER) cc_final: 0.4998 (m) REVERT: X 601 GLU cc_start: 0.8424 (tp30) cc_final: 0.7017 (tp30) REVERT: X 921 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7378 (mmtm) REVERT: X 933 MET cc_start: 0.7196 (ttt) cc_final: 0.6845 (ttt) REVERT: X 977 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8398 (mmtt) REVERT: X 983 GLU cc_start: 0.8359 (tp30) cc_final: 0.7984 (tp30) REVERT: X 1003 GLN cc_start: 0.8320 (mm-40) cc_final: 0.7170 (mp10) REVERT: X 1045 TRP cc_start: 0.8384 (m100) cc_final: 0.7869 (m100) REVERT: X 1169 MET cc_start: 0.7667 (mtp) cc_final: 0.7417 (mtt) REVERT: 1 20 MET cc_start: 0.9282 (mmt) cc_final: 0.8974 (mmm) REVERT: 1 92 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8460 (mt) REVERT: 2 90 ASN cc_start: 0.8826 (t0) cc_final: 0.8478 (t0) REVERT: 2 104 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8031 (t0) REVERT: 2 172 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8433 (tt) REVERT: 2 186 MET cc_start: 0.8314 (ttp) cc_final: 0.8061 (ttp) REVERT: 3 51 THR cc_start: 0.5958 (OUTLIER) cc_final: 0.4728 (m) REVERT: 3 78 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9099 (tp) REVERT: 3 98 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8173 (pt0) REVERT: 3 108 ARG cc_start: 0.7727 (mtm-85) cc_final: 0.7195 (ttm110) REVERT: 3 601 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7393 (tp30) REVERT: 3 620 MET cc_start: 0.8571 (tpp) cc_final: 0.8368 (mtp) REVERT: 3 925 TYR cc_start: 0.8290 (m-80) cc_final: 0.7957 (m-80) REVERT: 3 983 GLU cc_start: 0.7779 (tp30) cc_final: 0.7415 (tp30) REVERT: 3 1003 GLN cc_start: 0.8814 (mt0) cc_final: 0.8453 (mt0) REVERT: 3 1020 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.4063 (m-80) REVERT: 3 1031 GLN cc_start: 0.8522 (tp40) cc_final: 0.8065 (tp40) REVERT: 3 1170 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8896 (mp) REVERT: 3 1205 TYR cc_start: 0.9117 (t80) cc_final: 0.8627 (t80) REVERT: 4 58 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7693 (mm) REVERT: 5 59 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7152 (tp) REVERT: 5 77 LEU cc_start: 0.8267 (mp) cc_final: 0.7611 (pp) REVERT: 6 39 GLU cc_start: 0.8450 (tt0) cc_final: 0.8074 (tt0) REVERT: 6 77 LEU cc_start: 0.7382 (tt) cc_final: 0.7129 (tt) REVERT: 7 39 GLN cc_start: 0.8653 (tt0) cc_final: 0.8388 (tt0) REVERT: 7 70 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9000 (mp) REVERT: 8 52 ASN cc_start: 0.9167 (m-40) cc_final: 0.8958 (m-40) REVERT: 8 90 ASN cc_start: 0.8896 (t0) cc_final: 0.8658 (t0) REVERT: 8 131 PHE cc_start: 0.7226 (t80) cc_final: 0.6979 (t80) REVERT: 9 35 GLU cc_start: 0.8337 (tt0) cc_final: 0.7995 (tt0) REVERT: 9 58 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7554 (tm-30) REVERT: 9 80 PRO cc_start: 0.9590 (Cg_exo) cc_final: 0.9318 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7084 (tp30) REVERT: 9 606 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8493 (mm) REVERT: 9 619 GLN cc_start: 0.8733 (mp10) cc_final: 0.7810 (mp10) REVERT: 9 673 TRP cc_start: 0.8319 (m-10) cc_final: 0.7672 (m-10) REVERT: 9 977 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8412 (mmtp) REVERT: 9 1004 ARG cc_start: 0.8524 (ptt-90) cc_final: 0.8197 (ptp90) REVERT: 9 1020 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.3946 (m-80) REVERT: 9 1099 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8115 (mt) REVERT: 9 1125 ASN cc_start: 0.8232 (OUTLIER) cc_final: 0.7865 (p0) REVERT: 9 1205 TYR cc_start: 0.9005 (t80) cc_final: 0.8641 (t80) REVERT: 9 1232 ARG cc_start: 0.5559 (mtt90) cc_final: 0.5293 (mtt-85) REVERT: b 22 LEU cc_start: 0.8569 (mp) cc_final: 0.8277 (mp) REVERT: b 77 LEU cc_start: 0.8424 (mt) cc_final: 0.7845 (tt) REVERT: c 77 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7038 (tt) REVERT: e 44 GLU cc_start: 0.8469 (tp30) cc_final: 0.7477 (mm-30) REVERT: e 90 ASN cc_start: 0.8888 (t0) cc_final: 0.8670 (t0) REVERT: e 152 MET cc_start: 0.8947 (mtt) cc_final: 0.8631 (ttm) REVERT: f 58 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7225 (tm-30) REVERT: f 108 ARG cc_start: 0.7581 (mtm-85) cc_final: 0.7052 (ttp-110) REVERT: f 588 TRP cc_start: 0.7216 (OUTLIER) cc_final: 0.5944 (m100) REVERT: f 601 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7584 (tp30) REVERT: f 615 SER cc_start: 0.8252 (p) cc_final: 0.8048 (m) REVERT: f 1099 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7594 (mt) REVERT: f 1205 TYR cc_start: 0.8997 (t80) cc_final: 0.8724 (t80) REVERT: f 1232 ARG cc_start: 0.5434 (mtt90) cc_final: 0.4849 (ttt90) outliers start: 473 outliers final: 364 residues processed: 1644 average time/residue: 0.4688 time to fit residues: 1349.8725 Evaluate side-chains 1708 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 400 poor density : 1308 time to evaluate : 4.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 TYR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 998 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1057 LEU Chi-restraints excluded: chain F residue 1064 THR Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1197 SER Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 117 ILE Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 620 MET Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 924 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 998 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1024 LEU Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1064 THR Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1199 VAL Chi-restraints excluded: chain L residue 1212 THR Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 26 SER Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 152 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 924 THR Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1085 VAL Chi-restraints excluded: chain R residue 1170 LEU Chi-restraints excluded: chain R residue 1213 TYR Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain R residue 1230 ILE Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 18 LEU Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 69 ILE Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 80 VAL Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 83 TYR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 98 GLN Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 111 TYR Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 906 SER Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1085 VAL Chi-restraints excluded: chain X residue 1098 VAL Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1212 THR Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain X residue 1225 MET Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 71 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 0 residue 59 LEU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 33 ASN Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 106 LEU Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 26 SER Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 104 ASN Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 152 MET Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 2 residue 195 ILE Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 98 GLN Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 106 ILE Chi-restraints excluded: chain 3 residue 111 TYR Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 931 LEU Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 988 ILE Chi-restraints excluded: chain 3 residue 1006 SER Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1091 THR Chi-restraints excluded: chain 3 residue 1098 VAL Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1170 LEU Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1197 SER Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 20 ILE Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 40 VAL Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 LEU Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 71 VAL Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 115 VAL Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 88 VAL Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 8 residue 174 ILE Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 657 ILE Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 988 ILE Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1099 LEU Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1213 TYR Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 54 SER Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 76 THR Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 195 ILE Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 658 THR Chi-restraints excluded: chain f residue 988 ILE Chi-restraints excluded: chain f residue 998 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1099 LEU Chi-restraints excluded: chain f residue 1108 GLU Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1162 THR Chi-restraints excluded: chain f residue 1178 VAL Chi-restraints excluded: chain f residue 1192 ILE Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 570 optimal weight: 0.9990 chunk 601 optimal weight: 0.9990 chunk 548 optimal weight: 3.9990 chunk 584 optimal weight: 0.6980 chunk 600 optimal weight: 0.7980 chunk 351 optimal weight: 2.9990 chunk 254 optimal weight: 0.9990 chunk 459 optimal weight: 0.9990 chunk 179 optimal weight: 0.9990 chunk 528 optimal weight: 0.9980 chunk 553 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN D 49 ASN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1025 GLN F1135 ASN J 39 GLN J 43 GLN L 64 ASN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R1139 GLN W 34 ASN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 616 GLN 31125 ASN 7 49 ASN 9 64 ASN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 GLN ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 55153 Z= 0.254 Angle : 0.737 15.423 75691 Z= 0.361 Chirality : 0.044 0.298 9030 Planarity : 0.006 0.162 9247 Dihedral : 4.839 36.009 7245 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.28 % Favored : 94.06 % Rotamer: Outliers : 6.84 % Allowed : 31.43 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.10), residues: 6664 helix: 1.70 (0.08), residues: 4081 sheet: 0.08 (0.21), residues: 532 loop : -2.29 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP 31045 HIS 0.006 0.001 HIS R 57 PHE 0.029 0.002 PHE 8 177 TYR 0.039 0.001 TYR f 917 ARG 0.006 0.000 ARG c 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1767 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 402 poor density : 1365 time to evaluate : 4.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 59 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8189 (mm) REVERT: B 22 LEU cc_start: 0.8478 (mp) cc_final: 0.7762 (mp) REVERT: B 23 PHE cc_start: 0.7359 (m-80) cc_final: 0.6959 (m-80) REVERT: B 77 LEU cc_start: 0.8618 (mp) cc_final: 0.7892 (pp) REVERT: D 106 LEU cc_start: 0.9379 (tp) cc_final: 0.9149 (tp) REVERT: D 108 PHE cc_start: 0.7289 (m-10) cc_final: 0.6677 (m-10) REVERT: E 172 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8472 (tt) REVERT: E 203 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7838 (ttmt) REVERT: F 35 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (tt0) REVERT: F 45 LEU cc_start: 0.8823 (tp) cc_final: 0.8615 (tp) REVERT: F 588 TRP cc_start: 0.7153 (OUTLIER) cc_final: 0.4508 (m100) REVERT: F 601 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.6997 (tp30) REVERT: F 619 GLN cc_start: 0.8744 (mt0) cc_final: 0.8455 (mt0) REVERT: F 673 TRP cc_start: 0.8373 (m-10) cc_final: 0.7929 (m-10) REVERT: F 933 MET cc_start: 0.7197 (ttt) cc_final: 0.6934 (ttt) REVERT: F 977 LYS cc_start: 0.8921 (mmtp) cc_final: 0.8694 (mmtp) REVERT: F 1000 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7860 (mmm160) REVERT: F 1044 THR cc_start: 0.9148 (p) cc_final: 0.8868 (p) REVERT: F 1121 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7278 (mt-10) REVERT: F 1205 TYR cc_start: 0.8933 (t80) cc_final: 0.8534 (t80) REVERT: G 61 LEU cc_start: 0.7788 (mp) cc_final: 0.7519 (mp) REVERT: H 77 LEU cc_start: 0.8542 (mt) cc_final: 0.8211 (tt) REVERT: H 81 MET cc_start: 0.7757 (ptt) cc_final: 0.7293 (ptt) REVERT: K 46 GLN cc_start: 0.9114 (tm-30) cc_final: 0.7856 (tm-30) REVERT: K 172 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8890 (tt) REVERT: L 649 MET cc_start: 0.8551 (tpp) cc_final: 0.8118 (mmm) REVERT: L 902 PHE cc_start: 0.7428 (m-80) cc_final: 0.7226 (m-10) REVERT: L 914 MET cc_start: 0.8040 (mmm) cc_final: 0.7693 (mmm) REVERT: L 933 MET cc_start: 0.7551 (ttp) cc_final: 0.7331 (mtp) REVERT: L 983 GLU cc_start: 0.8203 (tp30) cc_final: 0.7855 (tp30) REVERT: L 998 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8565 (tp) REVERT: L 1020 TYR cc_start: 0.7028 (OUTLIER) cc_final: 0.3542 (m-80) REVERT: L 1045 TRP cc_start: 0.8757 (m100) cc_final: 0.8182 (m100) REVERT: L 1114 MET cc_start: 0.8395 (ppp) cc_final: 0.8115 (tmm) REVERT: L 1203 ILE cc_start: 0.9010 (mt) cc_final: 0.8770 (mt) REVERT: L 1214 MET cc_start: 0.8375 (ttp) cc_final: 0.8167 (ttp) REVERT: N 23 PHE cc_start: 0.6801 (m-80) cc_final: 0.6364 (m-80) REVERT: N 77 LEU cc_start: 0.8505 (mp) cc_final: 0.8131 (pp) REVERT: N 82 TYR cc_start: 0.7234 (m-80) cc_final: 0.6990 (m-80) REVERT: P 43 GLN cc_start: 0.8196 (mt0) cc_final: 0.7826 (mt0) REVERT: P 68 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8394 (m-30) REVERT: Q 46 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8696 (tm-30) REVERT: Q 52 ASN cc_start: 0.9181 (m-40) cc_final: 0.8705 (m-40) REVERT: Q 90 ASN cc_start: 0.8532 (t0) cc_final: 0.8186 (t0) REVERT: Q 126 ASN cc_start: 0.7686 (m-40) cc_final: 0.7406 (m-40) REVERT: R 35 GLU cc_start: 0.8576 (tt0) cc_final: 0.7990 (tt0) REVERT: R 47 SER cc_start: 0.8742 (t) cc_final: 0.8082 (m) REVERT: R 73 LYS cc_start: 0.8488 (mttp) cc_final: 0.7458 (mmtp) REVERT: R 590 GLU cc_start: 0.8318 (pm20) cc_final: 0.8048 (pm20) REVERT: R 597 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7270 (m-80) REVERT: R 620 MET cc_start: 0.8610 (mtp) cc_final: 0.8410 (ttm) REVERT: R 917 TYR cc_start: 0.8289 (t80) cc_final: 0.7803 (t80) REVERT: R 976 TYR cc_start: 0.8558 (p90) cc_final: 0.7815 (p90) REVERT: R 977 LYS cc_start: 0.8568 (mmtt) cc_final: 0.8014 (mmtp) REVERT: R 980 LEU cc_start: 0.9253 (mp) cc_final: 0.8986 (mp) REVERT: R 983 GLU cc_start: 0.7917 (tp30) cc_final: 0.7378 (tp30) REVERT: R 1205 TYR cc_start: 0.9087 (t80) cc_final: 0.8630 (t80) REVERT: T 23 PHE cc_start: 0.7052 (m-80) cc_final: 0.6638 (m-80) REVERT: U 77 LEU cc_start: 0.7099 (tt) cc_final: 0.6816 (tt) REVERT: W 44 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: X 51 THR cc_start: 0.6116 (OUTLIER) cc_final: 0.4897 (m) REVERT: X 601 GLU cc_start: 0.8494 (tp30) cc_final: 0.7218 (tp30) REVERT: X 914 MET cc_start: 0.7976 (mmm) cc_final: 0.7754 (mmm) REVERT: X 921 LYS cc_start: 0.7730 (mtmm) cc_final: 0.7355 (mmtm) REVERT: X 933 MET cc_start: 0.7329 (ttt) cc_final: 0.7024 (ttt) REVERT: X 977 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8433 (mmtt) REVERT: X 995 SER cc_start: 0.8837 (m) cc_final: 0.8585 (m) REVERT: X 1045 TRP cc_start: 0.8293 (m100) cc_final: 0.7824 (m100) REVERT: X 1114 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8018 (tmm) REVERT: X 1169 MET cc_start: 0.7620 (mtp) cc_final: 0.7375 (mtt) REVERT: Y 81 MET cc_start: 0.7812 (mmp) cc_final: 0.7568 (mmm) REVERT: Z 23 PHE cc_start: 0.6816 (m-80) cc_final: 0.6611 (m-80) REVERT: 1 20 MET cc_start: 0.9213 (mmt) cc_final: 0.8966 (mmm) REVERT: 1 92 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8360 (mt) REVERT: 2 90 ASN cc_start: 0.8807 (t0) cc_final: 0.8440 (t0) REVERT: 2 172 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8369 (tt) REVERT: 2 186 MET cc_start: 0.8240 (ttp) cc_final: 0.7988 (ttp) REVERT: 3 51 THR cc_start: 0.6163 (OUTLIER) cc_final: 0.4934 (m) REVERT: 3 78 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9081 (tp) REVERT: 3 98 GLN cc_start: 0.8715 (OUTLIER) cc_final: 0.8272 (pt0) REVERT: 3 108 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7204 (ttm110) REVERT: 3 601 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: 3 673 TRP cc_start: 0.8219 (m-10) cc_final: 0.7285 (m-10) REVERT: 3 917 TYR cc_start: 0.8403 (t80) cc_final: 0.8074 (t80) REVERT: 3 983 GLU cc_start: 0.7755 (tp30) cc_final: 0.7394 (tp30) REVERT: 3 1000 ARG cc_start: 0.8459 (mmm-85) cc_final: 0.7996 (mmm160) REVERT: 3 1003 GLN cc_start: 0.8818 (mt0) cc_final: 0.8541 (mt0) REVERT: 3 1020 TYR cc_start: 0.7120 (OUTLIER) cc_final: 0.4255 (m-80) REVERT: 3 1205 TYR cc_start: 0.9113 (t80) cc_final: 0.8618 (t80) REVERT: 4 58 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7681 (mm) REVERT: 5 58 LEU cc_start: 0.8362 (mm) cc_final: 0.8015 (mt) REVERT: 5 59 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6938 (tp) REVERT: 5 77 LEU cc_start: 0.8254 (mp) cc_final: 0.7621 (pp) REVERT: 6 39 GLU cc_start: 0.8437 (tt0) cc_final: 0.8064 (tt0) REVERT: 6 77 LEU cc_start: 0.7387 (tt) cc_final: 0.7139 (tt) REVERT: 7 23 PHE cc_start: 0.8748 (m-80) cc_final: 0.8350 (m-80) REVERT: 7 39 GLN cc_start: 0.8665 (tt0) cc_final: 0.8373 (tt0) REVERT: 7 70 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8978 (mp) REVERT: 8 44 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8183 (tp30) REVERT: 8 52 ASN cc_start: 0.9114 (m-40) cc_final: 0.8896 (m-40) REVERT: 8 90 ASN cc_start: 0.8972 (t0) cc_final: 0.8714 (t0) REVERT: 9 35 GLU cc_start: 0.8342 (tt0) cc_final: 0.8022 (tt0) REVERT: 9 58 GLU cc_start: 0.8051 (tm-30) cc_final: 0.7563 (tm-30) REVERT: 9 80 PRO cc_start: 0.9581 (Cg_exo) cc_final: 0.9314 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: 9 606 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8434 (mm) REVERT: 9 619 GLN cc_start: 0.8694 (mp10) cc_final: 0.7755 (mp10) REVERT: 9 673 TRP cc_start: 0.8299 (m-10) cc_final: 0.7479 (m-10) REVERT: 9 977 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8535 (mmtp) REVERT: 9 1004 ARG cc_start: 0.8468 (ptt-90) cc_final: 0.8212 (ptp90) REVERT: 9 1020 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.3974 (m-80) REVERT: 9 1099 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8123 (mt) REVERT: 9 1114 MET cc_start: 0.8269 (tmm) cc_final: 0.8011 (tmm) REVERT: 9 1125 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7928 (p0) REVERT: 9 1205 TYR cc_start: 0.8998 (t80) cc_final: 0.8627 (t80) REVERT: 9 1232 ARG cc_start: 0.5528 (mtt90) cc_final: 0.5244 (mtt-85) REVERT: b 22 LEU cc_start: 0.8562 (mp) cc_final: 0.8283 (mp) REVERT: b 77 LEU cc_start: 0.8419 (mt) cc_final: 0.7856 (tt) REVERT: c 77 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.7029 (tt) REVERT: e 90 ASN cc_start: 0.8858 (t0) cc_final: 0.8616 (t0) REVERT: e 152 MET cc_start: 0.8934 (mtt) cc_final: 0.8687 (ttm) REVERT: f 58 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7187 (tm-30) REVERT: f 108 ARG cc_start: 0.7558 (mtm-85) cc_final: 0.7119 (ttp-110) REVERT: f 588 TRP cc_start: 0.7186 (OUTLIER) cc_final: 0.5979 (m100) REVERT: f 601 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7553 (tp30) REVERT: f 620 MET cc_start: 0.8550 (mtp) cc_final: 0.8084 (ttm) REVERT: f 1099 LEU cc_start: 0.8213 (OUTLIER) cc_final: 0.7626 (mt) REVERT: f 1232 ARG cc_start: 0.5466 (mtt90) cc_final: 0.5004 (tmm160) outliers start: 402 outliers final: 339 residues processed: 1612 average time/residue: 0.4638 time to fit residues: 1307.7253 Evaluate side-chains 1703 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 372 poor density : 1331 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 658 THR Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 998 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1024 LEU Chi-restraints excluded: chain F residue 1033 TRP Chi-restraints excluded: chain F residue 1057 LEU Chi-restraints excluded: chain F residue 1064 THR Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1197 SER Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 111 TYR Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 998 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1033 TRP Chi-restraints excluded: chain L residue 1064 THR Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1170 LEU Chi-restraints excluded: chain L residue 1178 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 78 SER Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 152 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 924 THR Chi-restraints excluded: chain R residue 988 ILE Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1213 TYR Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain R residue 1230 ILE Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 78 SER Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 83 TYR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 906 SER Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1085 VAL Chi-restraints excluded: chain X residue 1098 VAL Chi-restraints excluded: chain X residue 1114 MET Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 71 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 33 ASN Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 78 SER Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 152 MET Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 2 residue 195 ILE Chi-restraints excluded: chain 3 residue 41 GLU Chi-restraints excluded: chain 3 residue 51 THR Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 98 GLN Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 106 ILE Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 924 THR Chi-restraints excluded: chain 3 residue 931 LEU Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 988 ILE Chi-restraints excluded: chain 3 residue 1006 SER Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1114 MET Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1197 SER Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 LEU Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 71 VAL Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 70 LEU Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 115 VAL Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 88 VAL Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 8 residue 174 ILE Chi-restraints excluded: chain 9 residue 53 VAL Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 106 ILE Chi-restraints excluded: chain 9 residue 111 TYR Chi-restraints excluded: chain 9 residue 597 TYR Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 658 THR Chi-restraints excluded: chain 9 residue 988 ILE Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1033 TRP Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1099 LEU Chi-restraints excluded: chain 9 residue 1125 ASN Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1213 TYR Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 195 ILE Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 906 SER Chi-restraints excluded: chain f residue 988 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1099 LEU Chi-restraints excluded: chain f residue 1108 GLU Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1162 THR Chi-restraints excluded: chain f residue 1178 VAL Chi-restraints excluded: chain f residue 1192 ILE Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 582 optimal weight: 0.5980 chunk 383 optimal weight: 0.2980 chunk 618 optimal weight: 0.7980 chunk 377 optimal weight: 3.9990 chunk 293 optimal weight: 0.5980 chunk 429 optimal weight: 0.9980 chunk 648 optimal weight: 0.1980 chunk 596 optimal weight: 3.9990 chunk 516 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 398 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 43 GLN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 619 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN J 43 GLN L 64 ASN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 98 GLN ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 55 GLN 9 57 HIS 9 64 ASN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 55153 Z= 0.227 Angle : 0.737 13.811 75691 Z= 0.360 Chirality : 0.044 0.312 9030 Planarity : 0.006 0.145 9247 Dihedral : 4.819 37.751 7245 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.65 % Allowed : 5.37 % Favored : 93.98 % Rotamer: Outliers : 6.44 % Allowed : 31.93 % Favored : 61.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.10), residues: 6664 helix: 1.73 (0.08), residues: 4081 sheet: 0.06 (0.22), residues: 532 loop : -2.30 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP f1033 HIS 0.005 0.001 HIS R 57 PHE 0.026 0.002 PHE 8 177 TYR 0.034 0.001 TYR R 917 ARG 0.006 0.000 ARG 6 83 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13328 Ramachandran restraints generated. 6664 Oldfield, 0 Emsley, 6664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 378 poor density : 1348 time to evaluate : 4.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8871 (tt) REVERT: A 59 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8135 (mm) REVERT: B 22 LEU cc_start: 0.8517 (mp) cc_final: 0.7864 (mp) REVERT: B 77 LEU cc_start: 0.8594 (mp) cc_final: 0.7896 (pp) REVERT: D 106 LEU cc_start: 0.9368 (tp) cc_final: 0.9148 (tp) REVERT: D 108 PHE cc_start: 0.7107 (m-10) cc_final: 0.6571 (m-10) REVERT: E 172 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8486 (tt) REVERT: E 203 LYS cc_start: 0.8117 (mtpt) cc_final: 0.7873 (ttmt) REVERT: F 588 TRP cc_start: 0.7140 (OUTLIER) cc_final: 0.4497 (m100) REVERT: F 601 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.6973 (tp30) REVERT: F 619 GLN cc_start: 0.8716 (mt0) cc_final: 0.8277 (mt0) REVERT: F 673 TRP cc_start: 0.8360 (m-10) cc_final: 0.7923 (m-10) REVERT: F 977 LYS cc_start: 0.8930 (mmtp) cc_final: 0.8690 (mmtp) REVERT: F 1000 ARG cc_start: 0.8550 (mmm-85) cc_final: 0.8316 (mmm160) REVERT: F 1044 THR cc_start: 0.9122 (p) cc_final: 0.8808 (p) REVERT: F 1121 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7283 (mt-10) REVERT: F 1205 TYR cc_start: 0.8911 (t80) cc_final: 0.8510 (t80) REVERT: G 61 LEU cc_start: 0.7822 (mp) cc_final: 0.7542 (mp) REVERT: H 23 PHE cc_start: 0.7362 (m-80) cc_final: 0.6846 (m-80) REVERT: H 59 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6773 (pt) REVERT: H 77 LEU cc_start: 0.8545 (mt) cc_final: 0.8180 (tt) REVERT: H 81 MET cc_start: 0.7719 (ptt) cc_final: 0.7267 (ptt) REVERT: K 46 GLN cc_start: 0.9095 (tm-30) cc_final: 0.7828 (tm-30) REVERT: K 172 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8887 (tt) REVERT: L 601 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: L 649 MET cc_start: 0.8537 (tpp) cc_final: 0.8104 (mmm) REVERT: L 673 TRP cc_start: 0.8320 (m-10) cc_final: 0.7621 (m-10) REVERT: L 914 MET cc_start: 0.8032 (mmm) cc_final: 0.7691 (mmm) REVERT: L 925 TYR cc_start: 0.7984 (m-80) cc_final: 0.7697 (m-80) REVERT: L 983 GLU cc_start: 0.8176 (tp30) cc_final: 0.7826 (tp30) REVERT: L 1020 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.3531 (m-80) REVERT: L 1029 GLU cc_start: 0.8484 (tt0) cc_final: 0.8203 (tt0) REVERT: L 1045 TRP cc_start: 0.8718 (m100) cc_final: 0.8397 (m100) REVERT: L 1114 MET cc_start: 0.8356 (ppp) cc_final: 0.8123 (tmm) REVERT: L 1203 ILE cc_start: 0.8966 (mt) cc_final: 0.8730 (mt) REVERT: N 23 PHE cc_start: 0.6796 (m-80) cc_final: 0.6353 (m-80) REVERT: N 77 LEU cc_start: 0.8405 (mp) cc_final: 0.8100 (pp) REVERT: N 82 TYR cc_start: 0.7236 (m-80) cc_final: 0.7018 (m-80) REVERT: P 43 GLN cc_start: 0.8138 (mt0) cc_final: 0.7787 (mt0) REVERT: P 68 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: Q 46 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8665 (tm-30) REVERT: Q 52 ASN cc_start: 0.9138 (m-40) cc_final: 0.8689 (m-40) REVERT: Q 90 ASN cc_start: 0.8560 (t0) cc_final: 0.8231 (t0) REVERT: Q 126 ASN cc_start: 0.7491 (m-40) cc_final: 0.7256 (m-40) REVERT: R 35 GLU cc_start: 0.8567 (tt0) cc_final: 0.7995 (tt0) REVERT: R 47 SER cc_start: 0.8697 (t) cc_final: 0.8049 (m) REVERT: R 73 LYS cc_start: 0.8496 (mttp) cc_final: 0.7417 (mmtp) REVERT: R 590 GLU cc_start: 0.8298 (pm20) cc_final: 0.8051 (pm20) REVERT: R 597 TYR cc_start: 0.8395 (OUTLIER) cc_final: 0.7231 (m-80) REVERT: R 917 TYR cc_start: 0.8237 (t80) cc_final: 0.7654 (t80) REVERT: R 976 TYR cc_start: 0.8504 (p90) cc_final: 0.8111 (p90) REVERT: R 980 LEU cc_start: 0.9254 (mp) cc_final: 0.8980 (mp) REVERT: R 983 GLU cc_start: 0.7903 (tp30) cc_final: 0.7356 (tp30) REVERT: R 1205 TYR cc_start: 0.9069 (t80) cc_final: 0.8629 (t80) REVERT: R 1233 ARG cc_start: 0.6484 (ppt170) cc_final: 0.6189 (ppt170) REVERT: T 23 PHE cc_start: 0.6967 (m-80) cc_final: 0.6542 (m-80) REVERT: U 77 LEU cc_start: 0.7101 (tt) cc_final: 0.6821 (tt) REVERT: W 44 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8340 (mm-30) REVERT: W 176 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7786 (mmm) REVERT: X 47 SER cc_start: 0.8408 (t) cc_final: 0.7671 (m) REVERT: X 51 THR cc_start: 0.6136 (OUTLIER) cc_final: 0.4908 (m) REVERT: X 601 GLU cc_start: 0.8435 (tp30) cc_final: 0.7200 (tp30) REVERT: X 921 LYS cc_start: 0.7516 (mtmm) cc_final: 0.7159 (mmtm) REVERT: X 977 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8399 (mmtt) REVERT: X 995 SER cc_start: 0.8783 (m) cc_final: 0.8537 (m) REVERT: X 1003 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7132 (mp10) REVERT: X 1045 TRP cc_start: 0.8227 (m100) cc_final: 0.7825 (m100) REVERT: X 1114 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8001 (tmm) REVERT: X 1169 MET cc_start: 0.7597 (mtp) cc_final: 0.7356 (mtt) REVERT: Y 81 MET cc_start: 0.7778 (mmp) cc_final: 0.7540 (mmm) REVERT: Z 23 PHE cc_start: 0.6711 (m-80) cc_final: 0.6239 (m-80) REVERT: 1 20 MET cc_start: 0.9202 (mmt) cc_final: 0.8961 (mmm) REVERT: 1 92 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8270 (mt) REVERT: 2 90 ASN cc_start: 0.8772 (t0) cc_final: 0.8395 (t0) REVERT: 2 172 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8319 (tt) REVERT: 2 186 MET cc_start: 0.8214 (ttp) cc_final: 0.7954 (ttp) REVERT: 3 78 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9028 (tp) REVERT: 3 108 ARG cc_start: 0.7724 (mtm-85) cc_final: 0.7235 (ttm110) REVERT: 3 590 GLU cc_start: 0.8701 (pm20) cc_final: 0.8379 (pm20) REVERT: 3 601 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.7321 (tp30) REVERT: 3 673 TRP cc_start: 0.8218 (m-10) cc_final: 0.7287 (m-10) REVERT: 3 925 TYR cc_start: 0.8207 (m-80) cc_final: 0.7932 (m-80) REVERT: 3 983 GLU cc_start: 0.7831 (tp30) cc_final: 0.7437 (tp30) REVERT: 3 1000 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7986 (mmm160) REVERT: 3 1003 GLN cc_start: 0.8751 (mt0) cc_final: 0.8460 (mt0) REVERT: 3 1020 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.3814 (m-80) REVERT: 3 1205 TYR cc_start: 0.9077 (t80) cc_final: 0.8592 (t80) REVERT: 4 58 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7661 (mm) REVERT: 5 23 PHE cc_start: 0.7080 (m-80) cc_final: 0.6422 (m-80) REVERT: 5 58 LEU cc_start: 0.8353 (mm) cc_final: 0.7997 (mt) REVERT: 5 59 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6911 (tp) REVERT: 5 77 LEU cc_start: 0.8232 (mp) cc_final: 0.7604 (pp) REVERT: 6 39 GLU cc_start: 0.8418 (tt0) cc_final: 0.8059 (tt0) REVERT: 6 77 LEU cc_start: 0.7394 (tt) cc_final: 0.7135 (tt) REVERT: 7 39 GLN cc_start: 0.8614 (tt0) cc_final: 0.8323 (tt0) REVERT: 8 52 ASN cc_start: 0.9070 (m-40) cc_final: 0.8844 (m-40) REVERT: 8 55 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7951 (mm110) REVERT: 8 90 ASN cc_start: 0.8897 (t0) cc_final: 0.8666 (t0) REVERT: 9 35 GLU cc_start: 0.8337 (tt0) cc_final: 0.7993 (tt0) REVERT: 9 58 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7500 (tm-30) REVERT: 9 80 PRO cc_start: 0.9583 (Cg_exo) cc_final: 0.9328 (Cg_endo) REVERT: 9 601 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: 9 606 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8430 (mm) REVERT: 9 619 GLN cc_start: 0.8693 (mp10) cc_final: 0.7770 (mp10) REVERT: 9 631 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8043 (tm-30) REVERT: 9 673 TRP cc_start: 0.8244 (m-10) cc_final: 0.7530 (m-10) REVERT: 9 1020 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.3776 (m-80) REVERT: 9 1046 SER cc_start: 0.8471 (t) cc_final: 0.8210 (t) REVERT: 9 1099 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8108 (mt) REVERT: 9 1114 MET cc_start: 0.8253 (tmm) cc_final: 0.7974 (tmm) REVERT: 9 1175 ILE cc_start: 0.9188 (mt) cc_final: 0.8963 (mt) REVERT: 9 1205 TYR cc_start: 0.8937 (t80) cc_final: 0.8561 (t80) REVERT: 9 1232 ARG cc_start: 0.5366 (mtt90) cc_final: 0.5105 (mtt-85) REVERT: b 22 LEU cc_start: 0.8547 (mp) cc_final: 0.8297 (mp) REVERT: b 77 LEU cc_start: 0.8404 (mt) cc_final: 0.7852 (tt) REVERT: c 77 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.7026 (tt) REVERT: e 90 ASN cc_start: 0.8833 (t0) cc_final: 0.8613 (t0) REVERT: f 58 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7139 (tm-30) REVERT: f 108 ARG cc_start: 0.7556 (mtm-85) cc_final: 0.7137 (ttp-110) REVERT: f 588 TRP cc_start: 0.7175 (OUTLIER) cc_final: 0.5973 (m100) REVERT: f 601 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: f 620 MET cc_start: 0.8481 (mtp) cc_final: 0.8050 (ttm) REVERT: f 1099 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7622 (mt) REVERT: f 1232 ARG cc_start: 0.5590 (mtt90) cc_final: 0.5139 (tmm160) outliers start: 378 outliers final: 314 residues processed: 1580 average time/residue: 0.4639 time to fit residues: 1281.7603 Evaluate side-chains 1670 residues out of total 5873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 1326 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain B residue 59 LEU Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain C residue 28 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 61 TRP Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 119 THR Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 82 TRP Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 588 TRP Chi-restraints excluded: chain F residue 597 TYR Chi-restraints excluded: chain F residue 601 GLU Chi-restraints excluded: chain F residue 988 ILE Chi-restraints excluded: chain F residue 999 SER Chi-restraints excluded: chain F residue 1057 LEU Chi-restraints excluded: chain F residue 1064 THR Chi-restraints excluded: chain F residue 1082 GLN Chi-restraints excluded: chain F residue 1125 ASN Chi-restraints excluded: chain F residue 1197 SER Chi-restraints excluded: chain F residue 1199 VAL Chi-restraints excluded: chain F residue 1213 TYR Chi-restraints excluded: chain F residue 1217 ILE Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain H residue 59 LEU Chi-restraints excluded: chain H residue 67 ILE Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain J residue 5 ILE Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 18 LEU Chi-restraints excluded: chain J residue 36 THR Chi-restraints excluded: chain J residue 61 TRP Chi-restraints excluded: chain J residue 76 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain J residue 106 LEU Chi-restraints excluded: chain J residue 120 VAL Chi-restraints excluded: chain J residue 124 ILE Chi-restraints excluded: chain K residue 24 THR Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 119 THR Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 176 MET Chi-restraints excluded: chain K residue 195 ILE Chi-restraints excluded: chain L residue 82 TRP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain L residue 588 TRP Chi-restraints excluded: chain L residue 597 TYR Chi-restraints excluded: chain L residue 601 GLU Chi-restraints excluded: chain L residue 641 THR Chi-restraints excluded: chain L residue 658 THR Chi-restraints excluded: chain L residue 988 ILE Chi-restraints excluded: chain L residue 1020 TYR Chi-restraints excluded: chain L residue 1064 THR Chi-restraints excluded: chain L residue 1082 GLN Chi-restraints excluded: chain L residue 1098 VAL Chi-restraints excluded: chain L residue 1125 ASN Chi-restraints excluded: chain L residue 1178 VAL Chi-restraints excluded: chain L residue 1213 TYR Chi-restraints excluded: chain L residue 1217 ILE Chi-restraints excluded: chain M residue 20 ILE Chi-restraints excluded: chain M residue 27 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 51 VAL Chi-restraints excluded: chain M residue 59 LEU Chi-restraints excluded: chain M residue 77 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 67 ILE Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain P residue 31 ILE Chi-restraints excluded: chain P residue 61 TRP Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 77 ILE Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 98 VAL Chi-restraints excluded: chain P residue 124 ILE Chi-restraints excluded: chain Q residue 24 THR Chi-restraints excluded: chain Q residue 25 ILE Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 81 THR Chi-restraints excluded: chain Q residue 119 THR Chi-restraints excluded: chain Q residue 135 LEU Chi-restraints excluded: chain Q residue 152 MET Chi-restraints excluded: chain Q residue 159 MET Chi-restraints excluded: chain R residue 82 TRP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain R residue 111 TYR Chi-restraints excluded: chain R residue 588 TRP Chi-restraints excluded: chain R residue 597 TYR Chi-restraints excluded: chain R residue 988 ILE Chi-restraints excluded: chain R residue 1082 GLN Chi-restraints excluded: chain R residue 1213 TYR Chi-restraints excluded: chain R residue 1217 ILE Chi-restraints excluded: chain R residue 1230 ILE Chi-restraints excluded: chain S residue 27 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain T residue 58 LEU Chi-restraints excluded: chain T residue 59 LEU Chi-restraints excluded: chain T residue 67 ILE Chi-restraints excluded: chain T residue 71 VAL Chi-restraints excluded: chain T residue 72 ILE Chi-restraints excluded: chain U residue 28 VAL Chi-restraints excluded: chain U residue 70 LEU Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain V residue 5 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 25 SER Chi-restraints excluded: chain V residue 49 ASN Chi-restraints excluded: chain V residue 61 TRP Chi-restraints excluded: chain V residue 76 THR Chi-restraints excluded: chain V residue 77 ILE Chi-restraints excluded: chain V residue 95 LEU Chi-restraints excluded: chain V residue 120 VAL Chi-restraints excluded: chain V residue 124 ILE Chi-restraints excluded: chain W residue 24 THR Chi-restraints excluded: chain W residue 25 ILE Chi-restraints excluded: chain W residue 44 GLU Chi-restraints excluded: chain W residue 53 THR Chi-restraints excluded: chain W residue 61 VAL Chi-restraints excluded: chain W residue 81 THR Chi-restraints excluded: chain W residue 83 TYR Chi-restraints excluded: chain W residue 106 THR Chi-restraints excluded: chain W residue 119 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 176 MET Chi-restraints excluded: chain W residue 195 ILE Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 53 VAL Chi-restraints excluded: chain X residue 82 TRP Chi-restraints excluded: chain X residue 104 LEU Chi-restraints excluded: chain X residue 106 ILE Chi-restraints excluded: chain X residue 588 TRP Chi-restraints excluded: chain X residue 596 ASN Chi-restraints excluded: chain X residue 597 TYR Chi-restraints excluded: chain X residue 606 LEU Chi-restraints excluded: chain X residue 641 THR Chi-restraints excluded: chain X residue 658 THR Chi-restraints excluded: chain X residue 906 SER Chi-restraints excluded: chain X residue 988 ILE Chi-restraints excluded: chain X residue 1011 THR Chi-restraints excluded: chain X residue 1020 TYR Chi-restraints excluded: chain X residue 1033 TRP Chi-restraints excluded: chain X residue 1085 VAL Chi-restraints excluded: chain X residue 1114 MET Chi-restraints excluded: chain X residue 1125 ASN Chi-restraints excluded: chain X residue 1162 THR Chi-restraints excluded: chain X residue 1178 VAL Chi-restraints excluded: chain X residue 1199 VAL Chi-restraints excluded: chain X residue 1213 TYR Chi-restraints excluded: chain X residue 1217 ILE Chi-restraints excluded: chain Y residue 16 VAL Chi-restraints excluded: chain Y residue 51 VAL Chi-restraints excluded: chain Y residue 59 LEU Chi-restraints excluded: chain Y residue 77 LEU Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 71 VAL Chi-restraints excluded: chain Z residue 76 VAL Chi-restraints excluded: chain 0 residue 28 VAL Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 1 residue 14 ILE Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 33 ASN Chi-restraints excluded: chain 1 residue 61 TRP Chi-restraints excluded: chain 1 residue 76 THR Chi-restraints excluded: chain 1 residue 77 ILE Chi-restraints excluded: chain 1 residue 92 LEU Chi-restraints excluded: chain 1 residue 95 LEU Chi-restraints excluded: chain 1 residue 98 VAL Chi-restraints excluded: chain 1 residue 120 VAL Chi-restraints excluded: chain 1 residue 124 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 25 ILE Chi-restraints excluded: chain 2 residue 53 THR Chi-restraints excluded: chain 2 residue 61 VAL Chi-restraints excluded: chain 2 residue 81 THR Chi-restraints excluded: chain 2 residue 106 THR Chi-restraints excluded: chain 2 residue 135 LEU Chi-restraints excluded: chain 2 residue 152 MET Chi-restraints excluded: chain 2 residue 172 LEU Chi-restraints excluded: chain 2 residue 195 ILE Chi-restraints excluded: chain 3 residue 78 ILE Chi-restraints excluded: chain 3 residue 82 TRP Chi-restraints excluded: chain 3 residue 104 LEU Chi-restraints excluded: chain 3 residue 106 ILE Chi-restraints excluded: chain 3 residue 596 ASN Chi-restraints excluded: chain 3 residue 597 TYR Chi-restraints excluded: chain 3 residue 601 GLU Chi-restraints excluded: chain 3 residue 658 THR Chi-restraints excluded: chain 3 residue 931 LEU Chi-restraints excluded: chain 3 residue 982 SER Chi-restraints excluded: chain 3 residue 988 ILE Chi-restraints excluded: chain 3 residue 1006 SER Chi-restraints excluded: chain 3 residue 1020 TYR Chi-restraints excluded: chain 3 residue 1033 TRP Chi-restraints excluded: chain 3 residue 1082 GLN Chi-restraints excluded: chain 3 residue 1114 MET Chi-restraints excluded: chain 3 residue 1125 ASN Chi-restraints excluded: chain 3 residue 1162 THR Chi-restraints excluded: chain 3 residue 1181 MET Chi-restraints excluded: chain 3 residue 1213 TYR Chi-restraints excluded: chain 3 residue 1217 ILE Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 27 LEU Chi-restraints excluded: chain 4 residue 51 VAL Chi-restraints excluded: chain 4 residue 58 LEU Chi-restraints excluded: chain 4 residue 59 LEU Chi-restraints excluded: chain 5 residue 59 LEU Chi-restraints excluded: chain 5 residue 67 ILE Chi-restraints excluded: chain 5 residue 71 VAL Chi-restraints excluded: chain 5 residue 76 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 5 ILE Chi-restraints excluded: chain 7 residue 6 ILE Chi-restraints excluded: chain 7 residue 84 ILE Chi-restraints excluded: chain 7 residue 95 LEU Chi-restraints excluded: chain 7 residue 115 VAL Chi-restraints excluded: chain 7 residue 120 VAL Chi-restraints excluded: chain 7 residue 124 ILE Chi-restraints excluded: chain 8 residue 24 THR Chi-restraints excluded: chain 8 residue 25 ILE Chi-restraints excluded: chain 8 residue 53 THR Chi-restraints excluded: chain 8 residue 61 VAL Chi-restraints excluded: chain 8 residue 81 THR Chi-restraints excluded: chain 8 residue 106 THR Chi-restraints excluded: chain 8 residue 119 THR Chi-restraints excluded: chain 8 residue 135 LEU Chi-restraints excluded: chain 8 residue 152 MET Chi-restraints excluded: chain 8 residue 166 ILE Chi-restraints excluded: chain 9 residue 82 TRP Chi-restraints excluded: chain 9 residue 104 LEU Chi-restraints excluded: chain 9 residue 106 ILE Chi-restraints excluded: chain 9 residue 601 GLU Chi-restraints excluded: chain 9 residue 606 LEU Chi-restraints excluded: chain 9 residue 988 ILE Chi-restraints excluded: chain 9 residue 1020 TYR Chi-restraints excluded: chain 9 residue 1064 THR Chi-restraints excluded: chain 9 residue 1099 LEU Chi-restraints excluded: chain 9 residue 1162 THR Chi-restraints excluded: chain 9 residue 1199 VAL Chi-restraints excluded: chain 9 residue 1213 TYR Chi-restraints excluded: chain 9 residue 1217 ILE Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 35 VAL Chi-restraints excluded: chain a residue 40 VAL Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 59 LEU Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 59 LEU Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain c residue 18 LEU Chi-restraints excluded: chain c residue 77 LEU Chi-restraints excluded: chain d residue 5 ILE Chi-restraints excluded: chain d residue 6 ILE Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 31 ILE Chi-restraints excluded: chain d residue 33 ASN Chi-restraints excluded: chain d residue 61 TRP Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 106 LEU Chi-restraints excluded: chain d residue 117 ILE Chi-restraints excluded: chain d residue 124 ILE Chi-restraints excluded: chain e residue 24 THR Chi-restraints excluded: chain e residue 70 GLU Chi-restraints excluded: chain e residue 81 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 89 ILE Chi-restraints excluded: chain e residue 106 THR Chi-restraints excluded: chain e residue 195 ILE Chi-restraints excluded: chain f residue 35 GLU Chi-restraints excluded: chain f residue 78 ILE Chi-restraints excluded: chain f residue 82 TRP Chi-restraints excluded: chain f residue 104 LEU Chi-restraints excluded: chain f residue 588 TRP Chi-restraints excluded: chain f residue 596 ASN Chi-restraints excluded: chain f residue 597 TYR Chi-restraints excluded: chain f residue 601 GLU Chi-restraints excluded: chain f residue 906 SER Chi-restraints excluded: chain f residue 988 ILE Chi-restraints excluded: chain f residue 1024 LEU Chi-restraints excluded: chain f residue 1082 GLN Chi-restraints excluded: chain f residue 1098 VAL Chi-restraints excluded: chain f residue 1099 LEU Chi-restraints excluded: chain f residue 1108 GLU Chi-restraints excluded: chain f residue 1125 ASN Chi-restraints excluded: chain f residue 1162 THR Chi-restraints excluded: chain f residue 1178 VAL Chi-restraints excluded: chain f residue 1199 VAL Chi-restraints excluded: chain f residue 1212 THR Chi-restraints excluded: chain f residue 1217 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 651 random chunks: chunk 316 optimal weight: 3.9990 chunk 410 optimal weight: 0.8980 chunk 550 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 476 optimal weight: 1.9990 chunk 76 optimal weight: 0.0040 chunk 143 optimal weight: 0.0070 chunk 517 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 531 optimal weight: 0.4980 chunk 65 optimal weight: 8.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 39 GLN D 49 ASN ** F 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1135 ASN J 39 GLN J 43 GLN L 64 ASN ** L 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 GLN ** X 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 616 GLN 3 991 ASN ** 4 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 49 ASN 9 64 ASN 9 98 GLN ** 9 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 91135 ASN d 39 GLN ** f 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.135421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.105606 restraints weight = 81242.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.108005 restraints weight = 45826.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.109518 restraints weight = 30890.481| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 55153 Z= 0.221 Angle : 0.736 13.598 75691 Z= 0.359 Chirality : 0.044 0.293 9030 Planarity : 0.006 0.132 9247 Dihedral : 4.786 38.353 7245 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.21 % Favored : 94.19 % Rotamer: Outliers : 6.01 % Allowed : 32.40 % Favored : 61.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.28 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.10), residues: 6664 helix: 1.74 (0.08), residues: 4081 sheet: 0.15 (0.22), residues: 518 loop : -2.25 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP 31045 HIS 0.005 0.001 HIS R 57 PHE 0.028 0.002 PHE 8 177 TYR 0.041 0.001 TYR X 917 ARG 0.007 0.000 ARG F1004 =============================================================================== Job complete usr+sys time: 17536.05 seconds wall clock time: 300 minutes 55.47 seconds (18055.47 seconds total)