Starting phenix.real_space_refine on Sun Sep 29 21:11:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v3z_42961/09_2024/8v3z_42961.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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 300 5.16 5 C 48846 2.51 5 N 12378 2.21 5 O 14898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 76422 Number of models: 1 Model: "" Number of chains: 42 Chain: "b" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "E" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "a" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "A" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "C" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "D" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "B" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "n" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "Y" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "k" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "V" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "P" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "o" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "Z" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "l" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "N" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "T" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "W" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "Q" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "L" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "J" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "K" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "F" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "I" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "G" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "p" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "c" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "m" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "O" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "U" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "X" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "R" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "j" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 3, 'TRANS': 143} Chain: "h" Number of atoms: 1081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1081 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 3, 'TRANS': 132} Chain: "i" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "d" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1111 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "f" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "g" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Chain: "e" Number of atoms: 2743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2743 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 6, 'TRANS': 346} Time building chain proxies: 33.95, per 1000 atoms: 0.44 Number of scatterers: 76422 At special positions: 0 Unit cell: (225.5, 218.9, 180.4, 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 300 16.00 O 14898 8.00 N 12378 7.00 C 48846 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: 13.52 Conformation dependent library (CDL) restraints added in 7.4 seconds 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18312 Finding SS restraints... Secondary structure from input PDB file: 246 helices and 97 sheets defined 31.7% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.23 Creating SS restraints... Processing helix chain 'b' and resid 3 through 19 removed outlier: 3.507A pdb=" N ILE b 7 " --> pdb=" O LYS b 3 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 33 removed outlier: 3.581A pdb=" N VAL b 30 " --> pdb=" O ASP b 26 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 85 removed outlier: 3.842A pdb=" N ASP b 81 " --> pdb=" O TYR b 77 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU b 82 " --> pdb=" O GLU b 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 82 removed outlier: 3.664A pdb=" N LYS E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS E 78 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 5 through 9 Processing helix chain 'a' and resid 11 through 13 No H-bonds generated for 'chain 'a' and resid 11 through 13' Processing helix chain 'a' and resid 69 through 82 removed outlier: 3.982A pdb=" N LYS a 73 " --> pdb=" O SER a 69 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU a 74 " --> pdb=" O ARG a 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE a 75 " --> pdb=" O MET a 71 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU a 77 " --> pdb=" O LYS a 73 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N LYS a 78 " --> pdb=" O LEU a 74 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS a 80 " --> pdb=" O GLY a 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG a 81 " --> pdb=" O GLU a 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 69 through 82 removed outlier: 4.001A pdb=" N LYS A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 75 " --> pdb=" O MET A 71 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 85 through 96 removed outlier: 4.500A pdb=" N ALA C 89 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR C 95 " --> pdb=" O ASP C 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS C 96 " --> pdb=" O PHE C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.620A pdb=" N THR C 112 " --> pdb=" O GLU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 174 removed outlier: 4.146A pdb=" N SER C 165 " --> pdb=" O ASP C 161 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ARG C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 207 removed outlier: 3.969A pdb=" N GLU C 207 " --> pdb=" O VAL C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 removed outlier: 3.659A pdb=" N GLN C 238 " --> pdb=" O GLU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 253 Processing helix chain 'C' and resid 253 through 261 removed outlier: 4.348A pdb=" N ASP C 259 " --> pdb=" O LYS C 255 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP C 260 " --> pdb=" O VAL C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 289 removed outlier: 3.731A pdb=" N GLU C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 286 " --> pdb=" O TYR C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 312 Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'D' and resid 54 through 66 removed outlier: 3.617A pdb=" N ALA D 64 " --> pdb=" O TYR D 60 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N MET D 66 " --> pdb=" O ASN D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 96 removed outlier: 3.748A pdb=" N PHE D 92 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR D 95 " --> pdb=" O ASP D 91 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS D 96 " --> pdb=" O PHE D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 124 Processing helix chain 'D' and resid 163 through 174 removed outlier: 3.532A pdb=" N THR D 174 " --> pdb=" O LEU D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 Processing helix chain 'D' and resid 234 through 238 removed outlier: 3.740A pdb=" N PHE D 237 " --> pdb=" O GLY D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 239 through 261 removed outlier: 3.700A pdb=" N ASP D 260 " --> pdb=" O VAL D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 3.613A pdb=" N LYS D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N SER D 289 " --> pdb=" O GLU D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 320 through 326 removed outlier: 3.639A pdb=" N LYS D 325 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 326 " --> pdb=" O GLN D 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.622A pdb=" N MET B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 94 Processing helix chain 'B' and resid 107 through 125 Processing helix chain 'B' and resid 159 through 174 removed outlier: 4.069A pdb=" N SER B 165 " --> pdb=" O ASP B 161 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 174 " --> pdb=" O LEU B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.660A pdb=" N PHE B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 261 Processing helix chain 'B' and resid 268 through 289 Processing helix chain 'B' and resid 301 through 313 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'n' and resid 3 through 19 Processing helix chain 'n' and resid 26 through 33 removed outlier: 3.530A pdb=" N VAL n 30 " --> pdb=" O ASP n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 85 removed outlier: 3.815A pdb=" N ASP n 81 " --> pdb=" O TYR n 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU n 82 " --> pdb=" O GLU n 78 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 82 removed outlier: 3.709A pdb=" N LYS Y 73 " --> pdb=" O SER Y 69 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU Y 77 " --> pdb=" O LYS Y 73 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LYS Y 78 " --> pdb=" O LEU Y 74 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 9 Processing helix chain 'k' and resid 11 through 13 No H-bonds generated for 'chain 'k' and resid 11 through 13' Processing helix chain 'k' and resid 69 through 82 removed outlier: 4.010A pdb=" N LYS k 73 " --> pdb=" O SER k 69 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU k 74 " --> pdb=" O ARG k 70 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU k 77 " --> pdb=" O LYS k 73 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LYS k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS k 80 " --> pdb=" O GLY k 76 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG k 81 " --> pdb=" O GLU k 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 11 through 13 No H-bonds generated for 'chain 'M' and resid 11 through 13' Processing helix chain 'M' and resid 69 through 82 removed outlier: 4.009A pdb=" N LYS M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU M 74 " --> pdb=" O ARG M 70 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE M 75 " --> pdb=" O MET M 71 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N LYS M 78 " --> pdb=" O LEU M 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS M 80 " --> pdb=" O GLY M 76 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 65 Processing helix chain 'S' and resid 85 through 96 removed outlier: 4.495A pdb=" N ALA S 89 " --> pdb=" O ASP S 85 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR S 95 " --> pdb=" O ASP S 91 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS S 96 " --> pdb=" O PHE S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 124 removed outlier: 3.505A pdb=" N THR S 112 " --> pdb=" O GLU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 174 removed outlier: 4.113A pdb=" N SER S 165 " --> pdb=" O ASP S 161 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG S 166 " --> pdb=" O GLU S 162 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 206 Processing helix chain 'S' and resid 234 through 238 removed outlier: 3.632A pdb=" N GLN S 238 " --> pdb=" O GLU S 235 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 253 Processing helix chain 'S' and resid 253 through 261 removed outlier: 4.340A pdb=" N ASP S 259 " --> pdb=" O LYS S 255 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASP S 260 " --> pdb=" O VAL S 256 " (cutoff:3.500A) Processing helix chain 'S' and resid 268 through 289 removed outlier: 3.740A pdb=" N GLU S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU S 286 " --> pdb=" O TYR S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 312 Processing helix chain 'S' and resid 320 through 327 Processing helix chain 'V' and resid 54 through 66 removed outlier: 3.642A pdb=" N ALA V 64 " --> pdb=" O TYR V 60 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET V 66 " --> pdb=" O ASN V 62 " (cutoff:3.500A) Processing helix chain 'V' and resid 86 through 96 removed outlier: 3.735A pdb=" N PHE V 92 " --> pdb=" O THR V 88 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR V 95 " --> pdb=" O ASP V 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS V 96 " --> pdb=" O PHE V 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 124 Processing helix chain 'V' and resid 163 through 174 removed outlier: 3.535A pdb=" N THR V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) Processing helix chain 'V' and resid 195 through 205 Processing helix chain 'V' and resid 235 through 238 Processing helix chain 'V' and resid 239 through 261 removed outlier: 3.697A pdb=" N ASP V 260 " --> pdb=" O VAL V 256 " (cutoff:3.500A) Processing helix chain 'V' and resid 268 through 289 removed outlier: 3.623A pdb=" N LYS V 288 " --> pdb=" O GLU V 284 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER V 289 " --> pdb=" O GLU V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 301 through 313 Processing helix chain 'V' and resid 320 through 326 removed outlier: 3.608A pdb=" N LYS V 325 " --> pdb=" O LEU V 321 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU V 326 " --> pdb=" O GLN V 322 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 66 removed outlier: 3.500A pdb=" N TYR P 60 " --> pdb=" O GLU P 56 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET P 66 " --> pdb=" O ASN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 86 through 96 removed outlier: 4.363A pdb=" N THR P 95 " --> pdb=" O ASP P 91 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS P 96 " --> pdb=" O PHE P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 107 through 125 Processing helix chain 'P' and resid 159 through 174 removed outlier: 4.073A pdb=" N SER P 165 " --> pdb=" O ASP P 161 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG P 166 " --> pdb=" O GLU P 162 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR P 174 " --> pdb=" O LEU P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 206 Processing helix chain 'P' and resid 234 through 238 removed outlier: 3.676A pdb=" N PHE P 237 " --> pdb=" O GLY P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 239 through 261 Processing helix chain 'P' and resid 268 through 289 Processing helix chain 'P' and resid 301 through 313 Processing helix chain 'P' and resid 320 through 326 Processing helix chain 'o' and resid 3 through 19 removed outlier: 3.504A pdb=" N ILE o 7 " --> pdb=" O LYS o 3 " (cutoff:3.500A) Processing helix chain 'o' and resid 26 through 33 removed outlier: 3.586A pdb=" N VAL o 30 " --> pdb=" O ASP o 26 " (cutoff:3.500A) Processing helix chain 'o' and resid 72 through 85 removed outlier: 3.894A pdb=" N ASP o 81 " --> pdb=" O TYR o 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU o 82 " --> pdb=" O GLU o 78 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 82 removed outlier: 3.696A pdb=" N LYS Z 73 " --> pdb=" O SER Z 69 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLU Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS Z 78 " --> pdb=" O LEU Z 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 5 through 9 Processing helix chain 'l' and resid 11 through 13 No H-bonds generated for 'chain 'l' and resid 11 through 13' Processing helix chain 'l' and resid 69 through 82 removed outlier: 3.991A pdb=" N LYS l 73 " --> pdb=" O SER l 69 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU l 74 " --> pdb=" O ARG l 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE l 75 " --> pdb=" O MET l 71 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N GLU l 77 " --> pdb=" O LYS l 73 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LYS l 78 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS l 80 " --> pdb=" O GLY l 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG l 81 " --> pdb=" O GLU l 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 9 Processing helix chain 'N' and resid 11 through 13 No H-bonds generated for 'chain 'N' and resid 11 through 13' Processing helix chain 'N' and resid 69 through 82 removed outlier: 4.007A pdb=" N LYS N 73 " --> pdb=" O SER N 69 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU N 74 " --> pdb=" O ARG N 70 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE N 75 " --> pdb=" O MET N 71 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU N 77 " --> pdb=" O LYS N 73 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LYS N 78 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS N 80 " --> pdb=" O GLY N 76 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG N 81 " --> pdb=" O GLU N 77 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 65 Processing helix chain 'T' and resid 85 through 96 removed outlier: 4.519A pdb=" N ALA T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR T 95 " --> pdb=" O ASP T 91 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS T 96 " --> pdb=" O PHE T 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 124 Processing helix chain 'T' and resid 159 through 174 removed outlier: 4.127A pdb=" N SER T 165 " --> pdb=" O ASP T 161 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG T 166 " --> pdb=" O GLU T 162 " (cutoff:3.500A) Processing helix chain 'T' and resid 195 through 206 Processing helix chain 'T' and resid 234 through 238 removed outlier: 3.594A pdb=" N GLN T 238 " --> pdb=" O GLU T 235 " (cutoff:3.500A) Processing helix chain 'T' and resid 239 through 253 Processing helix chain 'T' and resid 253 through 261 removed outlier: 4.306A pdb=" N ASP T 259 " --> pdb=" O LYS T 255 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP T 260 " --> pdb=" O VAL T 256 " (cutoff:3.500A) Processing helix chain 'T' and resid 268 through 289 removed outlier: 3.744A pdb=" N GLU T 285 " --> pdb=" O SER T 281 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU T 286 " --> pdb=" O TYR T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 301 through 312 Processing helix chain 'T' and resid 320 through 327 Processing helix chain 'W' and resid 54 through 66 removed outlier: 3.564A pdb=" N ALA W 64 " --> pdb=" O TYR W 60 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N MET W 66 " --> pdb=" O ASN W 62 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 96 removed outlier: 3.732A pdb=" N PHE W 92 " --> pdb=" O THR W 88 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR W 95 " --> pdb=" O ASP W 91 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS W 96 " --> pdb=" O PHE W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 107 through 124 Processing helix chain 'W' and resid 163 through 174 removed outlier: 3.524A pdb=" N THR W 174 " --> pdb=" O LEU W 170 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 205 Processing helix chain 'W' and resid 234 through 238 removed outlier: 3.670A pdb=" N PHE W 237 " --> pdb=" O GLY W 234 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 261 removed outlier: 3.704A pdb=" N ASP W 260 " --> pdb=" O VAL W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 268 through 289 removed outlier: 3.532A pdb=" N LYS W 288 " --> pdb=" O GLU W 284 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER W 289 " --> pdb=" O GLU W 285 " (cutoff:3.500A) Processing helix chain 'W' and resid 301 through 313 Processing helix chain 'W' and resid 320 through 326 removed outlier: 3.611A pdb=" N LYS W 325 " --> pdb=" O LEU W 321 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU W 326 " --> pdb=" O GLN W 322 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 66 removed outlier: 3.576A pdb=" N MET Q 66 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 96 removed outlier: 4.389A pdb=" N THR Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LYS Q 96 " --> pdb=" O PHE Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 125 Processing helix chain 'Q' and resid 159 through 174 removed outlier: 4.051A pdb=" N SER Q 165 " --> pdb=" O ASP Q 161 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR Q 174 " --> pdb=" O LEU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 206 Processing helix chain 'Q' and resid 234 through 238 removed outlier: 3.676A pdb=" N PHE Q 237 " --> pdb=" O GLY Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 261 Processing helix chain 'Q' and resid 268 through 289 Processing helix chain 'Q' and resid 301 through 313 Processing helix chain 'Q' and resid 320 through 326 Processing helix chain 'L' and resid 3 through 19 removed outlier: 3.511A pdb=" N ILE L 7 " --> pdb=" O LYS L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 33 removed outlier: 3.568A pdb=" N VAL L 30 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 85 removed outlier: 3.837A pdb=" N ASP L 81 " --> pdb=" O TYR L 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU L 82 " --> pdb=" O GLU L 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 82 removed outlier: 3.692A pdb=" N LYS J 73 " --> pdb=" O SER J 69 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLU J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS J 78 " --> pdb=" O LEU J 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 13 No H-bonds generated for 'chain 'K' and resid 11 through 13' Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.983A pdb=" N LYS K 73 " --> pdb=" O SER K 69 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU K 74 " --> pdb=" O ARG K 70 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE K 75 " --> pdb=" O MET K 71 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LYS K 78 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS K 80 " --> pdb=" O GLY K 76 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 9 Processing helix chain 'F' and resid 11 through 13 No H-bonds generated for 'chain 'F' and resid 11 through 13' Processing helix chain 'F' and resid 69 through 82 removed outlier: 4.003A pdb=" N LYS F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU F 74 " --> pdb=" O ARG F 70 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE F 75 " --> pdb=" O MET F 71 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LYS F 78 " --> pdb=" O LEU F 74 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 80 " --> pdb=" O GLY F 76 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 65 Processing helix chain 'H' and resid 85 through 96 removed outlier: 4.499A pdb=" N ALA H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR H 95 " --> pdb=" O ASP H 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS H 96 " --> pdb=" O PHE H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.612A pdb=" N THR H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 174 removed outlier: 4.137A pdb=" N SER H 165 " --> pdb=" O ASP H 161 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 207 removed outlier: 3.971A pdb=" N GLU H 207 " --> pdb=" O VAL H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 238 removed outlier: 3.662A pdb=" N GLN H 238 " --> pdb=" O GLU H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 253 Processing helix chain 'H' and resid 253 through 261 removed outlier: 4.329A pdb=" N ASP H 259 " --> pdb=" O LYS H 255 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP H 260 " --> pdb=" O VAL H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 289 removed outlier: 3.730A pdb=" N GLU H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU H 286 " --> pdb=" O TYR H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 312 Processing helix chain 'H' and resid 320 through 327 Processing helix chain 'I' and resid 54 through 66 removed outlier: 3.615A pdb=" N ALA I 64 " --> pdb=" O TYR I 60 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET I 66 " --> pdb=" O ASN I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 96 removed outlier: 3.746A pdb=" N PHE I 92 " --> pdb=" O THR I 88 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS I 96 " --> pdb=" O PHE I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 124 Processing helix chain 'I' and resid 163 through 174 removed outlier: 3.527A pdb=" N THR I 174 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 205 Processing helix chain 'I' and resid 234 through 238 removed outlier: 3.740A pdb=" N PHE I 237 " --> pdb=" O GLY I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 261 removed outlier: 3.695A pdb=" N ASP I 260 " --> pdb=" O VAL I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 289 removed outlier: 3.612A pdb=" N LYS I 288 " --> pdb=" O GLU I 284 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER I 289 " --> pdb=" O GLU I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 313 Processing helix chain 'I' and resid 320 through 326 removed outlier: 3.638A pdb=" N LYS I 325 " --> pdb=" O LEU I 321 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU I 326 " --> pdb=" O GLN I 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 66 removed outlier: 3.628A pdb=" N MET G 66 " --> pdb=" O ASN G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 94 Processing helix chain 'G' and resid 107 through 125 Processing helix chain 'G' and resid 159 through 174 removed outlier: 4.062A pdb=" N SER G 165 " --> pdb=" O ASP G 161 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR G 174 " --> pdb=" O LEU G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 234 through 238 removed outlier: 3.677A pdb=" N PHE G 237 " --> pdb=" O GLY G 234 " (cutoff:3.500A) Processing helix chain 'G' and resid 239 through 261 Processing helix chain 'G' and resid 268 through 289 Processing helix chain 'G' and resid 301 through 313 Processing helix chain 'G' and resid 320 through 326 Processing helix chain 'p' and resid 3 through 19 removed outlier: 3.504A pdb=" N ILE p 7 " --> pdb=" O LYS p 3 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 33 removed outlier: 3.522A pdb=" N VAL p 30 " --> pdb=" O ASP p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 85 removed outlier: 3.813A pdb=" N ASP p 81 " --> pdb=" O TYR p 77 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU p 82 " --> pdb=" O GLU p 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 82 removed outlier: 3.713A pdb=" N LYS c 73 " --> pdb=" O SER c 69 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU c 77 " --> pdb=" O LYS c 73 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS c 78 " --> pdb=" O LEU c 74 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 9 Processing helix chain 'm' and resid 11 through 13 No H-bonds generated for 'chain 'm' and resid 11 through 13' Processing helix chain 'm' and resid 69 through 82 removed outlier: 4.006A pdb=" N LYS m 73 " --> pdb=" O SER m 69 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLU m 77 " --> pdb=" O LYS m 73 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LYS m 78 " --> pdb=" O LEU m 74 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS m 80 " --> pdb=" O GLY m 76 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG m 81 " --> pdb=" O GLU m 77 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 11 through 13 No H-bonds generated for 'chain 'O' and resid 11 through 13' Processing helix chain 'O' and resid 69 through 82 removed outlier: 4.016A pdb=" N LYS O 73 " --> pdb=" O SER O 69 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU O 74 " --> pdb=" O ARG O 70 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE O 75 " --> pdb=" O MET O 71 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N GLU O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS O 78 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS O 80 " --> pdb=" O GLY O 76 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG O 81 " --> pdb=" O GLU O 77 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 65 Processing helix chain 'U' and resid 85 through 96 removed outlier: 4.493A pdb=" N ALA U 89 " --> pdb=" O ASP U 85 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR U 95 " --> pdb=" O ASP U 91 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS U 96 " --> pdb=" O PHE U 92 " (cutoff:3.500A) Processing helix chain 'U' and resid 107 through 124 removed outlier: 3.503A pdb=" N THR U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 174 removed outlier: 4.112A pdb=" N SER U 165 " --> pdb=" O ASP U 161 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG U 166 " --> pdb=" O GLU U 162 " (cutoff:3.500A) Processing helix chain 'U' and resid 195 through 206 Processing helix chain 'U' and resid 234 through 238 removed outlier: 3.504A pdb=" N PHE U 237 " --> pdb=" O GLY U 234 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN U 238 " --> pdb=" O GLU U 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 234 through 238' Processing helix chain 'U' and resid 239 through 253 Processing helix chain 'U' and resid 253 through 261 removed outlier: 4.340A pdb=" N ASP U 259 " --> pdb=" O LYS U 255 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP U 260 " --> pdb=" O VAL U 256 " (cutoff:3.500A) Processing helix chain 'U' and resid 268 through 289 removed outlier: 3.741A pdb=" N GLU U 285 " --> pdb=" O SER U 281 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU U 286 " --> pdb=" O TYR U 282 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 312 Processing helix chain 'U' and resid 320 through 327 Processing helix chain 'X' and resid 54 through 66 removed outlier: 3.642A pdb=" N ALA X 64 " --> pdb=" O TYR X 60 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N MET X 66 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 96 removed outlier: 3.714A pdb=" N PHE X 92 " --> pdb=" O THR X 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR X 95 " --> pdb=" O ASP X 91 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS X 96 " --> pdb=" O PHE X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 124 Processing helix chain 'X' and resid 163 through 174 removed outlier: 3.537A pdb=" N THR X 174 " --> pdb=" O LEU X 170 " (cutoff:3.500A) Processing helix chain 'X' and resid 195 through 205 Processing helix chain 'X' and resid 235 through 238 Processing helix chain 'X' and resid 239 through 261 removed outlier: 3.692A pdb=" N ASP X 260 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Processing helix chain 'X' and resid 268 through 289 removed outlier: 3.628A pdb=" N LYS X 288 " --> pdb=" O GLU X 284 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER X 289 " --> pdb=" O GLU X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 301 through 313 Processing helix chain 'X' and resid 320 through 326 removed outlier: 3.618A pdb=" N LYS X 325 " --> pdb=" O LEU X 321 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU X 326 " --> pdb=" O GLN X 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 54 through 66 removed outlier: 3.609A pdb=" N MET R 66 " --> pdb=" O ASN R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 96 removed outlier: 4.359A pdb=" N THR R 95 " --> pdb=" O ASP R 91 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS R 96 " --> pdb=" O PHE R 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 125 Processing helix chain 'R' and resid 159 through 174 removed outlier: 4.079A pdb=" N SER R 165 " --> pdb=" O ASP R 161 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 206 Processing helix chain 'R' and resid 234 through 238 removed outlier: 3.689A pdb=" N PHE R 237 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 239 through 261 Processing helix chain 'R' and resid 268 through 289 Processing helix chain 'R' and resid 301 through 313 Processing helix chain 'R' and resid 320 through 326 Processing helix chain 'j' and resid 3 through 19 removed outlier: 3.503A pdb=" N ILE j 7 " --> pdb=" O LYS j 3 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 33 removed outlier: 3.589A pdb=" N VAL j 30 " --> pdb=" O ASP j 26 " (cutoff:3.500A) Processing helix chain 'j' and resid 72 through 85 removed outlier: 3.896A pdb=" N ASP j 81 " --> pdb=" O TYR j 77 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU j 82 " --> pdb=" O GLU j 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 82 removed outlier: 3.717A pdb=" N LYS h 73 " --> pdb=" O SER h 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU h 77 " --> pdb=" O LYS h 73 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS h 78 " --> pdb=" O LEU h 74 " (cutoff:3.500A) Processing helix chain 'i' and resid 5 through 9 Processing helix chain 'i' and resid 11 through 13 No H-bonds generated for 'chain 'i' and resid 11 through 13' Processing helix chain 'i' and resid 69 through 82 removed outlier: 3.977A pdb=" N LYS i 73 " --> pdb=" O SER i 69 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE i 75 " --> pdb=" O MET i 71 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLU i 77 " --> pdb=" O LYS i 73 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LYS i 78 " --> pdb=" O LEU i 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS i 80 " --> pdb=" O GLY i 76 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG i 81 " --> pdb=" O GLU i 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 5 through 9 Processing helix chain 'd' and resid 11 through 13 No H-bonds generated for 'chain 'd' and resid 11 through 13' Processing helix chain 'd' and resid 69 through 82 removed outlier: 4.003A pdb=" N LYS d 73 " --> pdb=" O SER d 69 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE d 75 " --> pdb=" O MET d 71 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLU d 77 " --> pdb=" O LYS d 73 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LYS d 78 " --> pdb=" O LEU d 74 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LYS d 80 " --> pdb=" O GLY d 76 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG d 81 " --> pdb=" O GLU d 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 54 through 65 Processing helix chain 'f' and resid 85 through 96 removed outlier: 4.511A pdb=" N ALA f 89 " --> pdb=" O ASP f 85 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR f 95 " --> pdb=" O ASP f 91 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS f 96 " --> pdb=" O PHE f 92 " (cutoff:3.500A) Processing helix chain 'f' and resid 107 through 124 Processing helix chain 'f' and resid 159 through 174 removed outlier: 4.125A pdb=" N SER f 165 " --> pdb=" O ASP f 161 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG f 166 " --> pdb=" O GLU f 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 195 through 207 removed outlier: 3.968A pdb=" N GLU f 207 " --> pdb=" O VAL f 203 " (cutoff:3.500A) Processing helix chain 'f' and resid 234 through 238 removed outlier: 3.616A pdb=" N GLN f 238 " --> pdb=" O GLU f 235 " (cutoff:3.500A) Processing helix chain 'f' and resid 239 through 253 Processing helix chain 'f' and resid 253 through 261 removed outlier: 4.301A pdb=" N ASP f 259 " --> pdb=" O LYS f 255 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ASP f 260 " --> pdb=" O VAL f 256 " (cutoff:3.500A) Processing helix chain 'f' and resid 268 through 289 removed outlier: 3.743A pdb=" N GLU f 285 " --> pdb=" O SER f 281 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU f 286 " --> pdb=" O TYR f 282 " (cutoff:3.500A) Processing helix chain 'f' and resid 301 through 312 Processing helix chain 'f' and resid 320 through 327 Processing helix chain 'g' and resid 54 through 66 removed outlier: 3.564A pdb=" N ALA g 64 " --> pdb=" O TYR g 60 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N MET g 66 " --> pdb=" O ASN g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 96 removed outlier: 3.712A pdb=" N PHE g 92 " --> pdb=" O THR g 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR g 95 " --> pdb=" O ASP g 91 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS g 96 " --> pdb=" O PHE g 92 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 124 Processing helix chain 'g' and resid 163 through 174 removed outlier: 3.524A pdb=" N THR g 174 " --> pdb=" O LEU g 170 " (cutoff:3.500A) Processing helix chain 'g' and resid 195 through 205 Processing helix chain 'g' and resid 234 through 238 removed outlier: 3.674A pdb=" N PHE g 237 " --> pdb=" O GLY g 234 " (cutoff:3.500A) Processing helix chain 'g' and resid 239 through 261 removed outlier: 3.704A pdb=" N ASP g 260 " --> pdb=" O VAL g 256 " (cutoff:3.500A) Processing helix chain 'g' and resid 268 through 289 removed outlier: 3.528A pdb=" N LYS g 288 " --> pdb=" O GLU g 284 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER g 289 " --> pdb=" O GLU g 285 " (cutoff:3.500A) Processing helix chain 'g' and resid 301 through 313 Processing helix chain 'g' and resid 320 through 326 removed outlier: 3.617A pdb=" N LYS g 325 " --> pdb=" O LEU g 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU g 326 " --> pdb=" O GLN g 322 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 66 removed outlier: 3.544A pdb=" N MET e 66 " --> pdb=" O ASN e 62 " (cutoff:3.500A) Processing helix chain 'e' and resid 86 through 96 removed outlier: 4.385A pdb=" N THR e 95 " --> pdb=" O ASP e 91 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYS e 96 " --> pdb=" O PHE e 92 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 125 Processing helix chain 'e' and resid 159 through 174 removed outlier: 4.040A pdb=" N SER e 165 " --> pdb=" O ASP e 161 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG e 166 " --> pdb=" O GLU e 162 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR e 174 " --> pdb=" O LEU e 170 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 206 Processing helix chain 'e' and resid 234 through 238 removed outlier: 3.640A pdb=" N PHE e 237 " --> pdb=" O GLY e 234 " (cutoff:3.500A) Processing helix chain 'e' and resid 239 through 261 Processing helix chain 'e' and resid 268 through 289 Processing helix chain 'e' and resid 301 through 313 Processing helix chain 'e' and resid 320 through 326 Processing sheet with id=AA1, first strand: chain 'b' and resid 23 through 24 removed outlier: 6.839A pdb=" N PHE b 24 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 9.312A pdb=" N ILE b 42 " --> pdb=" O PHE b 24 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE b 38 " --> pdb=" O LEU b 66 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU b 66 " --> pdb=" O PHE b 38 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N VAL b 40 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS b 64 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE b 42 " --> pdb=" O SER b 62 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER b 62 " --> pdb=" O ILE b 42 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER b 44 " --> pdb=" O VAL b 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 54 through 66 current: chain 'b' and resid 96 through 110 removed outlier: 14.894A pdb=" N ARG b 96 " --> pdb=" O SER b 127 " (cutoff:3.500A) removed outlier: 13.673A pdb=" N SER b 127 " --> pdb=" O ARG b 96 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N LEU b 98 " --> pdb=" O LEU b 125 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N LEU b 125 " --> pdb=" O LEU b 98 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE b 100 " --> pdb=" O ASN b 123 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ASN b 123 " --> pdb=" O ILE b 100 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS b 102 " --> pdb=" O THR b 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 113 through 127 current: chain 'n' and resid 37 through 49 removed outlier: 3.817A pdb=" N CYS n 37 " --> pdb=" O LEU n 66 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL n 60 " --> pdb=" O LEU n 43 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL n 45 " --> pdb=" O ASP n 58 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP n 58 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS n 47 " --> pdb=" O ASN n 56 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ASN n 56 " --> pdb=" O CYS n 47 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR n 54 " --> pdb=" O PRO n 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 54 through 66 current: chain 'n' and resid 96 through 110 removed outlier: 14.900A pdb=" N ARG n 96 " --> pdb=" O SER n 127 " (cutoff:3.500A) removed outlier: 13.663A pdb=" N SER n 127 " --> pdb=" O ARG n 96 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N LEU n 98 " --> pdb=" O LEU n 125 " (cutoff:3.500A) removed outlier: 9.929A pdb=" N LEU n 125 " --> pdb=" O LEU n 98 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE n 100 " --> pdb=" O ASN n 123 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN n 123 " --> pdb=" O ILE n 100 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS n 102 " --> pdb=" O THR n 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 113 through 127 current: chain 'o' and resid 37 through 49 removed outlier: 3.804A pdb=" N CYS o 37 " --> pdb=" O LEU o 66 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL o 60 " --> pdb=" O LEU o 43 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL o 45 " --> pdb=" O ASP o 58 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASP o 58 " --> pdb=" O VAL o 45 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N CYS o 47 " --> pdb=" O ASN o 56 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN o 56 " --> pdb=" O CYS o 47 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N THR o 54 " --> pdb=" O PRO o 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 54 through 66 current: chain 'o' and resid 96 through 110 removed outlier: 14.915A pdb=" N ARG o 96 " --> pdb=" O SER o 127 " (cutoff:3.500A) removed outlier: 13.622A pdb=" N SER o 127 " --> pdb=" O ARG o 96 " (cutoff:3.500A) removed outlier: 9.647A pdb=" N LEU o 98 " --> pdb=" O LEU o 125 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N LEU o 125 " --> pdb=" O LEU o 98 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ILE o 100 " --> pdb=" O ASN o 123 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASN o 123 " --> pdb=" O ILE o 100 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS o 102 " --> pdb=" O THR o 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 113 through 127 current: chain 'L' and resid 37 through 49 removed outlier: 6.283A pdb=" N PHE L 38 " --> pdb=" O LEU L 66 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU L 66 " --> pdb=" O PHE L 38 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL L 40 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LYS L 64 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE L 42 " --> pdb=" O SER L 62 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER L 62 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER L 44 " --> pdb=" O VAL L 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 54 through 66 current: chain 'L' and resid 96 through 110 removed outlier: 14.895A pdb=" N ARG L 96 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 13.673A pdb=" N SER L 127 " --> pdb=" O ARG L 96 " (cutoff:3.500A) removed outlier: 9.555A pdb=" N LEU L 98 " --> pdb=" O LEU L 125 " (cutoff:3.500A) removed outlier: 9.943A pdb=" N LEU L 125 " --> pdb=" O LEU L 98 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE L 100 " --> pdb=" O ASN L 123 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ASN L 123 " --> pdb=" O ILE L 100 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LYS L 102 " --> pdb=" O THR L 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 113 through 127 current: chain 'p' and resid 37 through 49 removed outlier: 3.814A pdb=" N CYS p 37 " --> pdb=" O LEU p 66 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL p 60 " --> pdb=" O LEU p 43 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL p 45 " --> pdb=" O ASP p 58 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ASP p 58 " --> pdb=" O VAL p 45 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N CYS p 47 " --> pdb=" O ASN p 56 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ASN p 56 " --> pdb=" O CYS p 47 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR p 54 " --> pdb=" O PRO p 49 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 54 through 66 current: chain 'p' and resid 96 through 110 removed outlier: 14.893A pdb=" N ARG p 96 " --> pdb=" O SER p 127 " (cutoff:3.500A) removed outlier: 13.663A pdb=" N SER p 127 " --> pdb=" O ARG p 96 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N LEU p 98 " --> pdb=" O LEU p 125 " (cutoff:3.500A) removed outlier: 9.934A pdb=" N LEU p 125 " --> pdb=" O LEU p 98 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ILE p 100 " --> pdb=" O ASN p 123 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASN p 123 " --> pdb=" O ILE p 100 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS p 102 " --> pdb=" O THR p 121 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'p' and resid 113 through 127 current: chain 'j' and resid 37 through 49 removed outlier: 6.250A pdb=" N PHE j 38 " --> pdb=" O LEU j 66 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU j 66 " --> pdb=" O PHE j 38 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL j 40 " --> pdb=" O LYS j 64 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS j 64 " --> pdb=" O VAL j 40 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE j 42 " --> pdb=" O SER j 62 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N SER j 62 " --> pdb=" O ILE j 42 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER j 44 " --> pdb=" O VAL j 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'j' and resid 54 through 66 current: chain 'j' and resid 96 through 110 removed outlier: 14.922A pdb=" N ARG j 96 " --> pdb=" O SER j 127 " (cutoff:3.500A) removed outlier: 13.622A pdb=" N SER j 127 " --> pdb=" O ARG j 96 " (cutoff:3.500A) removed outlier: 9.651A pdb=" N LEU j 98 " --> pdb=" O LEU j 125 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N LEU j 125 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ILE j 100 " --> pdb=" O ASN j 123 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN j 123 " --> pdb=" O ILE j 100 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LYS j 102 " --> pdb=" O THR j 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 140 through 146 Processing sheet with id=AA3, first strand: chain 'E' and resid 15 through 19 removed outlier: 4.700A pdb=" N LEU E 17 " --> pdb=" O VAL E 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 22 through 24 current: chain 'E' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 65 current: chain 'E' and resid 102 through 111 Processing sheet with id=AA4, first strand: chain 'E' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 113 through 120 current: chain 'h' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 22 through 24 current: chain 'h' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 50 through 65 current: chain 'h' and resid 102 through 111 Processing sheet with id=AA5, first strand: chain 'a' and resid 15 through 19 removed outlier: 4.466A pdb=" N LEU a 17 " --> pdb=" O VAL a 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 22 through 24 current: chain 'a' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 50 through 65 current: chain 'a' and resid 102 through 111 Processing sheet with id=AA6, first strand: chain 'a' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 113 through 120 current: chain 'i' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 22 through 24 current: chain 'i' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 50 through 65 current: chain 'i' and resid 102 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 15 through 19 removed outlier: 4.455A pdb=" N LEU A 17 " --> pdb=" O VAL A 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 22 through 24 current: chain 'A' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 50 through 65 current: chain 'A' and resid 101 through 111 Processing sheet with id=AA8, first strand: chain 'A' and resid 113 through 120 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 113 through 120 current: chain 'd' and resid 22 through 24 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 22 through 24 current: chain 'd' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'd' and resid 50 through 65 current: chain 'd' and resid 101 through 111 Processing sheet with id=AA9, first strand: chain 'C' and resid 8 through 13 removed outlier: 6.240A pdb=" N ASN C 9 " --> pdb=" O LEU f 350 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ILE f 352 " --> pdb=" O ASN C 9 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N SER C 11 " --> pdb=" O ILE f 352 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 43 removed outlier: 6.751A pdb=" N ILE C 28 " --> pdb=" O LEU C 76 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N TYR C 78 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N MET C 30 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ILE C 80 " --> pdb=" O MET C 30 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU C 32 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 31 " --> pdb=" O CYS C 102 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU C 101 " --> pdb=" O VAL C 132 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 153 removed outlier: 3.590A pdb=" N VAL C 153 " --> pdb=" O LYS C 156 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 210 through 213 removed outlier: 3.600A pdb=" N ALA C 216 " --> pdb=" O GLU C 213 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 297 through 300 removed outlier: 3.571A pdb=" N ASN S 9 " --> pdb=" O ILE C 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 8 through 13 removed outlier: 3.675A pdb=" N ASN D 9 " --> pdb=" O ILE g 348 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU g 350 " --> pdb=" O ASN D 9 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE g 352 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 41 through 43 removed outlier: 3.611A pdb=" N VAL D 77 " --> pdb=" O ASN D 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU D 101 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA D 131 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 157 through 158 removed outlier: 7.234A pdb=" N LEU D 152 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 210 through 211 Processing sheet with id=AB9, first strand: chain 'B' and resid 297 through 300 removed outlier: 3.696A pdb=" N ASN V 9 " --> pdb=" O ILE D 348 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU D 350 " --> pdb=" O ASN V 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 9 through 13 removed outlier: 6.804A pdb=" N ASN B 9 " --> pdb=" O LEU e 350 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ILE e 352 " --> pdb=" O ASN B 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER B 11 " --> pdb=" O ILE e 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 39 through 43 removed outlier: 3.787A pdb=" N CYS B 102 " --> pdb=" O ALA B 29 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL B 31 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 101 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA B 131 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 156 through 158 removed outlier: 7.301A pdb=" N LEU B 152 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 210 through 211 removed outlier: 3.533A pdb=" N ILE B 211 " --> pdb=" O ARG B 218 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 349 through 353 removed outlier: 3.688A pdb=" N LYS P 13 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'n' and resid 140 through 146 Processing sheet with id=AC7, first strand: chain 'Y' and resid 15 through 19 removed outlier: 4.703A pdb=" N LEU Y 17 " --> pdb=" O VAL Y 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 22 through 24 current: chain 'Y' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 50 through 65 current: chain 'Y' and resid 102 through 111 Processing sheet with id=AC8, first strand: chain 'k' and resid 15 through 19 removed outlier: 4.519A pdb=" N LEU k 17 " --> pdb=" O VAL k 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 22 through 24 current: chain 'k' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'k' and resid 50 through 65 current: chain 'k' and resid 102 through 111 Processing sheet with id=AC9, first strand: chain 'M' and resid 15 through 19 removed outlier: 4.391A pdb=" N LEU M 17 " --> pdb=" O VAL M 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 22 through 24 current: chain 'M' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 50 through 65 current: chain 'M' and resid 101 through 111 Processing sheet with id=AD1, first strand: chain 'S' and resid 39 through 43 removed outlier: 6.778A pdb=" N ILE S 28 " --> pdb=" O LEU S 76 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N TYR S 78 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET S 30 " --> pdb=" O TYR S 78 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE S 80 " --> pdb=" O MET S 30 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU S 32 " --> pdb=" O ILE S 80 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL S 31 " --> pdb=" O CYS S 102 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU S 101 " --> pdb=" O VAL S 132 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 151 through 153 removed outlier: 3.562A pdb=" N VAL S 153 " --> pdb=" O LYS S 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'S' and resid 210 through 213 removed outlier: 3.600A pdb=" N ALA S 216 " --> pdb=" O GLU S 213 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 297 through 300 removed outlier: 6.826A pdb=" N ASP S 347 " --> pdb=" O VAL V 333 " (cutoff:3.500A) removed outlier: 8.161A pdb=" N LEU V 335 " --> pdb=" O ASP S 347 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP S 349 " --> pdb=" O LEU V 335 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA V 337 " --> pdb=" O ASP S 349 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER S 351 " --> pdb=" O ALA V 337 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN T 9 " --> pdb=" O ILE S 348 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 41 through 43 removed outlier: 3.585A pdb=" N VAL V 77 " --> pdb=" O ASN V 41 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU V 101 " --> pdb=" O VAL V 132 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'V' and resid 157 through 158 removed outlier: 7.193A pdb=" N LEU V 152 " --> pdb=" O VAL V 189 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 210 through 211 Processing sheet with id=AD8, first strand: chain 'P' and resid 297 through 300 removed outlier: 6.657A pdb=" N ILE V 348 " --> pdb=" O ASN W 9 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER W 11 " --> pdb=" O ILE V 348 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU V 350 " --> pdb=" O SER W 11 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LYS W 13 " --> pdb=" O LEU V 350 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ILE V 352 " --> pdb=" O LYS W 13 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 39 through 43 removed outlier: 3.843A pdb=" N CYS P 102 " --> pdb=" O ALA P 29 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL P 31 " --> pdb=" O CYS P 102 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU P 101 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA P 131 " --> pdb=" O ILE P 144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 151 through 153 Processing sheet with id=AE2, first strand: chain 'P' and resid 210 through 211 Processing sheet with id=AE3, first strand: chain 'P' and resid 349 through 353 removed outlier: 3.674A pdb=" N LYS Q 13 " --> pdb=" O ILE P 352 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'o' and resid 140 through 146 Processing sheet with id=AE5, first strand: chain 'Z' and resid 15 through 19 removed outlier: 4.747A pdb=" N LEU Z 17 " --> pdb=" O VAL Z 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 22 through 24 current: chain 'Z' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 50 through 65 current: chain 'Z' and resid 102 through 111 Processing sheet with id=AE6, first strand: chain 'l' and resid 15 through 19 removed outlier: 4.527A pdb=" N LEU l 17 " --> pdb=" O VAL l 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 22 through 24 current: chain 'l' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 50 through 65 current: chain 'l' and resid 102 through 111 Processing sheet with id=AE7, first strand: chain 'N' and resid 15 through 19 removed outlier: 4.418A pdb=" N LEU N 17 " --> pdb=" O VAL N 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 22 through 24 current: chain 'N' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 50 through 65 current: chain 'N' and resid 101 through 111 Processing sheet with id=AE8, first strand: chain 'T' and resid 39 through 43 removed outlier: 6.723A pdb=" N ILE T 28 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR T 78 " --> pdb=" O ILE T 28 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET T 30 " --> pdb=" O TYR T 78 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N ILE T 80 " --> pdb=" O MET T 30 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU T 32 " --> pdb=" O ILE T 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL T 31 " --> pdb=" O CYS T 102 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU T 101 " --> pdb=" O VAL T 132 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 151 through 153 removed outlier: 3.562A pdb=" N VAL T 153 " --> pdb=" O LYS T 156 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 210 through 213 removed outlier: 3.594A pdb=" N ALA T 216 " --> pdb=" O GLU T 213 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'W' and resid 297 through 300 removed outlier: 3.561A pdb=" N ASN H 9 " --> pdb=" O ILE T 348 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'W' and resid 41 through 43 removed outlier: 3.604A pdb=" N VAL W 77 " --> pdb=" O ASN W 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N CYS W 102 " --> pdb=" O ALA W 29 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL W 31 " --> pdb=" O CYS W 102 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU W 101 " --> pdb=" O VAL W 132 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'W' and resid 157 through 158 removed outlier: 7.234A pdb=" N LEU W 152 " --> pdb=" O VAL W 189 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'W' and resid 210 through 211 removed outlier: 3.525A pdb=" N ARG W 218 " --> pdb=" O ILE W 211 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Q' and resid 297 through 300 removed outlier: 3.591A pdb=" N GLU W 353 " --> pdb=" O ALA Q 337 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE W 348 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 39 through 43 removed outlier: 3.762A pdb=" N CYS Q 102 " --> pdb=" O ALA Q 29 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL Q 31 " --> pdb=" O CYS Q 102 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU Q 101 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA Q 131 " --> pdb=" O ILE Q 144 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 156 through 158 removed outlier: 7.306A pdb=" N LEU Q 152 " --> pdb=" O VAL Q 189 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 210 through 211 removed outlier: 3.548A pdb=" N ILE Q 211 " --> pdb=" O ARG Q 218 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'Q' and resid 349 through 353 removed outlier: 3.538A pdb=" N SER G 11 " --> pdb=" O LEU Q 350 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS G 13 " --> pdb=" O ILE Q 352 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 140 through 146 Processing sheet with id=AG3, first strand: chain 'J' and resid 15 through 19 removed outlier: 4.697A pdb=" N LEU J 17 " --> pdb=" O VAL J 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 22 through 24 current: chain 'J' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 50 through 65 current: chain 'J' and resid 102 through 111 Processing sheet with id=AG4, first strand: chain 'K' and resid 15 through 19 removed outlier: 4.469A pdb=" N LEU K 17 " --> pdb=" O VAL K 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 22 through 24 current: chain 'K' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 50 through 65 current: chain 'K' and resid 102 through 111 Processing sheet with id=AG5, first strand: chain 'F' and resid 15 through 19 removed outlier: 4.457A pdb=" N LEU F 17 " --> pdb=" O VAL F 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 22 through 24 current: chain 'F' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 50 through 65 current: chain 'F' and resid 101 through 111 Processing sheet with id=AG6, first strand: chain 'H' and resid 39 through 43 removed outlier: 6.709A pdb=" N ILE H 28 " --> pdb=" O LEU H 76 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR H 78 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET H 30 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ILE H 80 " --> pdb=" O MET H 30 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU H 32 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL H 31 " --> pdb=" O CYS H 102 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU H 101 " --> pdb=" O VAL H 132 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 151 through 153 removed outlier: 3.594A pdb=" N VAL H 153 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS H 156 " --> pdb=" O VAL H 153 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 210 through 213 removed outlier: 3.600A pdb=" N ALA H 216 " --> pdb=" O GLU H 213 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 297 through 300 removed outlier: 3.560A pdb=" N ASN U 9 " --> pdb=" O ILE H 348 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 41 through 43 removed outlier: 3.613A pdb=" N VAL I 77 " --> pdb=" O ASN I 41 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU I 101 " --> pdb=" O VAL I 132 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA I 131 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 157 through 158 removed outlier: 7.225A pdb=" N LEU I 152 " --> pdb=" O VAL I 189 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 210 through 211 Processing sheet with id=AH4, first strand: chain 'G' and resid 297 through 300 removed outlier: 3.693A pdb=" N ASN X 9 " --> pdb=" O ILE I 348 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU I 350 " --> pdb=" O ASN X 9 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 39 through 43 removed outlier: 3.786A pdb=" N CYS G 102 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N VAL G 31 " --> pdb=" O CYS G 102 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU G 101 " --> pdb=" O VAL G 132 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA G 131 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 156 through 158 removed outlier: 7.298A pdb=" N LEU G 152 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 210 through 211 removed outlier: 3.528A pdb=" N ILE G 211 " --> pdb=" O ARG G 218 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 349 through 353 removed outlier: 3.692A pdb=" N LYS R 13 " --> pdb=" O ILE G 352 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'p' and resid 140 through 146 Processing sheet with id=AI1, first strand: chain 'c' and resid 15 through 19 removed outlier: 4.698A pdb=" N LEU c 17 " --> pdb=" O VAL c 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 22 through 24 current: chain 'c' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 50 through 65 current: chain 'c' and resid 102 through 111 Processing sheet with id=AI2, first strand: chain 'm' and resid 15 through 19 removed outlier: 4.512A pdb=" N LEU m 17 " --> pdb=" O VAL m 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 22 through 24 current: chain 'm' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'm' and resid 50 through 65 current: chain 'm' and resid 102 through 111 Processing sheet with id=AI3, first strand: chain 'O' and resid 15 through 19 removed outlier: 4.390A pdb=" N LEU O 17 " --> pdb=" O VAL O 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 22 through 24 current: chain 'O' and resid 50 through 65 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 50 through 65 current: chain 'O' and resid 101 through 111 Processing sheet with id=AI4, first strand: chain 'U' and resid 39 through 43 removed outlier: 6.771A pdb=" N ILE U 28 " --> pdb=" O LEU U 76 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR U 78 " --> pdb=" O ILE U 28 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET U 30 " --> pdb=" O TYR U 78 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE U 80 " --> pdb=" O MET U 30 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU U 32 " --> pdb=" O ILE U 80 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL U 31 " --> pdb=" O CYS U 102 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU U 101 " --> pdb=" O VAL U 132 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 151 through 153 removed outlier: 3.562A pdb=" N VAL U 153 " --> pdb=" O LYS U 156 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 210 through 213 removed outlier: 3.600A pdb=" N ALA U 216 " --> pdb=" O GLU U 213 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'X' and resid 297 through 300 removed outlier: 6.818A pdb=" N ASP U 347 " --> pdb=" O VAL X 333 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU X 335 " --> pdb=" O ASP U 347 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASP U 349 " --> pdb=" O LEU X 335 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N ALA X 337 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER U 351 " --> pdb=" O ALA X 337 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN f 9 " --> pdb=" O ILE U 348 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'X' and resid 41 through 43 removed outlier: 3.584A pdb=" N VAL X 77 " --> pdb=" O ASN X 41 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU X 101 " --> pdb=" O VAL X 132 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'X' and resid 157 through 158 removed outlier: 7.192A pdb=" N LEU X 152 " --> pdb=" O VAL X 189 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'X' and resid 210 through 211 Processing sheet with id=AJ2, first strand: chain 'R' and resid 297 through 300 removed outlier: 3.590A pdb=" N ASN g 9 " --> pdb=" O ILE X 348 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU X 350 " --> pdb=" O ASN g 9 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'R' and resid 39 through 43 removed outlier: 3.810A pdb=" N CYS R 102 " --> pdb=" O ALA R 29 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL R 31 " --> pdb=" O CYS R 102 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU R 101 " --> pdb=" O VAL R 132 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA R 131 " --> pdb=" O ILE R 144 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 151 through 153 Processing sheet with id=AJ5, first strand: chain 'R' and resid 210 through 211 removed outlier: 3.548A pdb=" N ILE R 211 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 348 through 353 removed outlier: 3.706A pdb=" N LYS e 13 " --> pdb=" O ILE R 352 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'j' and resid 140 through 146 Processing sheet with id=AJ8, first strand: chain 'f' and resid 39 through 43 removed outlier: 6.723A pdb=" N ILE f 28 " --> pdb=" O LEU f 76 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N TYR f 78 " --> pdb=" O ILE f 28 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N MET f 30 " --> pdb=" O TYR f 78 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE f 80 " --> pdb=" O MET f 30 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU f 32 " --> pdb=" O ILE f 80 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL f 31 " --> pdb=" O CYS f 102 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU f 101 " --> pdb=" O VAL f 132 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'f' and resid 151 through 153 removed outlier: 3.569A pdb=" N VAL f 153 " --> pdb=" O LYS f 156 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'f' and resid 210 through 213 removed outlier: 3.599A pdb=" N ALA f 216 " --> pdb=" O GLU f 213 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'g' and resid 41 through 43 removed outlier: 3.596A pdb=" N VAL g 77 " --> pdb=" O ASN g 41 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU g 101 " --> pdb=" O VAL g 132 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'g' and resid 157 through 158 removed outlier: 7.235A pdb=" N LEU g 152 " --> pdb=" O VAL g 189 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'g' and resid 210 through 211 removed outlier: 3.529A pdb=" N ARG g 218 " --> pdb=" O ILE g 211 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'e' and resid 39 through 43 removed outlier: 3.801A pdb=" N CYS e 102 " --> pdb=" O ALA e 29 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL e 31 " --> pdb=" O CYS e 102 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU e 101 " --> pdb=" O VAL e 132 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA e 131 " --> pdb=" O ILE e 144 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'e' and resid 156 through 158 removed outlier: 7.306A pdb=" N LEU e 152 " --> pdb=" O VAL e 189 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'e' and resid 210 through 211 removed outlier: 3.546A pdb=" N ILE e 211 " --> pdb=" O ARG e 218 " (cutoff:3.500A) 2533 hydrogen bonds defined for protein. 7134 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: 35.86 Time building geometry restraints manager: 16.45 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: 24486 1.34 - 1.45: 7981 1.45 - 1.57: 44399 1.57 - 1.69: 0 1.69 - 1.81: 552 Bond restraints: 77418 Sorted by residual: bond pdb=" N THR P 18 " pdb=" CA THR P 18 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.69e+00 bond pdb=" N THR B 18 " pdb=" CA THR B 18 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.61e+00 bond pdb=" N THR R 18 " pdb=" CA THR R 18 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.57e+00 bond pdb=" N THR e 18 " pdb=" CA THR e 18 " ideal model delta sigma weight residual 1.457 1.482 -0.024 1.29e-02 6.01e+03 3.56e+00 bond pdb=" N THR Q 18 " pdb=" CA THR Q 18 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.41e+00 ... (remaining 77413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 103333 2.03 - 4.07: 850 4.07 - 6.10: 68 6.10 - 8.13: 14 8.13 - 10.16: 3 Bond angle restraints: 104268 Sorted by residual: angle pdb=" CA GLN n 70 " pdb=" CB GLN n 70 " pdb=" CG GLN n 70 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLN p 70 " pdb=" CB GLN p 70 " pdb=" CG GLN p 70 " ideal model delta sigma weight residual 114.10 120.82 -6.72 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CA GLY X 82 " pdb=" C GLY X 82 " pdb=" O GLY X 82 " ideal model delta sigma weight residual 122.37 120.11 2.26 7.30e-01 1.88e+00 9.57e+00 angle pdb=" CA ILE g 191 " pdb=" C ILE g 191 " pdb=" N PRO g 192 " ideal model delta sigma weight residual 116.57 119.56 -2.99 9.80e-01 1.04e+00 9.30e+00 angle pdb=" CA ILE W 191 " pdb=" C ILE W 191 " pdb=" N PRO W 192 " ideal model delta sigma weight residual 116.57 119.53 -2.96 9.80e-01 1.04e+00 9.14e+00 ... (remaining 104263 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 41248 17.98 - 35.96: 5106 35.96 - 53.93: 1053 53.93 - 71.91: 181 71.91 - 89.89: 76 Dihedral angle restraints: 47664 sinusoidal: 19350 harmonic: 28314 Sorted by residual: dihedral pdb=" CA LEU Z 74 " pdb=" C LEU Z 74 " pdb=" N ILE Z 75 " pdb=" CA ILE Z 75 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU h 74 " pdb=" C LEU h 74 " pdb=" N ILE h 75 " pdb=" CA ILE h 75 " ideal model delta harmonic sigma weight residual -180.00 -161.18 -18.82 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA LEU Y 74 " pdb=" C LEU Y 74 " pdb=" N ILE Y 75 " pdb=" CA ILE Y 75 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 47661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 8752 0.035 - 0.071: 2255 0.071 - 0.106: 906 0.106 - 0.142: 408 0.142 - 0.177: 21 Chirality restraints: 12342 Sorted by residual: chirality pdb=" CB VAL T 137 " pdb=" CA VAL T 137 " pdb=" CG1 VAL T 137 " pdb=" CG2 VAL T 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CB VAL f 137 " pdb=" CA VAL f 137 " pdb=" CG1 VAL f 137 " pdb=" CG2 VAL f 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.75e-01 chirality pdb=" CB VAL H 137 " pdb=" CA VAL H 137 " pdb=" CG1 VAL H 137 " pdb=" CG2 VAL H 137 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.17 2.00e-01 2.50e+01 7.63e-01 ... (remaining 12339 not shown) Planarity restraints: 13056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 83 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" CD GLU D 83 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU D 83 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU D 83 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET P 103 " 0.035 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO P 104 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO P 104 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO P 104 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU I 83 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" CD GLU I 83 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU I 83 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU I 83 " -0.013 2.00e-02 2.50e+03 ... (remaining 13053 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1652 2.69 - 3.24: 71803 3.24 - 3.79: 109742 3.79 - 4.35: 144014 4.35 - 4.90: 250645 Nonbonded interactions: 577856 Sorted by model distance: nonbonded pdb=" OE1 GLN p 70 " pdb=" N SER p 71 " model vdw 2.135 3.120 nonbonded pdb=" OE1 GLN n 70 " pdb=" N SER n 71 " model vdw 2.168 3.120 nonbonded pdb=" OE2 GLU f 287 " pdb=" OG SER f 296 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU T 287 " pdb=" OG SER T 296 " model vdw 2.200 3.040 nonbonded pdb=" OE2 GLU U 287 " pdb=" OG SER U 296 " model vdw 2.200 3.040 ... (remaining 577851 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 142) selection = chain 'E' selection = (chain 'F' and resid 7 through 142) selection = chain 'J' selection = (chain 'K' and resid 7 through 142) selection = (chain 'M' and resid 7 through 142) selection = (chain 'N' and resid 7 through 142) selection = (chain 'O' and resid 7 through 142) selection = chain 'Y' selection = chain 'Z' selection = (chain 'a' and resid 7 through 142) selection = chain 'c' selection = (chain 'd' and resid 7 through 142) selection = chain 'h' selection = (chain 'i' and resid 7 through 142) selection = (chain 'k' and resid 7 through 142) selection = (chain 'l' and resid 7 through 142) selection = (chain 'm' and resid 7 through 142) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'L' selection = chain 'b' selection = chain 'j' selection = chain 'n' selection = chain 'o' selection = chain 'p' } 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.180 Check model and map are aligned: 0.450 Set scattering table: 0.540 Process input model: 138.710 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.670 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 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 0.030 77418 Z= 0.190 Angle : 0.503 10.164 104268 Z= 0.282 Chirality : 0.042 0.177 12342 Planarity : 0.003 0.054 13056 Dihedral : 16.099 89.890 29352 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.24 % Allowed : 23.65 % Favored : 76.12 % 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: -0.02 (0.08), residues: 9648 helix: 2.02 (0.10), residues: 2646 sheet: 0.10 (0.11), residues: 2034 loop : -1.24 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 119 HIS 0.004 0.001 HIS R 250 PHE 0.020 0.001 PHE g 12 TYR 0.037 0.001 TYR T 318 ARG 0.004 0.000 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1033 time to evaluate : 6.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 13 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7904 (mm-30) REVERT: E 68 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (p) REVERT: a 68 SER cc_start: 0.8403 (t) cc_final: 0.8072 (p) REVERT: C 95 THR cc_start: 0.8372 (m) cc_final: 0.8167 (p) REVERT: C 202 ARG cc_start: 0.7456 (ttm110) cc_final: 0.7252 (mtp180) REVERT: B 46 LYS cc_start: 0.6037 (tmtt) cc_final: 0.5013 (tptt) REVERT: n 13 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7875 (mm-30) REVERT: M 71 MET cc_start: 0.9160 (tpp) cc_final: 0.8898 (mmt) REVERT: V 196 LYS cc_start: 0.6719 (tptm) cc_final: 0.6203 (mmtp) REVERT: V 200 GLU cc_start: 0.7391 (tp30) cc_final: 0.7158 (mm-30) REVERT: P 149 GLU cc_start: 0.6075 (pm20) cc_final: 0.4862 (mm-30) REVERT: P 207 GLU cc_start: 0.6338 (mt-10) cc_final: 0.6113 (tt0) REVERT: P 295 ASP cc_start: 0.6229 (t70) cc_final: 0.5854 (t70) REVERT: Z 137 ASP cc_start: 0.7686 (t0) cc_final: 0.7486 (t0) REVERT: N 118 ASP cc_start: 0.8297 (t0) cc_final: 0.8026 (t0) REVERT: T 30 MET cc_start: 0.7957 (ttm) cc_final: 0.7578 (ttm) REVERT: T 31 VAL cc_start: 0.7100 (t) cc_final: 0.6827 (t) REVERT: T 103 MET cc_start: 0.6909 (ttm) cc_final: 0.6180 (ttt) REVERT: T 254 ARG cc_start: 0.7560 (tpt170) cc_final: 0.7350 (mmt180) REVERT: T 338 LYS cc_start: 0.8061 (mtmt) cc_final: 0.7805 (mtmm) REVERT: W 196 LYS cc_start: 0.6311 (tptm) cc_final: 0.5824 (mmtm) REVERT: W 288 LYS cc_start: 0.7874 (mttp) cc_final: 0.7445 (mttp) REVERT: Q 295 ASP cc_start: 0.6060 (t70) cc_final: 0.5709 (t70) REVERT: L 13 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7902 (mm-30) REVERT: K 68 SER cc_start: 0.8396 (t) cc_final: 0.8059 (p) REVERT: H 95 THR cc_start: 0.8396 (m) cc_final: 0.8185 (p) REVERT: G 46 LYS cc_start: 0.6029 (tmtt) cc_final: 0.5008 (tptt) REVERT: G 73 ASN cc_start: 0.6636 (t0) cc_final: 0.6404 (m-40) REVERT: p 13 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7889 (mm-30) REVERT: m 81 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8246 (mtm-85) REVERT: X 87 GLN cc_start: 0.6507 (mm-40) cc_final: 0.5698 (tp40) REVERT: X 196 LYS cc_start: 0.6718 (tptm) cc_final: 0.6216 (mmtp) REVERT: X 284 GLU cc_start: 0.7202 (tt0) cc_final: 0.7001 (mm-30) REVERT: R 103 MET cc_start: 0.6535 (tpt) cc_final: 0.5943 (tpt) REVERT: R 149 GLU cc_start: 0.6157 (pm20) cc_final: 0.5007 (mm-30) REVERT: R 178 GLN cc_start: 0.7031 (mt0) cc_final: 0.6696 (mt0) REVERT: R 207 GLU cc_start: 0.6402 (mt-10) cc_final: 0.6184 (tt0) REVERT: R 295 ASP cc_start: 0.6255 (t70) cc_final: 0.5927 (t70) REVERT: i 47 MET cc_start: 0.8109 (mmt) cc_final: 0.7777 (mmt) REVERT: d 118 ASP cc_start: 0.8286 (t0) cc_final: 0.8006 (t0) REVERT: f 15 LEU cc_start: 0.7850 (tt) cc_final: 0.7592 (mt) REVERT: f 103 MET cc_start: 0.6891 (ttm) cc_final: 0.6258 (ttt) REVERT: f 338 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7846 (mtmm) REVERT: g 196 LYS cc_start: 0.6273 (tptm) cc_final: 0.5803 (mmtm) REVERT: g 288 LYS cc_start: 0.7891 (mttp) cc_final: 0.7443 (mttp) REVERT: e 295 ASP cc_start: 0.6007 (t70) cc_final: 0.5648 (t70) outliers start: 20 outliers final: 7 residues processed: 1051 average time/residue: 0.7045 time to fit residues: 1266.3216 Evaluate side-chains 737 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 729 time to evaluate : 6.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 SER Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain n residue 20 THR Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain e residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 810 optimal weight: 5.9990 chunk 727 optimal weight: 7.9990 chunk 403 optimal weight: 0.8980 chunk 248 optimal weight: 9.9990 chunk 490 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 752 optimal weight: 2.9990 chunk 291 optimal weight: 0.3980 chunk 457 optimal weight: 0.0670 chunk 560 optimal weight: 6.9990 chunk 871 optimal weight: 10.0000 overall best weight: 1.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN B 238 GLN n 70 GLN k 46 GLN V 44 HIS P 238 GLN ** P 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 62 ASN T 271 ASN W 73 ASN W 140 HIS Q 238 GLN L 70 GLN K 46 GLN G 238 GLN p 70 GLN m 46 GLN R 238 GLN f 62 ASN f 271 ASN g 73 ASN g 140 HIS e 238 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 77418 Z= 0.159 Angle : 0.500 8.751 104268 Z= 0.275 Chirality : 0.043 0.163 12342 Planarity : 0.003 0.041 13056 Dihedral : 4.194 38.145 10268 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.15 % Allowed : 22.82 % Favored : 75.02 % 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: 0.02 (0.08), residues: 9648 helix: 2.28 (0.10), residues: 2652 sheet: 0.12 (0.11), residues: 1938 loop : -1.35 (0.08), residues: 5058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 119 HIS 0.003 0.001 HIS R 250 PHE 0.014 0.001 PHE I 12 TYR 0.018 0.001 TYR I 60 ARG 0.005 0.000 ARG I 254 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 798 time to evaluate : 6.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 GLU cc_start: 0.7836 (tt0) cc_final: 0.7591 (tt0) REVERT: a 68 SER cc_start: 0.8272 (t) cc_final: 0.7969 (p) REVERT: a 136 TYR cc_start: 0.8385 (p90) cc_final: 0.7994 (p90) REVERT: a 140 ASP cc_start: 0.8340 (t0) cc_final: 0.8082 (t0) REVERT: C 95 THR cc_start: 0.8415 (m) cc_final: 0.8210 (p) REVERT: C 217 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7946 (mm) REVERT: C 252 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7506 (m-30) REVERT: D 152 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5304 (mp) REVERT: D 196 LYS cc_start: 0.6576 (tptm) cc_final: 0.6182 (mmtp) REVERT: B 46 LYS cc_start: 0.5940 (tmtt) cc_final: 0.4954 (tptt) REVERT: n 13 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7884 (mm-30) REVERT: n 23 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8818 (mp) REVERT: n 145 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8389 (pp) REVERT: Y 138 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.6602 (t80) REVERT: M 71 MET cc_start: 0.9147 (tpp) cc_final: 0.8910 (mmt) REVERT: S 13 LYS cc_start: 0.7994 (pttt) cc_final: 0.7573 (ptpt) REVERT: S 152 LEU cc_start: 0.8238 (mt) cc_final: 0.7945 (mt) REVERT: S 217 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8186 (mp) REVERT: V 152 LEU cc_start: 0.6195 (OUTLIER) cc_final: 0.5248 (mp) REVERT: V 196 LYS cc_start: 0.6645 (tptm) cc_final: 0.6196 (mmtp) REVERT: P 66 MET cc_start: 0.4642 (pmm) cc_final: 0.3103 (ttm) REVERT: P 92 PHE cc_start: 0.7604 (t80) cc_final: 0.7361 (t80) REVERT: P 149 GLU cc_start: 0.6009 (pm20) cc_final: 0.4831 (mm-30) REVERT: P 295 ASP cc_start: 0.6215 (t70) cc_final: 0.5726 (t70) REVERT: o 1 MET cc_start: 0.5461 (OUTLIER) cc_final: 0.5150 (mtp) REVERT: o 145 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8504 (pp) REVERT: l 34 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8420 (mtm) REVERT: l 68 SER cc_start: 0.8238 (t) cc_final: 0.8004 (p) REVERT: T 30 MET cc_start: 0.7840 (ttm) cc_final: 0.7349 (ttm) REVERT: T 74 LYS cc_start: 0.8122 (ttpp) cc_final: 0.7522 (ttpp) REVERT: T 103 MET cc_start: 0.6971 (ttm) cc_final: 0.6263 (ttt) REVERT: T 217 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8200 (mm) REVERT: W 87 GLN cc_start: 0.7291 (mp10) cc_final: 0.6597 (mm-40) REVERT: W 152 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5326 (mp) REVERT: W 196 LYS cc_start: 0.6144 (tptm) cc_final: 0.5731 (mmtm) REVERT: W 288 LYS cc_start: 0.7752 (mttp) cc_final: 0.7450 (mtmt) REVERT: Q 92 PHE cc_start: 0.7547 (t80) cc_final: 0.7196 (t80) REVERT: Q 295 ASP cc_start: 0.5969 (t70) cc_final: 0.5552 (t70) REVERT: L 13 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7953 (mm-30) REVERT: J 102 GLU cc_start: 0.7835 (tt0) cc_final: 0.7578 (tt0) REVERT: K 68 SER cc_start: 0.8262 (t) cc_final: 0.7956 (p) REVERT: K 136 TYR cc_start: 0.8388 (p90) cc_final: 0.8088 (p90) REVERT: K 140 ASP cc_start: 0.8359 (t0) cc_final: 0.8104 (t0) REVERT: F 71 MET cc_start: 0.9006 (tpp) cc_final: 0.8681 (mmt) REVERT: H 152 LEU cc_start: 0.8295 (mt) cc_final: 0.7922 (tt) REVERT: H 217 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7908 (mm) REVERT: H 252 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: I 152 LEU cc_start: 0.6297 (OUTLIER) cc_final: 0.5316 (mp) REVERT: I 196 LYS cc_start: 0.6570 (tptm) cc_final: 0.6118 (mmtp) REVERT: G 46 LYS cc_start: 0.5946 (tmtt) cc_final: 0.4961 (tptt) REVERT: G 211 ILE cc_start: 0.6590 (tp) cc_final: 0.6320 (tt) REVERT: p 13 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7928 (mm-30) REVERT: p 23 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (mp) REVERT: p 145 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8353 (pp) REVERT: c 138 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.6591 (t80) REVERT: m 34 MET cc_start: 0.8822 (mtp) cc_final: 0.8611 (mtm) REVERT: m 81 ARG cc_start: 0.8298 (mtm-85) cc_final: 0.8040 (ttp-110) REVERT: O 71 MET cc_start: 0.9155 (tpp) cc_final: 0.8926 (mmt) REVERT: U 13 LYS cc_start: 0.7984 (pttt) cc_final: 0.7574 (ptpt) REVERT: X 87 GLN cc_start: 0.6525 (mm-40) cc_final: 0.5710 (tp40) REVERT: X 152 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5304 (mp) REVERT: X 196 LYS cc_start: 0.6627 (tptm) cc_final: 0.6171 (mmtp) REVERT: X 284 GLU cc_start: 0.7246 (tt0) cc_final: 0.7000 (mm-30) REVERT: R 92 PHE cc_start: 0.7589 (t80) cc_final: 0.7353 (t80) REVERT: R 103 MET cc_start: 0.6518 (tpt) cc_final: 0.6119 (tpt) REVERT: R 149 GLU cc_start: 0.5707 (pm20) cc_final: 0.4837 (mm-30) REVERT: R 295 ASP cc_start: 0.6257 (t70) cc_final: 0.5778 (t70) REVERT: R 319 MET cc_start: 0.6088 (mtp) cc_final: 0.5861 (mtp) REVERT: j 1 MET cc_start: 0.5500 (OUTLIER) cc_final: 0.5188 (mtp) REVERT: j 145 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8508 (pp) REVERT: i 68 SER cc_start: 0.8249 (t) cc_final: 0.8027 (p) REVERT: f 15 LEU cc_start: 0.8003 (tt) cc_final: 0.7794 (mt) REVERT: f 74 LYS cc_start: 0.8152 (ttpp) cc_final: 0.7522 (ttpp) REVERT: f 103 MET cc_start: 0.6915 (ttm) cc_final: 0.6259 (ttt) REVERT: f 217 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8159 (mm) REVERT: g 30 MET cc_start: 0.6565 (ptm) cc_final: 0.6298 (ptm) REVERT: g 152 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5248 (mp) REVERT: g 196 LYS cc_start: 0.6055 (tptm) cc_final: 0.5675 (mmtm) REVERT: g 288 LYS cc_start: 0.7760 (mttp) cc_final: 0.7449 (mtmt) REVERT: g 352 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7851 (mt) REVERT: e 92 PHE cc_start: 0.7591 (t80) cc_final: 0.7265 (t80) REVERT: e 295 ASP cc_start: 0.5924 (t70) cc_final: 0.5507 (t70) outliers start: 183 outliers final: 71 residues processed: 946 average time/residue: 0.6789 time to fit residues: 1116.3204 Evaluate side-chains 798 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 702 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 232 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain l residue 34 MET Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 152 LEU Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain J residue 79 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 232 GLU Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 345 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 35 GLU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 484 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 725 optimal weight: 9.9990 chunk 593 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 873 optimal weight: 4.9990 chunk 943 optimal weight: 7.9990 chunk 777 optimal weight: 7.9990 chunk 866 optimal weight: 9.9990 chunk 297 optimal weight: 3.9990 chunk 700 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN V 87 GLN W 73 ASN L 70 GLN K 46 GLN H 271 ASN g 73 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 77418 Z= 0.283 Angle : 0.541 8.646 104268 Z= 0.296 Chirality : 0.044 0.168 12342 Planarity : 0.003 0.038 13056 Dihedral : 4.478 38.966 10262 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.50 % Allowed : 22.62 % Favored : 73.88 % 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: -0.22 (0.08), residues: 9648 helix: 2.09 (0.10), residues: 2652 sheet: -0.20 (0.11), residues: 2022 loop : -1.43 (0.08), residues: 4974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 119 HIS 0.005 0.001 HIS N 66 PHE 0.023 0.001 PHE I 12 TYR 0.018 0.002 TYR O 99 ARG 0.007 0.000 ARG R 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 297 poor density : 694 time to evaluate : 6.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7318 (t80) REVERT: a 68 SER cc_start: 0.8246 (t) cc_final: 0.7880 (p) REVERT: a 136 TYR cc_start: 0.8516 (p90) cc_final: 0.8061 (p90) REVERT: a 140 ASP cc_start: 0.8477 (t0) cc_final: 0.8232 (t0) REVERT: C 152 LEU cc_start: 0.8184 (mt) cc_final: 0.7904 (mm) REVERT: C 217 ILE cc_start: 0.8350 (OUTLIER) cc_final: 0.8146 (mm) REVERT: C 252 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7546 (m-30) REVERT: D 87 GLN cc_start: 0.7609 (mp10) cc_final: 0.7281 (mp10) REVERT: D 196 LYS cc_start: 0.6594 (tptm) cc_final: 0.6199 (mmtp) REVERT: B 295 ASP cc_start: 0.6418 (t70) cc_final: 0.5883 (t70) REVERT: n 23 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8847 (mp) REVERT: n 98 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8323 (mt) REVERT: n 145 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8335 (pp) REVERT: Y 138 PHE cc_start: 0.8627 (OUTLIER) cc_final: 0.6724 (t80) REVERT: k 34 MET cc_start: 0.8961 (mtp) cc_final: 0.8746 (mtm) REVERT: M 71 MET cc_start: 0.9177 (tpp) cc_final: 0.8971 (mmt) REVERT: S 13 LYS cc_start: 0.8010 (pttt) cc_final: 0.7618 (ptpt) REVERT: S 119 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.8046 (mt) REVERT: S 152 LEU cc_start: 0.8252 (mt) cc_final: 0.7972 (mt) REVERT: S 217 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8247 (mp) REVERT: V 196 LYS cc_start: 0.6695 (tptm) cc_final: 0.6139 (mmtp) REVERT: V 352 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7663 (mt) REVERT: P 66 MET cc_start: 0.5077 (pmm) cc_final: 0.3628 (ttm) REVERT: P 182 TYR cc_start: 0.6459 (OUTLIER) cc_final: 0.5525 (t80) REVERT: P 295 ASP cc_start: 0.6472 (t70) cc_final: 0.6180 (t70) REVERT: o 1 MET cc_start: 0.5604 (OUTLIER) cc_final: 0.5116 (mtp) REVERT: o 145 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8434 (pp) REVERT: Z 77 GLU cc_start: 0.7120 (pm20) cc_final: 0.6786 (mp0) REVERT: l 34 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8700 (mtm) REVERT: l 68 SER cc_start: 0.8269 (t) cc_final: 0.7949 (p) REVERT: T 103 MET cc_start: 0.6890 (ttm) cc_final: 0.6257 (ttm) REVERT: T 152 LEU cc_start: 0.8161 (mt) cc_final: 0.7944 (mp) REVERT: T 217 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8343 (mm) REVERT: W 87 GLN cc_start: 0.7402 (mp10) cc_final: 0.7158 (mp10) REVERT: W 97 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6884 (mt-10) REVERT: W 196 LYS cc_start: 0.6165 (tptm) cc_final: 0.5772 (mmtm) REVERT: W 288 LYS cc_start: 0.7648 (mttp) cc_final: 0.7365 (mtmt) REVERT: Q 92 PHE cc_start: 0.7543 (t80) cc_final: 0.7167 (t80) REVERT: Q 295 ASP cc_start: 0.6267 (t70) cc_final: 0.5835 (t70) REVERT: J 138 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7322 (t80) REVERT: K 17 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8944 (tp) REVERT: K 68 SER cc_start: 0.8249 (t) cc_final: 0.7872 (p) REVERT: K 136 TYR cc_start: 0.8567 (p90) cc_final: 0.8125 (p90) REVERT: K 140 ASP cc_start: 0.8477 (t0) cc_final: 0.8232 (t0) REVERT: F 71 MET cc_start: 0.9070 (tpp) cc_final: 0.8784 (mmt) REVERT: H 217 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8121 (mm) REVERT: H 252 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: I 30 MET cc_start: 0.7383 (ttp) cc_final: 0.7149 (ttp) REVERT: I 87 GLN cc_start: 0.7629 (mp10) cc_final: 0.7321 (mp10) REVERT: I 196 LYS cc_start: 0.6489 (tptm) cc_final: 0.6113 (mmtp) REVERT: G 295 ASP cc_start: 0.6501 (t70) cc_final: 0.5989 (t70) REVERT: p 23 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8851 (mp) REVERT: p 98 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8336 (mt) REVERT: p 145 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8328 (pp) REVERT: c 138 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.6655 (t80) REVERT: U 13 LYS cc_start: 0.7999 (pttt) cc_final: 0.7624 (ptpt) REVERT: U 119 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.8060 (mt) REVERT: X 196 LYS cc_start: 0.6831 (tptm) cc_final: 0.6264 (mmtp) REVERT: X 284 GLU cc_start: 0.7310 (tt0) cc_final: 0.7072 (mm-30) REVERT: R 66 MET cc_start: 0.4851 (pmm) cc_final: 0.3175 (ttm) REVERT: R 103 MET cc_start: 0.6477 (tpt) cc_final: 0.6139 (tpt) REVERT: R 150 ASP cc_start: 0.4706 (t0) cc_final: 0.4472 (t70) REVERT: R 295 ASP cc_start: 0.6518 (t70) cc_final: 0.6219 (t70) REVERT: R 319 MET cc_start: 0.5849 (mtp) cc_final: 0.5567 (mtp) REVERT: j 1 MET cc_start: 0.5515 (OUTLIER) cc_final: 0.5001 (mtp) REVERT: j 145 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8438 (pp) REVERT: h 77 GLU cc_start: 0.7177 (pm20) cc_final: 0.6840 (mp0) REVERT: i 68 SER cc_start: 0.8299 (t) cc_final: 0.7987 (p) REVERT: d 103 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.8250 (ttm170) REVERT: f 15 LEU cc_start: 0.8034 (tt) cc_final: 0.7812 (mt) REVERT: f 103 MET cc_start: 0.6914 (ttm) cc_final: 0.6321 (ttm) REVERT: f 152 LEU cc_start: 0.8143 (mt) cc_final: 0.7922 (mp) REVERT: f 217 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8321 (mm) REVERT: g 12 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7739 (p90) REVERT: g 30 MET cc_start: 0.6505 (ptm) cc_final: 0.6240 (ptm) REVERT: g 97 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6869 (mt-10) REVERT: g 152 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5015 (mp) REVERT: g 196 LYS cc_start: 0.6110 (tptm) cc_final: 0.5745 (mmtm) REVERT: g 288 LYS cc_start: 0.7674 (mttp) cc_final: 0.7386 (mtmt) REVERT: g 352 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7905 (mt) REVERT: e 92 PHE cc_start: 0.7757 (t80) cc_final: 0.7386 (t80) REVERT: e 232 GLU cc_start: 0.6328 (tm-30) cc_final: 0.6001 (mp0) REVERT: e 295 ASP cc_start: 0.6179 (t70) cc_final: 0.5775 (t70) outliers start: 297 outliers final: 165 residues processed: 962 average time/residue: 0.6775 time to fit residues: 1145.6451 Evaluate side-chains 841 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 643 time to evaluate : 6.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 217 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 256 VAL Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 208 LEU Chi-restraints excluded: chain V residue 232 GLU Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain l residue 34 MET Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 217 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 208 LEU Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 98 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 256 VAL Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 208 LEU Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 345 MET Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 103 ARG Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 152 LEU Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 862 optimal weight: 6.9990 chunk 656 optimal weight: 0.9990 chunk 453 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 chunk 586 optimal weight: 10.0000 chunk 876 optimal weight: 9.9990 chunk 927 optimal weight: 10.0000 chunk 457 optimal weight: 10.0000 chunk 830 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN A 8 ASN D 73 ASN M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN W 73 ASN L 70 GLN K 46 GLN F 8 ASN I 73 ASN p 70 GLN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN g 73 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 77418 Z= 0.372 Angle : 0.592 8.477 104268 Z= 0.323 Chirality : 0.046 0.179 12342 Planarity : 0.004 0.049 13056 Dihedral : 4.841 46.648 10262 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.83 % Allowed : 22.80 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.08), residues: 9648 helix: 1.76 (0.10), residues: 2652 sheet: -0.58 (0.11), residues: 1986 loop : -1.57 (0.08), residues: 5010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 119 HIS 0.007 0.002 HIS P 44 PHE 0.027 0.002 PHE I 12 TYR 0.021 0.002 TYR O 99 ARG 0.006 0.001 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 410 poor density : 672 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5089 (mtp) REVERT: E 54 MET cc_start: 0.9145 (mmm) cc_final: 0.8938 (mmt) REVERT: E 138 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.7419 (t80) REVERT: a 68 SER cc_start: 0.8312 (t) cc_final: 0.7956 (p) REVERT: a 136 TYR cc_start: 0.8518 (p90) cc_final: 0.8147 (p90) REVERT: a 140 ASP cc_start: 0.8497 (t0) cc_final: 0.8246 (t0) REVERT: C 152 LEU cc_start: 0.8223 (mt) cc_final: 0.7953 (mm) REVERT: C 252 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7814 (t0) REVERT: D 30 MET cc_start: 0.7464 (ttp) cc_final: 0.7238 (ttp) REVERT: D 87 GLN cc_start: 0.7678 (mp10) cc_final: 0.7305 (mp10) REVERT: D 152 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.5084 (mp) REVERT: D 196 LYS cc_start: 0.6593 (tptm) cc_final: 0.6194 (mmtp) REVERT: D 352 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7676 (mt) REVERT: B 36 LYS cc_start: 0.6228 (pttm) cc_final: 0.5878 (pttt) REVERT: B 119 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6193 (pt) REVERT: B 213 GLU cc_start: 0.6344 (tm-30) cc_final: 0.5933 (tp30) REVERT: B 295 ASP cc_start: 0.6683 (t70) cc_final: 0.6133 (t70) REVERT: n 23 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8865 (mp) REVERT: n 145 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8232 (pp) REVERT: Y 138 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.6732 (t80) REVERT: k 75 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.8889 (pt) REVERT: k 128 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8058 (tt0) REVERT: S 13 LYS cc_start: 0.8072 (pttt) cc_final: 0.7671 (ptpt) REVERT: S 119 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8103 (mt) REVERT: S 152 LEU cc_start: 0.8316 (mt) cc_final: 0.8065 (mt) REVERT: S 217 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8295 (mp) REVERT: V 152 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5187 (mp) REVERT: V 196 LYS cc_start: 0.6776 (tptm) cc_final: 0.6157 (mmtp) REVERT: V 352 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7753 (mt) REVERT: P 66 MET cc_start: 0.5185 (pmm) cc_final: 0.3790 (ttm) REVERT: P 182 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5686 (t80) REVERT: o 1 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.5268 (mtp) REVERT: o 145 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8414 (pp) REVERT: Z 138 PHE cc_start: 0.8683 (OUTLIER) cc_final: 0.8272 (t80) REVERT: l 68 SER cc_start: 0.8328 (t) cc_final: 0.8031 (p) REVERT: l 136 TYR cc_start: 0.8595 (p90) cc_final: 0.8299 (p90) REVERT: N 47 MET cc_start: 0.8815 (mmp) cc_final: 0.8427 (mmp) REVERT: T 103 MET cc_start: 0.7150 (ttm) cc_final: 0.6752 (ttm) REVERT: T 152 LEU cc_start: 0.8272 (mt) cc_final: 0.8009 (mm) REVERT: T 217 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8421 (mm) REVERT: W 87 GLN cc_start: 0.7393 (mp10) cc_final: 0.7040 (mp10) REVERT: W 97 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6956 (mt-10) REVERT: W 196 LYS cc_start: 0.6146 (tptm) cc_final: 0.5765 (mmtm) REVERT: W 288 LYS cc_start: 0.7942 (mttp) cc_final: 0.7583 (mttp) REVERT: Q 92 PHE cc_start: 0.7633 (t80) cc_final: 0.7236 (t80) REVERT: Q 218 ARG cc_start: 0.6081 (OUTLIER) cc_final: 0.5740 (mtt-85) REVERT: Q 295 ASP cc_start: 0.6688 (t70) cc_final: 0.6163 (t70) REVERT: L 1 MET cc_start: 0.5628 (OUTLIER) cc_final: 0.4585 (mtp) REVERT: J 54 MET cc_start: 0.9149 (mmm) cc_final: 0.8945 (mmt) REVERT: J 138 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7432 (t80) REVERT: K 68 SER cc_start: 0.8308 (t) cc_final: 0.7944 (p) REVERT: K 136 TYR cc_start: 0.8563 (p90) cc_final: 0.8187 (p90) REVERT: K 140 ASP cc_start: 0.8498 (t0) cc_final: 0.8244 (t0) REVERT: H 252 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7820 (t0) REVERT: I 30 MET cc_start: 0.7344 (ttp) cc_final: 0.7119 (ttp) REVERT: I 87 GLN cc_start: 0.7691 (mp10) cc_final: 0.7309 (mp10) REVERT: I 152 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5031 (mp) REVERT: I 196 LYS cc_start: 0.6521 (tptm) cc_final: 0.6181 (mmtp) REVERT: G 36 LYS cc_start: 0.6242 (pttm) cc_final: 0.5837 (pttt) REVERT: G 119 ILE cc_start: 0.6402 (OUTLIER) cc_final: 0.6200 (pt) REVERT: G 295 ASP cc_start: 0.6684 (t70) cc_final: 0.6136 (t70) REVERT: p 1 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5617 (mtp) REVERT: p 23 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8872 (mp) REVERT: p 145 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8229 (pp) REVERT: c 138 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.6735 (t80) REVERT: m 75 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8888 (pt) REVERT: m 128 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8050 (tt0) REVERT: U 13 LYS cc_start: 0.8070 (pttt) cc_final: 0.7689 (ptpt) REVERT: U 119 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8086 (mt) REVERT: U 258 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.7057 (tt) REVERT: X 152 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.5166 (mp) REVERT: X 196 LYS cc_start: 0.6859 (tptm) cc_final: 0.6239 (mmtp) REVERT: X 284 GLU cc_start: 0.7390 (tt0) cc_final: 0.7051 (mm-30) REVERT: R 213 GLU cc_start: 0.6296 (OUTLIER) cc_final: 0.5284 (tt0) REVERT: R 218 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.5541 (mtt180) REVERT: R 319 MET cc_start: 0.5891 (mtp) cc_final: 0.5645 (mtp) REVERT: j 1 MET cc_start: 0.5834 (OUTLIER) cc_final: 0.5345 (mtp) REVERT: j 145 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8393 (pp) REVERT: h 54 MET cc_start: 0.9290 (mmt) cc_final: 0.9016 (mmt) REVERT: h 138 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8274 (t80) REVERT: i 68 SER cc_start: 0.8325 (t) cc_final: 0.8047 (p) REVERT: i 136 TYR cc_start: 0.8589 (p90) cc_final: 0.8278 (p90) REVERT: d 47 MET cc_start: 0.8796 (mmp) cc_final: 0.8368 (mmp) REVERT: f 15 LEU cc_start: 0.8189 (tt) cc_final: 0.7910 (mt) REVERT: f 103 MET cc_start: 0.7182 (ttm) cc_final: 0.6801 (ttm) REVERT: f 152 LEU cc_start: 0.8237 (mt) cc_final: 0.7970 (mm) REVERT: f 217 ILE cc_start: 0.8641 (OUTLIER) cc_final: 0.8402 (mm) REVERT: g 30 MET cc_start: 0.6646 (ptm) cc_final: 0.6352 (ptm) REVERT: g 97 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: g 196 LYS cc_start: 0.6113 (tptm) cc_final: 0.5748 (mmtm) REVERT: g 288 LYS cc_start: 0.7907 (mttp) cc_final: 0.7541 (mttp) REVERT: g 352 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8000 (mt) REVERT: e 92 PHE cc_start: 0.7645 (t80) cc_final: 0.7252 (t80) REVERT: e 119 ILE cc_start: 0.6464 (OUTLIER) cc_final: 0.6257 (pt) REVERT: e 218 ARG cc_start: 0.6256 (OUTLIER) cc_final: 0.5789 (mtt-85) REVERT: e 295 ASP cc_start: 0.6611 (t70) cc_final: 0.6151 (t70) outliers start: 410 outliers final: 255 residues processed: 1041 average time/residue: 0.6506 time to fit residues: 1200.7368 Evaluate side-chains 927 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 626 time to evaluate : 6.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 123 ASN Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 62 ASN Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 66 MET Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain P residue 249 ILE Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 70 GLN Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 258 ILE Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 74 LYS Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 249 ILE Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 352 ILE Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 119 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 66 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 258 ILE Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 62 ASN Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 12 PHE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 213 GLU Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 62 ASN Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 219 ILE Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 74 LYS Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 119 ILE Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 186 SER Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 249 ILE Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 772 optimal weight: 7.9990 chunk 526 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 690 optimal weight: 5.9990 chunk 382 optimal weight: 6.9990 chunk 791 optimal weight: 9.9990 chunk 641 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 473 optimal weight: 7.9990 chunk 832 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN D 73 ASN B 140 HIS M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN P 44 HIS W 73 ASN L 70 GLN K 46 GLN I 73 ASN G 140 HIS ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN R 44 HIS g 73 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 77418 Z= 0.229 Angle : 0.504 7.905 104268 Z= 0.277 Chirality : 0.044 0.207 12342 Planarity : 0.003 0.037 13056 Dihedral : 4.519 49.300 10262 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.94 % Allowed : 24.15 % Favored : 71.90 % 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: -0.47 (0.08), residues: 9648 helix: 1.94 (0.10), residues: 2724 sheet: -0.51 (0.11), residues: 1956 loop : -1.59 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 119 HIS 0.005 0.001 HIS A 66 PHE 0.018 0.001 PHE I 12 TYR 0.017 0.001 TYR M 99 ARG 0.005 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 687 time to evaluate : 6.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 PHE cc_start: 0.8526 (OUTLIER) cc_final: 0.7365 (t80) REVERT: a 68 SER cc_start: 0.8264 (t) cc_final: 0.7890 (p) REVERT: a 136 TYR cc_start: 0.8500 (p90) cc_final: 0.8131 (p90) REVERT: a 140 ASP cc_start: 0.8465 (t0) cc_final: 0.8205 (t0) REVERT: C 152 LEU cc_start: 0.8184 (mt) cc_final: 0.7949 (mm) REVERT: C 252 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: D 30 MET cc_start: 0.7537 (ttp) cc_final: 0.7335 (ttp) REVERT: D 40 LEU cc_start: 0.7973 (tt) cc_final: 0.7740 (tp) REVERT: D 87 GLN cc_start: 0.7621 (mp10) cc_final: 0.7210 (mp10) REVERT: D 196 LYS cc_start: 0.6610 (tptm) cc_final: 0.6228 (mmtp) REVERT: D 352 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7570 (mt) REVERT: B 36 LYS cc_start: 0.6228 (pttm) cc_final: 0.5946 (pttt) REVERT: B 108 GLU cc_start: 0.6701 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: n 23 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8767 (mp) REVERT: n 98 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8334 (mt) REVERT: n 145 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8312 (pp) REVERT: Y 138 PHE cc_start: 0.8567 (OUTLIER) cc_final: 0.6648 (t80) REVERT: k 128 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8049 (tt0) REVERT: S 13 LYS cc_start: 0.8056 (pttt) cc_final: 0.7676 (ptpt) REVERT: S 119 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8106 (mt) REVERT: S 152 LEU cc_start: 0.8324 (mt) cc_final: 0.8018 (mt) REVERT: S 217 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8239 (mp) REVERT: S 258 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7045 (tt) REVERT: V 152 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.5088 (mp) REVERT: V 196 LYS cc_start: 0.6845 (tptm) cc_final: 0.6218 (mmtp) REVERT: V 352 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7710 (mt) REVERT: P 66 MET cc_start: 0.5105 (pmm) cc_final: 0.3830 (ttm) REVERT: P 182 TYR cc_start: 0.6454 (OUTLIER) cc_final: 0.5771 (t80) REVERT: o 1 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5227 (mtp) REVERT: o 145 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8434 (pp) REVERT: Z 138 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8373 (t80) REVERT: l 68 SER cc_start: 0.8305 (t) cc_final: 0.8044 (p) REVERT: T 74 LYS cc_start: 0.8080 (ttpp) cc_final: 0.7428 (ttpp) REVERT: T 103 MET cc_start: 0.6943 (ttm) cc_final: 0.6368 (ttt) REVERT: T 152 LEU cc_start: 0.8252 (mt) cc_final: 0.8046 (mm) REVERT: T 217 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8271 (mm) REVERT: W 30 MET cc_start: 0.6545 (ptm) cc_final: 0.6277 (ptm) REVERT: W 87 GLN cc_start: 0.7345 (mp10) cc_final: 0.6955 (mp10) REVERT: W 97 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: W 150 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: W 196 LYS cc_start: 0.6029 (tptm) cc_final: 0.5823 (mmtm) REVERT: W 288 LYS cc_start: 0.7936 (mttp) cc_final: 0.7583 (mttp) REVERT: Q 92 PHE cc_start: 0.7709 (t80) cc_final: 0.7280 (t80) REVERT: Q 149 GLU cc_start: 0.5993 (OUTLIER) cc_final: 0.5060 (mm-30) REVERT: Q 295 ASP cc_start: 0.6605 (t70) cc_final: 0.6062 (t70) REVERT: J 138 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7375 (t80) REVERT: K 68 SER cc_start: 0.8258 (t) cc_final: 0.7870 (p) REVERT: K 136 TYR cc_start: 0.8554 (p90) cc_final: 0.8211 (p90) REVERT: K 140 ASP cc_start: 0.8499 (t0) cc_final: 0.8206 (t0) REVERT: F 71 MET cc_start: 0.9067 (tpp) cc_final: 0.8848 (mmt) REVERT: H 252 ASP cc_start: 0.8066 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: I 87 GLN cc_start: 0.7620 (mp10) cc_final: 0.7225 (mp10) REVERT: I 152 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5142 (mp) REVERT: I 196 LYS cc_start: 0.6481 (tptm) cc_final: 0.6175 (mmtp) REVERT: G 36 LYS cc_start: 0.6380 (pttm) cc_final: 0.6054 (pttt) REVERT: G 108 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: G 182 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.5528 (t80) REVERT: p 1 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5304 (mtp) REVERT: p 23 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8834 (mp) REVERT: p 145 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8270 (pp) REVERT: c 138 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.6624 (t80) REVERT: m 128 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.8034 (tt0) REVERT: U 13 LYS cc_start: 0.8039 (pttt) cc_final: 0.7683 (ptpt) REVERT: U 119 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8130 (mt) REVERT: U 152 LEU cc_start: 0.8261 (mt) cc_final: 0.8056 (mm) REVERT: U 252 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7795 (t0) REVERT: X 152 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5074 (mp) REVERT: X 196 LYS cc_start: 0.6738 (tptm) cc_final: 0.6128 (mmtp) REVERT: X 202 ARG cc_start: 0.7675 (ttt90) cc_final: 0.7459 (ttt90) REVERT: X 284 GLU cc_start: 0.7305 (tt0) cc_final: 0.7015 (mm-30) REVERT: R 66 MET cc_start: 0.4799 (pmm) cc_final: 0.3838 (ttm) REVERT: R 149 GLU cc_start: 0.5495 (OUTLIER) cc_final: 0.4941 (mm-30) REVERT: R 218 ARG cc_start: 0.5943 (OUTLIER) cc_final: 0.5385 (mtt180) REVERT: R 319 MET cc_start: 0.5912 (mtp) cc_final: 0.5647 (mtp) REVERT: j 1 MET cc_start: 0.5846 (OUTLIER) cc_final: 0.5389 (mtp) REVERT: j 145 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8432 (pp) REVERT: h 54 MET cc_start: 0.9289 (mmt) cc_final: 0.9001 (mmt) REVERT: h 138 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8372 (t80) REVERT: i 68 SER cc_start: 0.8281 (t) cc_final: 0.8000 (p) REVERT: f 15 LEU cc_start: 0.8098 (tt) cc_final: 0.7785 (mt) REVERT: f 74 LYS cc_start: 0.8087 (ttpp) cc_final: 0.7431 (ttpp) REVERT: f 103 MET cc_start: 0.7027 (ttm) cc_final: 0.6541 (ttt) REVERT: f 152 LEU cc_start: 0.8210 (mt) cc_final: 0.7986 (mm) REVERT: f 217 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8263 (mm) REVERT: g 65 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7017 (mm) REVERT: g 97 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: g 196 LYS cc_start: 0.6024 (tptm) cc_final: 0.5779 (mmtm) REVERT: g 288 LYS cc_start: 0.7934 (mttp) cc_final: 0.7585 (mttp) REVERT: g 352 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7700 (mt) REVERT: e 92 PHE cc_start: 0.7717 (t80) cc_final: 0.7286 (t80) REVERT: e 149 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5030 (mm-30) REVERT: e 218 ARG cc_start: 0.6180 (OUTLIER) cc_final: 0.5864 (mtt-85) REVERT: e 295 ASP cc_start: 0.6518 (t70) cc_final: 0.6037 (t70) outliers start: 335 outliers final: 227 residues processed: 990 average time/residue: 0.6398 time to fit residues: 1123.6964 Evaluate side-chains 915 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 642 time to evaluate : 6.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 32 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 232 GLU Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 70 GLN Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 62 ASN Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 93 LEU Chi-restraints excluded: chain Q residue 146 PHE Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 217 ILE Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 143 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 211 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 232 GLU Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 12 PHE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 258 ILE Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 87 GLN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 93 LEU Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 217 ILE Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 345 MET Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 312 optimal weight: 10.0000 chunk 835 optimal weight: 7.9990 chunk 183 optimal weight: 10.0000 chunk 544 optimal weight: 5.9990 chunk 229 optimal weight: 5.9990 chunk 928 optimal weight: 20.0000 chunk 771 optimal weight: 20.0000 chunk 430 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 307 optimal weight: 5.9990 chunk 487 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN E 72 HIS a 46 GLN D 73 ASN M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN P 44 HIS P 68 ASN N 8 ASN L 70 GLN J 72 HIS K 46 GLN I 73 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN d 8 ASN g 73 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 77418 Z= 0.362 Angle : 0.578 9.354 104268 Z= 0.315 Chirality : 0.045 0.258 12342 Planarity : 0.003 0.042 13056 Dihedral : 4.813 52.585 10262 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.21 % Allowed : 23.71 % Favored : 71.08 % 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: -0.72 (0.08), residues: 9648 helix: 1.70 (0.10), residues: 2646 sheet: -0.68 (0.11), residues: 1956 loop : -1.65 (0.08), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP k 119 HIS 0.006 0.001 HIS g 250 PHE 0.026 0.002 PHE I 12 TYR 0.020 0.002 TYR M 99 ARG 0.006 0.000 ARG R 166 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 443 poor density : 637 time to evaluate : 6.740 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: b 1 MET cc_start: 0.5653 (OUTLIER) cc_final: 0.4615 (mtp) REVERT: b 98 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8425 (mt) REVERT: b 116 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9073 (tp) REVERT: E 138 PHE cc_start: 0.8514 (OUTLIER) cc_final: 0.7425 (t80) REVERT: a 68 SER cc_start: 0.8359 (t) cc_final: 0.7956 (p) REVERT: a 75 ILE cc_start: 0.9188 (OUTLIER) cc_final: 0.8878 (pt) REVERT: a 136 TYR cc_start: 0.8522 (p90) cc_final: 0.8178 (p90) REVERT: a 140 ASP cc_start: 0.8452 (t0) cc_final: 0.8177 (t0) REVERT: C 152 LEU cc_start: 0.8208 (mt) cc_final: 0.7986 (mm) REVERT: C 252 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7772 (t0) REVERT: D 87 GLN cc_start: 0.7669 (mp10) cc_final: 0.7226 (mp10) REVERT: D 152 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.5180 (mp) REVERT: D 196 LYS cc_start: 0.6635 (tptm) cc_final: 0.6260 (mmtp) REVERT: D 352 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.7732 (mt) REVERT: B 36 LYS cc_start: 0.6339 (pttm) cc_final: 0.5882 (pttt) REVERT: B 68 ASN cc_start: 0.5609 (t0) cc_final: 0.5309 (t0) REVERT: B 108 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: B 149 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.4958 (mm-30) REVERT: B 182 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5555 (t80) REVERT: n 1 MET cc_start: 0.5548 (OUTLIER) cc_final: 0.5293 (mtp) REVERT: n 23 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8785 (mp) REVERT: n 145 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8202 (pp) REVERT: Y 138 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.6766 (t80) REVERT: k 75 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8891 (pt) REVERT: k 128 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8080 (tt0) REVERT: M 35 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8221 (mm-30) REVERT: S 13 LYS cc_start: 0.8111 (pttt) cc_final: 0.7734 (ptpt) REVERT: S 119 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8112 (mt) REVERT: S 152 LEU cc_start: 0.8393 (mt) cc_final: 0.8129 (mt) REVERT: S 217 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8296 (mm) REVERT: S 258 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7081 (tt) REVERT: V 152 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.5124 (mp) REVERT: V 196 LYS cc_start: 0.6841 (tptm) cc_final: 0.6143 (mmtp) REVERT: V 352 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.7807 (mt) REVERT: P 28 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7794 (mm) REVERT: P 66 MET cc_start: 0.5118 (pmm) cc_final: 0.3739 (ttm) REVERT: P 108 GLU cc_start: 0.6638 (OUTLIER) cc_final: 0.6316 (tt0) REVERT: P 149 GLU cc_start: 0.5604 (OUTLIER) cc_final: 0.5073 (mm-30) REVERT: o 145 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8399 (pp) REVERT: Z 77 GLU cc_start: 0.7162 (pm20) cc_final: 0.6766 (mp0) REVERT: Z 138 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.8314 (t80) REVERT: l 68 SER cc_start: 0.8347 (t) cc_final: 0.8047 (p) REVERT: l 75 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8803 (pt) REVERT: T 74 LYS cc_start: 0.8106 (ttpp) cc_final: 0.7872 (ttpp) REVERT: T 103 MET cc_start: 0.7078 (ttm) cc_final: 0.6639 (ttm) REVERT: T 217 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8419 (mm) REVERT: W 87 GLN cc_start: 0.7471 (mp10) cc_final: 0.7031 (mp10) REVERT: W 97 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: W 150 ASP cc_start: 0.7838 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: W 196 LYS cc_start: 0.6200 (tptm) cc_final: 0.5922 (mmtm) REVERT: W 288 LYS cc_start: 0.7787 (mttp) cc_final: 0.7466 (mttt) REVERT: Q 92 PHE cc_start: 0.7826 (t80) cc_final: 0.7396 (t80) REVERT: Q 149 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5025 (mm-30) REVERT: Q 182 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5505 (t80) REVERT: Q 218 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5796 (mtt-85) REVERT: Q 295 ASP cc_start: 0.6513 (OUTLIER) cc_final: 0.5845 (t70) REVERT: J 138 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.7434 (t80) REVERT: K 68 SER cc_start: 0.8346 (t) cc_final: 0.7941 (p) REVERT: K 75 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8889 (pt) REVERT: K 136 TYR cc_start: 0.8576 (p90) cc_final: 0.8238 (p90) REVERT: K 140 ASP cc_start: 0.8466 (t0) cc_final: 0.8196 (t0) REVERT: F 71 MET cc_start: 0.9096 (tpp) cc_final: 0.8878 (mmt) REVERT: H 252 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7777 (t0) REVERT: I 87 GLN cc_start: 0.7678 (mp10) cc_final: 0.7216 (mp10) REVERT: I 152 LEU cc_start: 0.6258 (OUTLIER) cc_final: 0.5165 (mp) REVERT: I 196 LYS cc_start: 0.6507 (tptm) cc_final: 0.6216 (mmtp) REVERT: G 36 LYS cc_start: 0.6302 (pttm) cc_final: 0.5844 (pttt) REVERT: G 108 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: G 149 GLU cc_start: 0.5515 (OUTLIER) cc_final: 0.4906 (mm-30) REVERT: G 182 TYR cc_start: 0.5889 (OUTLIER) cc_final: 0.5486 (t80) REVERT: G 211 ILE cc_start: 0.6637 (tp) cc_final: 0.6399 (tt) REVERT: p 1 MET cc_start: 0.5597 (OUTLIER) cc_final: 0.5104 (mtp) REVERT: p 23 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8854 (mp) REVERT: p 98 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8360 (mt) REVERT: p 145 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8160 (pp) REVERT: c 138 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.6735 (t80) REVERT: m 75 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8904 (pt) REVERT: m 128 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: U 13 LYS cc_start: 0.8096 (pttt) cc_final: 0.7736 (ptpt) REVERT: U 119 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8109 (mt) REVERT: X 152 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5135 (mp) REVERT: X 196 LYS cc_start: 0.6804 (tptm) cc_final: 0.6136 (mmtp) REVERT: X 284 GLU cc_start: 0.7425 (tt0) cc_final: 0.7085 (mm-30) REVERT: R 66 MET cc_start: 0.5276 (pmm) cc_final: 0.3962 (ttm) REVERT: R 108 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6271 (tt0) REVERT: R 149 GLU cc_start: 0.5364 (OUTLIER) cc_final: 0.4844 (mm-30) REVERT: R 182 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5860 (t80) REVERT: R 218 ARG cc_start: 0.5915 (OUTLIER) cc_final: 0.5296 (mtt180) REVERT: R 319 MET cc_start: 0.5950 (mtp) cc_final: 0.5683 (mtp) REVERT: j 145 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8414 (pp) REVERT: h 138 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8286 (t80) REVERT: i 68 SER cc_start: 0.8362 (t) cc_final: 0.8094 (p) REVERT: i 75 ILE cc_start: 0.9171 (OUTLIER) cc_final: 0.8814 (pt) REVERT: f 74 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7797 (ttpp) REVERT: f 103 MET cc_start: 0.6988 (ttm) cc_final: 0.6611 (ttm) REVERT: f 152 LEU cc_start: 0.8266 (mt) cc_final: 0.8043 (mm) REVERT: f 217 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8401 (mm) REVERT: g 30 MET cc_start: 0.6675 (ptm) cc_final: 0.6400 (ptm) REVERT: g 97 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: g 150 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: g 196 LYS cc_start: 0.6094 (tptm) cc_final: 0.5831 (mmtm) REVERT: g 288 LYS cc_start: 0.7819 (mttp) cc_final: 0.7495 (mttt) REVERT: g 352 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7878 (mt) REVERT: e 92 PHE cc_start: 0.7827 (t80) cc_final: 0.7398 (t80) REVERT: e 149 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5033 (mm-30) REVERT: e 182 TYR cc_start: 0.6043 (OUTLIER) cc_final: 0.5508 (t80) REVERT: e 218 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5809 (mtt-85) REVERT: e 295 ASP cc_start: 0.6346 (t70) cc_final: 0.5797 (t70) outliers start: 443 outliers final: 314 residues processed: 1036 average time/residue: 0.6340 time to fit residues: 1167.4231 Evaluate side-chains 999 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 380 poor density : 619 time to evaluate : 6.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 88 ASN Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 123 ASN Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 149 GLU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 76 MET Chi-restraints excluded: chain n residue 88 ASN Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 217 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 62 ASN Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 179 SER Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain P residue 249 ILE Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 70 GLN Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 134 VAL Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain T residue 217 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 62 ASN Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 258 ILE Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 182 TYR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 217 ILE Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 249 ILE Chi-restraints excluded: chain Q residue 295 ASP Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 352 ILE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 76 MET Chi-restraints excluded: chain p residue 88 ASN Chi-restraints excluded: chain p residue 98 LEU Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain m residue 137 ASP Chi-restraints excluded: chain m residue 141 ILE Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 211 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 62 ASN Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 277 VAL Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 12 PHE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 108 GLU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 70 GLN Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 219 ILE Chi-restraints excluded: chain g residue 258 ILE Chi-restraints excluded: chain g residue 277 VAL Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 87 GLN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 146 PHE Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 186 SER Chi-restraints excluded: chain e residue 217 ILE Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 243 VAL Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 895 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 529 optimal weight: 5.9990 chunk 678 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 781 optimal weight: 30.0000 chunk 518 optimal weight: 9.9990 chunk 925 optimal weight: 20.0000 chunk 579 optimal weight: 10.0000 chunk 564 optimal weight: 8.9990 chunk 427 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN C 271 ASN D 73 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN L 70 GLN K 46 GLN I 73 ASN G 68 ASN O 8 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 77418 Z= 0.474 Angle : 0.643 8.982 104268 Z= 0.350 Chirality : 0.048 0.313 12342 Planarity : 0.004 0.056 13056 Dihedral : 5.143 52.559 10262 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 5.71 % Allowed : 23.91 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.08), residues: 9648 helix: 1.31 (0.10), residues: 2646 sheet: -0.97 (0.11), residues: 2016 loop : -1.75 (0.08), residues: 4986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP d 119 HIS 0.007 0.002 HIS F 66 PHE 0.030 0.002 PHE I 12 TYR 0.023 0.002 TYR M 99 ARG 0.006 0.001 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 485 poor density : 628 time to evaluate : 6.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 98 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8450 (mt) REVERT: b 116 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9087 (tp) REVERT: b 145 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8423 (pp) REVERT: E 138 PHE cc_start: 0.8560 (OUTLIER) cc_final: 0.7414 (t80) REVERT: a 68 SER cc_start: 0.8411 (t) cc_final: 0.7983 (p) REVERT: a 75 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8914 (pt) REVERT: a 136 TYR cc_start: 0.8519 (p90) cc_final: 0.8197 (p90) REVERT: a 140 ASP cc_start: 0.8480 (t0) cc_final: 0.8237 (t0) REVERT: C 152 LEU cc_start: 0.8297 (mt) cc_final: 0.8063 (mm) REVERT: C 252 ASP cc_start: 0.8174 (OUTLIER) cc_final: 0.7852 (t0) REVERT: D 87 GLN cc_start: 0.7730 (mp10) cc_final: 0.7240 (mp10) REVERT: D 150 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7207 (t0) REVERT: D 152 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5086 (mp) REVERT: D 196 LYS cc_start: 0.6649 (tptm) cc_final: 0.6258 (mmtp) REVERT: D 352 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7731 (mt) REVERT: B 36 LYS cc_start: 0.6262 (pttm) cc_final: 0.5823 (pttt) REVERT: B 108 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6297 (tm-30) REVERT: B 130 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6659 (mtmt) REVERT: B 182 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5489 (t80) REVERT: n 23 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8812 (mp) REVERT: n 104 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7208 (mt-10) REVERT: n 145 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8110 (pp) REVERT: Y 138 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.6778 (t80) REVERT: k 75 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8919 (pt) REVERT: k 128 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8102 (tt0) REVERT: M 35 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8203 (mm-30) REVERT: S 13 LYS cc_start: 0.8151 (pttt) cc_final: 0.7764 (ptpt) REVERT: S 119 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8123 (mt) REVERT: S 152 LEU cc_start: 0.8410 (mt) cc_final: 0.8110 (mt) REVERT: S 258 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7072 (tt) REVERT: V 152 LEU cc_start: 0.6482 (OUTLIER) cc_final: 0.5180 (mp) REVERT: V 196 LYS cc_start: 0.6780 (tptm) cc_final: 0.6133 (mmtp) REVERT: V 352 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7850 (mt) REVERT: P 28 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7793 (mm) REVERT: P 108 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6330 (tt0) REVERT: P 149 GLU cc_start: 0.5538 (OUTLIER) cc_final: 0.5055 (mm-30) REVERT: P 182 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.5670 (t80) REVERT: o 145 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8380 (pp) REVERT: Z 138 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8315 (t80) REVERT: l 75 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8834 (pt) REVERT: T 74 LYS cc_start: 0.8104 (ttpp) cc_final: 0.7864 (ttpp) REVERT: T 103 MET cc_start: 0.7092 (ttm) cc_final: 0.6814 (ttt) REVERT: W 87 GLN cc_start: 0.7623 (mp10) cc_final: 0.6931 (mm-40) REVERT: W 97 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7111 (mt-10) REVERT: W 150 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.7334 (m-30) REVERT: W 196 LYS cc_start: 0.6179 (tptm) cc_final: 0.5941 (mmtm) REVERT: W 288 LYS cc_start: 0.7999 (mttp) cc_final: 0.7726 (mttt) REVERT: W 331 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8686 (p) REVERT: Q 28 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7890 (mm) REVERT: Q 36 LYS cc_start: 0.6059 (pttm) cc_final: 0.5815 (pttm) REVERT: Q 108 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6556 (tm-30) REVERT: Q 149 GLU cc_start: 0.5997 (OUTLIER) cc_final: 0.4479 (tp30) REVERT: Q 218 ARG cc_start: 0.6420 (OUTLIER) cc_final: 0.5809 (mtt-85) REVERT: L 98 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8450 (mt) REVERT: L 116 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9110 (tp) REVERT: L 145 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8397 (pp) REVERT: J 138 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7453 (t80) REVERT: K 68 SER cc_start: 0.8407 (t) cc_final: 0.7968 (p) REVERT: K 75 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8919 (pt) REVERT: K 136 TYR cc_start: 0.8568 (p90) cc_final: 0.8240 (p90) REVERT: K 140 ASP cc_start: 0.8485 (t0) cc_final: 0.8239 (t0) REVERT: F 71 MET cc_start: 0.9089 (tpp) cc_final: 0.8847 (mmt) REVERT: H 152 LEU cc_start: 0.8375 (mt) cc_final: 0.8141 (mt) REVERT: H 252 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7855 (t0) REVERT: I 87 GLN cc_start: 0.7729 (mp10) cc_final: 0.7232 (mp10) REVERT: I 150 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7166 (t0) REVERT: I 152 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5158 (mp) REVERT: I 196 LYS cc_start: 0.6488 (tptm) cc_final: 0.6210 (mmtp) REVERT: G 36 LYS cc_start: 0.6281 (pttm) cc_final: 0.5829 (pttt) REVERT: G 108 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6483 (tm-30) REVERT: G 182 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5467 (t80) REVERT: p 23 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8812 (mp) REVERT: p 104 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7213 (mt-10) REVERT: p 145 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8108 (pp) REVERT: c 138 PHE cc_start: 0.8634 (OUTLIER) cc_final: 0.6778 (t80) REVERT: m 75 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8919 (pt) REVERT: m 128 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: O 35 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8175 (mm-30) REVERT: U 13 LYS cc_start: 0.8169 (pttt) cc_final: 0.7787 (ptpt) REVERT: U 119 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8123 (mt) REVERT: U 152 LEU cc_start: 0.8394 (mm) cc_final: 0.7952 (mt) REVERT: U 258 ILE cc_start: 0.7361 (OUTLIER) cc_final: 0.7050 (tt) REVERT: X 152 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.5184 (mp) REVERT: X 196 LYS cc_start: 0.6845 (tptm) cc_final: 0.6196 (mmtp) REVERT: X 284 GLU cc_start: 0.7446 (tt0) cc_final: 0.7047 (mm-30) REVERT: R 149 GLU cc_start: 0.5318 (OUTLIER) cc_final: 0.4803 (mm-30) REVERT: R 182 TYR cc_start: 0.6252 (OUTLIER) cc_final: 0.5559 (t80) REVERT: R 218 ARG cc_start: 0.5979 (OUTLIER) cc_final: 0.5405 (mtt180) REVERT: R 319 MET cc_start: 0.6027 (mtp) cc_final: 0.5773 (mtp) REVERT: j 145 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8378 (pp) REVERT: h 138 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8317 (t80) REVERT: i 75 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8853 (pt) REVERT: f 44 HIS cc_start: 0.6651 (t-90) cc_final: 0.6347 (t-90) REVERT: f 74 LYS cc_start: 0.8116 (ttpp) cc_final: 0.7867 (ttpp) REVERT: f 103 MET cc_start: 0.6994 (ttm) cc_final: 0.6761 (ttt) REVERT: f 152 LEU cc_start: 0.8327 (mt) cc_final: 0.8099 (mm) REVERT: f 217 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8431 (mm) REVERT: g 97 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: g 150 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: g 196 LYS cc_start: 0.6056 (tptm) cc_final: 0.5836 (mmtm) REVERT: g 288 LYS cc_start: 0.8004 (mttp) cc_final: 0.7692 (mttp) REVERT: g 352 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7937 (mt) REVERT: e 28 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7727 (mm) REVERT: e 36 LYS cc_start: 0.6129 (pttm) cc_final: 0.5525 (pttt) REVERT: e 108 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: e 149 GLU cc_start: 0.6038 (OUTLIER) cc_final: 0.5149 (mm-30) REVERT: e 182 TYR cc_start: 0.6104 (OUTLIER) cc_final: 0.5495 (t80) REVERT: e 218 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5863 (mtt-85) outliers start: 485 outliers final: 345 residues processed: 1068 average time/residue: 0.6339 time to fit residues: 1206.0084 Evaluate side-chains 1024 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 609 time to evaluate : 6.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 25 ILE Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 54 THR Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 76 MET Chi-restraints excluded: chain b residue 88 ASN Chi-restraints excluded: chain b residue 98 LEU Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 130 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 66 LEU Chi-restraints excluded: chain n residue 76 MET Chi-restraints excluded: chain n residue 88 ASN Chi-restraints excluded: chain n residue 121 THR Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain k residue 137 ASP Chi-restraints excluded: chain k residue 141 ILE Chi-restraints excluded: chain M residue 35 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 62 ASN Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 185 LEU Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 108 GLU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain P residue 249 ILE Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 52 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 88 ASN Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 134 VAL Chi-restraints excluded: chain o residue 144 ASN Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain Z residue 139 LEU Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 64 LEU Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 119 ILE Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 248 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 256 VAL Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 62 ASN Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 150 ASP Chi-restraints excluded: chain W residue 185 LEU Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 294 SER Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain W residue 331 SER Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 182 TYR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 195 THR Chi-restraints excluded: chain Q residue 217 ILE Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 249 ILE Chi-restraints excluded: chain Q residue 295 ASP Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain L residue 145 LEU Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 121 LEU Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 181 THR Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 303 GLU Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 323 GLU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 248 ILE Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain I residue 352 ILE Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 153 VAL Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 248 ILE Chi-restraints excluded: chain G residue 249 ILE Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 66 LEU Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 76 MET Chi-restraints excluded: chain p residue 88 ASN Chi-restraints excluded: chain p residue 121 THR Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 134 THR Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain m residue 137 ASP Chi-restraints excluded: chain m residue 141 ILE Chi-restraints excluded: chain O residue 35 GLU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain U residue 63 LEU Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 119 ILE Chi-restraints excluded: chain U residue 121 LEU Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 211 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 230 THR Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain U residue 258 ILE Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 62 ASN Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 66 MET Chi-restraints excluded: chain X residue 110 ASP Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 185 LEU Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 200 GLU Chi-restraints excluded: chain X residue 248 ILE Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 277 VAL Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 12 PHE Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 52 LEU Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 88 ASN Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 144 ASN Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain h residue 139 LEU Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 75 ILE Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 119 ILE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 97 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 150 ASP Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 219 ILE Chi-restraints excluded: chain g residue 277 VAL Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 291 LEU Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 331 SER Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 53 LEU Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 108 GLU Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 186 SER Chi-restraints excluded: chain e residue 195 THR Chi-restraints excluded: chain e residue 217 ILE Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 243 VAL Chi-restraints excluded: chain e residue 249 ILE Chi-restraints excluded: chain e residue 295 ASP Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 572 optimal weight: 8.9990 chunk 369 optimal weight: 5.9990 chunk 552 optimal weight: 8.9990 chunk 278 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 179 optimal weight: 6.9990 chunk 588 optimal weight: 6.9990 chunk 630 optimal weight: 0.9980 chunk 457 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 chunk 727 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN A 8 ASN D 73 ASN B 68 ASN M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN N 8 ASN L 70 GLN K 46 GLN I 73 ASN O 8 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN R 145 ASN d 8 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 77418 Z= 0.182 Angle : 0.495 10.148 104268 Z= 0.271 Chirality : 0.043 0.221 12342 Planarity : 0.003 0.039 13056 Dihedral : 4.508 54.505 10262 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.03 % Allowed : 25.80 % Favored : 70.17 % 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 (0.08), residues: 9648 helix: 1.81 (0.10), residues: 2718 sheet: -0.66 (0.11), residues: 1896 loop : -1.68 (0.08), residues: 5034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP d 119 HIS 0.004 0.001 HIS Q 250 PHE 0.016 0.001 PHE g 12 TYR 0.019 0.001 TYR Q 60 ARG 0.006 0.000 ARG B 166 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 679 time to evaluate : 6.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 116 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.9039 (tp) REVERT: E 138 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.7439 (t80) REVERT: a 68 SER cc_start: 0.8229 (t) cc_final: 0.7928 (p) REVERT: a 136 TYR cc_start: 0.8507 (p90) cc_final: 0.8197 (p90) REVERT: a 140 ASP cc_start: 0.8409 (t0) cc_final: 0.8083 (t0) REVERT: A 35 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: C 152 LEU cc_start: 0.8200 (mt) cc_final: 0.7971 (mm) REVERT: C 252 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7452 (m-30) REVERT: D 87 GLN cc_start: 0.7727 (mp10) cc_final: 0.7222 (mp10) REVERT: D 152 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.4899 (mp) REVERT: D 196 LYS cc_start: 0.6542 (tptm) cc_final: 0.6142 (mmtp) REVERT: D 200 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7198 (mm-30) REVERT: D 352 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7522 (mt) REVERT: B 27 ILE cc_start: 0.8415 (mm) cc_final: 0.8054 (mt) REVERT: B 36 LYS cc_start: 0.6384 (pttm) cc_final: 0.6102 (pttt) REVERT: B 182 TYR cc_start: 0.6170 (OUTLIER) cc_final: 0.5352 (t80) REVERT: n 1 MET cc_start: 0.5297 (OUTLIER) cc_final: 0.5005 (mtp) REVERT: n 23 ILE cc_start: 0.9043 (OUTLIER) cc_final: 0.8779 (mp) REVERT: n 145 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8267 (pp) REVERT: Y 138 PHE cc_start: 0.8544 (OUTLIER) cc_final: 0.6663 (t80) REVERT: k 128 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7981 (tt0) REVERT: S 13 LYS cc_start: 0.8091 (pttt) cc_final: 0.7711 (ptpt) REVERT: S 152 LEU cc_start: 0.8382 (mt) cc_final: 0.8027 (mt) REVERT: S 252 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7796 (t0) REVERT: S 258 ILE cc_start: 0.7396 (OUTLIER) cc_final: 0.7102 (tt) REVERT: V 152 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5228 (mp) REVERT: V 196 LYS cc_start: 0.6648 (tptm) cc_final: 0.6142 (mmtp) REVERT: P 66 MET cc_start: 0.5201 (pmm) cc_final: 0.3772 (ttm) REVERT: P 149 GLU cc_start: 0.5452 (OUTLIER) cc_final: 0.4975 (mm-30) REVERT: P 182 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5748 (t80) REVERT: o 145 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8444 (pp) REVERT: Z 138 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8333 (t80) REVERT: T 44 HIS cc_start: 0.6734 (t-90) cc_final: 0.6421 (t-90) REVERT: T 74 LYS cc_start: 0.7995 (ttpp) cc_final: 0.7779 (ttpp) REVERT: W 30 MET cc_start: 0.6588 (ptm) cc_final: 0.6244 (ptm) REVERT: W 87 GLN cc_start: 0.7402 (mp10) cc_final: 0.6657 (mm-40) REVERT: W 196 LYS cc_start: 0.6091 (tptm) cc_final: 0.5878 (mmtm) REVERT: W 288 LYS cc_start: 0.7826 (mttp) cc_final: 0.7616 (mttp) REVERT: Q 28 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7742 (mm) REVERT: Q 108 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5881 (tm-30) REVERT: Q 149 GLU cc_start: 0.5793 (OUTLIER) cc_final: 0.4973 (mm-30) REVERT: Q 218 ARG cc_start: 0.6109 (OUTLIER) cc_final: 0.5731 (mtt-85) REVERT: L 98 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8434 (mt) REVERT: J 138 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7366 (t80) REVERT: K 68 SER cc_start: 0.8227 (t) cc_final: 0.7916 (p) REVERT: K 136 TYR cc_start: 0.8558 (p90) cc_final: 0.8241 (p90) REVERT: K 140 ASP cc_start: 0.8436 (t0) cc_final: 0.8086 (t0) REVERT: F 71 MET cc_start: 0.9073 (tpp) cc_final: 0.8837 (mmt) REVERT: H 252 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7433 (m-30) REVERT: I 87 GLN cc_start: 0.7714 (mp10) cc_final: 0.7198 (mp10) REVERT: I 152 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.4977 (mp) REVERT: I 196 LYS cc_start: 0.6377 (tptm) cc_final: 0.6141 (mmtp) REVERT: G 36 LYS cc_start: 0.6375 (pttm) cc_final: 0.6051 (pttt) REVERT: p 23 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8774 (mp) REVERT: p 145 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8261 (pp) REVERT: c 138 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.6646 (t80) REVERT: m 128 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (tt0) REVERT: U 13 LYS cc_start: 0.8071 (pttt) cc_final: 0.7709 (ptpt) REVERT: X 152 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.5226 (mp) REVERT: X 196 LYS cc_start: 0.6739 (tptm) cc_final: 0.6018 (mmtp) REVERT: X 284 GLU cc_start: 0.7322 (tt0) cc_final: 0.7030 (mm-30) REVERT: R 149 GLU cc_start: 0.5403 (OUTLIER) cc_final: 0.4891 (mm-30) REVERT: R 182 TYR cc_start: 0.6287 (OUTLIER) cc_final: 0.5529 (t80) REVERT: R 217 ILE cc_start: 0.6714 (OUTLIER) cc_final: 0.6483 (mm) REVERT: R 218 ARG cc_start: 0.5950 (OUTLIER) cc_final: 0.5416 (mtt180) REVERT: R 319 MET cc_start: 0.5946 (mtp) cc_final: 0.5668 (mtp) REVERT: j 145 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8446 (pp) REVERT: h 138 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8398 (t80) REVERT: f 44 HIS cc_start: 0.6740 (t-90) cc_final: 0.6446 (t-90) REVERT: f 74 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7777 (ttpp) REVERT: f 103 MET cc_start: 0.6669 (ttm) cc_final: 0.6466 (ttt) REVERT: f 152 LEU cc_start: 0.8262 (mt) cc_final: 0.8061 (mm) REVERT: f 217 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8226 (mm) REVERT: g 65 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7025 (mm) REVERT: g 196 LYS cc_start: 0.6137 (tptm) cc_final: 0.5833 (mmtm) REVERT: g 288 LYS cc_start: 0.7835 (mttp) cc_final: 0.7633 (mttp) REVERT: g 352 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7681 (mt) REVERT: e 28 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7786 (mm) REVERT: e 92 PHE cc_start: 0.7752 (t80) cc_final: 0.7289 (t80) REVERT: e 108 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: e 149 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.4976 (mm-30) outliers start: 342 outliers final: 240 residues processed: 980 average time/residue: 0.6481 time to fit residues: 1118.6578 Evaluate side-chains 924 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 639 time to evaluate : 6.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 76 MET Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 76 MET Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 230 THR Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 62 ASN Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 259 ASP Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 62 ASN Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 258 ILE Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 182 TYR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 123 ASN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 76 MET Chi-restraints excluded: chain p residue 88 ASN Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 211 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 62 ASN Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 143 LEU Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 297 THR Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 219 ILE Chi-restraints excluded: chain g residue 258 ILE Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 108 GLU Chi-restraints excluded: chain e residue 146 PHE Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 186 SER Chi-restraints excluded: chain e residue 345 MET Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 841 optimal weight: 10.0000 chunk 886 optimal weight: 6.9990 chunk 808 optimal weight: 9.9990 chunk 862 optimal weight: 20.0000 chunk 518 optimal weight: 7.9990 chunk 375 optimal weight: 0.0980 chunk 677 optimal weight: 7.9990 chunk 264 optimal weight: 10.0000 chunk 779 optimal weight: 8.9990 chunk 815 optimal weight: 3.9990 chunk 859 optimal weight: 0.0970 overall best weight: 3.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN D 73 ASN ** B 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN L 70 GLN K 46 GLN I 73 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 77418 Z= 0.235 Angle : 0.516 10.068 104268 Z= 0.282 Chirality : 0.043 0.188 12342 Planarity : 0.003 0.037 13056 Dihedral : 4.518 56.665 10262 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.30 % Allowed : 25.68 % Favored : 70.02 % 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: -0.64 (0.08), residues: 9648 helix: 1.85 (0.10), residues: 2646 sheet: -0.63 (0.11), residues: 1956 loop : -1.65 (0.08), residues: 5046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP d 119 HIS 0.004 0.001 HIS W 250 PHE 0.019 0.001 PHE I 12 TYR 0.034 0.001 TYR B 60 ARG 0.008 0.000 ARG G 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1019 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 654 time to evaluate : 6.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 PHE cc_start: 0.8508 (OUTLIER) cc_final: 0.7336 (t80) REVERT: a 68 SER cc_start: 0.8260 (t) cc_final: 0.7960 (p) REVERT: a 75 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8833 (pt) REVERT: a 136 TYR cc_start: 0.8523 (p90) cc_final: 0.8204 (p90) REVERT: a 140 ASP cc_start: 0.8419 (t0) cc_final: 0.8116 (t0) REVERT: A 35 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: C 152 LEU cc_start: 0.8227 (mt) cc_final: 0.8018 (mm) REVERT: C 252 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7462 (m-30) REVERT: D 87 GLN cc_start: 0.7754 (mp10) cc_final: 0.7242 (mp10) REVERT: D 152 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5169 (mp) REVERT: D 196 LYS cc_start: 0.6518 (tptm) cc_final: 0.6169 (mmtp) REVERT: D 200 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7177 (mm-30) REVERT: D 352 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7604 (mt) REVERT: B 27 ILE cc_start: 0.8466 (mm) cc_final: 0.8075 (mt) REVERT: B 36 LYS cc_start: 0.6357 (pttm) cc_final: 0.6061 (pttt) REVERT: B 60 TYR cc_start: 0.5162 (m-80) cc_final: 0.4959 (m-80) REVERT: B 108 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6331 (tm-30) REVERT: B 182 TYR cc_start: 0.6206 (OUTLIER) cc_final: 0.5353 (t80) REVERT: n 1 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5079 (mtp) REVERT: n 23 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8777 (mp) REVERT: n 98 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8395 (mt) REVERT: n 145 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8217 (pp) REVERT: Y 138 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.6643 (t80) REVERT: k 128 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: S 13 LYS cc_start: 0.8090 (pttt) cc_final: 0.7725 (ptpt) REVERT: S 152 LEU cc_start: 0.8399 (mt) cc_final: 0.8083 (mt) REVERT: S 252 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7827 (t0) REVERT: S 258 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7116 (tt) REVERT: V 152 LEU cc_start: 0.6471 (OUTLIER) cc_final: 0.5206 (mp) REVERT: V 196 LYS cc_start: 0.6606 (tptm) cc_final: 0.6139 (mmtp) REVERT: P 28 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7786 (mm) REVERT: P 66 MET cc_start: 0.5072 (pmm) cc_final: 0.3701 (ttm) REVERT: P 149 GLU cc_start: 0.5386 (OUTLIER) cc_final: 0.4768 (mm-30) REVERT: P 182 TYR cc_start: 0.6392 (OUTLIER) cc_final: 0.5749 (t80) REVERT: o 145 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8432 (pp) REVERT: Z 138 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8359 (t80) REVERT: T 44 HIS cc_start: 0.6725 (t-90) cc_final: 0.6395 (t-90) REVERT: W 30 MET cc_start: 0.6587 (ptm) cc_final: 0.6244 (ptm) REVERT: W 65 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.7001 (mm) REVERT: W 87 GLN cc_start: 0.7405 (mp10) cc_final: 0.6672 (mm-40) REVERT: W 196 LYS cc_start: 0.6113 (tptm) cc_final: 0.5899 (mmtm) REVERT: W 288 LYS cc_start: 0.7837 (mttp) cc_final: 0.7487 (mttp) REVERT: Q 28 ILE cc_start: 0.7994 (OUTLIER) cc_final: 0.7762 (mm) REVERT: Q 108 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: Q 149 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.4979 (mm-30) REVERT: Q 218 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.5764 (mtt-85) REVERT: L 98 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8411 (mt) REVERT: J 138 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7340 (t80) REVERT: K 68 SER cc_start: 0.8259 (t) cc_final: 0.7941 (p) REVERT: K 75 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8835 (pt) REVERT: K 136 TYR cc_start: 0.8574 (p90) cc_final: 0.8251 (p90) REVERT: K 140 ASP cc_start: 0.8446 (t0) cc_final: 0.8119 (t0) REVERT: F 35 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: F 71 MET cc_start: 0.9083 (tpp) cc_final: 0.8857 (mmt) REVERT: H 252 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: I 87 GLN cc_start: 0.7733 (mp10) cc_final: 0.7227 (mp10) REVERT: I 152 LEU cc_start: 0.6055 (OUTLIER) cc_final: 0.5107 (mp) REVERT: I 196 LYS cc_start: 0.6393 (tptm) cc_final: 0.6186 (mmtp) REVERT: G 27 ILE cc_start: 0.8439 (mm) cc_final: 0.8140 (mt) REVERT: G 36 LYS cc_start: 0.6418 (pttm) cc_final: 0.6070 (pttt) REVERT: G 312 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7422 (mptt) REVERT: p 23 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8774 (mp) REVERT: p 145 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8170 (pp) REVERT: c 138 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.6605 (t80) REVERT: m 128 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: U 13 LYS cc_start: 0.8101 (pttt) cc_final: 0.7760 (ptpt) REVERT: X 152 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.5209 (mp) REVERT: X 196 LYS cc_start: 0.6629 (tptm) cc_final: 0.5974 (mmtp) REVERT: X 284 GLU cc_start: 0.7361 (tt0) cc_final: 0.7048 (mm-30) REVERT: R 44 HIS cc_start: 0.6915 (OUTLIER) cc_final: 0.6539 (m90) REVERT: R 149 GLU cc_start: 0.5323 (OUTLIER) cc_final: 0.4764 (mm-30) REVERT: R 182 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5490 (t80) REVERT: R 217 ILE cc_start: 0.6574 (OUTLIER) cc_final: 0.6368 (mm) REVERT: R 218 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.5383 (mtt180) REVERT: R 319 MET cc_start: 0.5942 (mtp) cc_final: 0.5659 (mtp) REVERT: j 145 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8434 (pp) REVERT: h 138 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8360 (t80) REVERT: f 44 HIS cc_start: 0.6683 (t-90) cc_final: 0.6367 (t-90) REVERT: f 152 LEU cc_start: 0.8325 (mt) cc_final: 0.8108 (mm) REVERT: f 217 ILE cc_start: 0.8505 (OUTLIER) cc_final: 0.8202 (mm) REVERT: g 65 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7041 (mm) REVERT: g 196 LYS cc_start: 0.6053 (tptm) cc_final: 0.5837 (mmtm) REVERT: g 288 LYS cc_start: 0.7844 (mttp) cc_final: 0.7506 (mttp) REVERT: g 352 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.7674 (mt) REVERT: e 28 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7779 (mm) REVERT: e 108 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5945 (tm-30) REVERT: e 149 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.4984 (mm-30) REVERT: e 218 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5778 (mtt-85) outliers start: 365 outliers final: 270 residues processed: 981 average time/residue: 0.6421 time to fit residues: 1116.5624 Evaluate side-chains 963 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 324 poor density : 639 time to evaluate : 6.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 52 LEU Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 76 MET Chi-restraints excluded: chain b residue 101 THR Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain b residue 143 LEU Chi-restraints excluded: chain E residue 128 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 141 ILE Chi-restraints excluded: chain a residue 50 ASP Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 91 SER Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 354 ILE Chi-restraints excluded: chain n residue 1 MET Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 76 MET Chi-restraints excluded: chain n residue 88 ASN Chi-restraints excluded: chain n residue 98 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 134 THR Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 79 ILE Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 230 THR Chi-restraints excluded: chain S residue 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU Chi-restraints excluded: chain S residue 323 GLU Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 62 ASN Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 150 ASP Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 311 SER Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain P residue 12 PHE Chi-restraints excluded: chain P residue 28 ILE Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain P residue 59 GLU Chi-restraints excluded: chain P residue 88 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 GLU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain o residue 1 MET Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 54 THR Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain o residue 145 LEU Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain l residue 49 THR Chi-restraints excluded: chain l residue 64 LEU Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain l residue 91 SER Chi-restraints excluded: chain l residue 141 ILE Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 153 VAL Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 170 LEU Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain T residue 297 THR Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 323 GLU Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 62 ASN Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 80 ILE Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 258 ILE Chi-restraints excluded: chain W residue 277 VAL Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 311 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 108 GLU Chi-restraints excluded: chain Q residue 146 PHE Chi-restraints excluded: chain Q residue 149 GLU Chi-restraints excluded: chain Q residue 177 SER Chi-restraints excluded: chain Q residue 182 TYR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 243 VAL Chi-restraints excluded: chain Q residue 354 ILE Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 66 LEU Chi-restraints excluded: chain L residue 76 MET Chi-restraints excluded: chain L residue 98 LEU Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 143 LEU Chi-restraints excluded: chain J residue 128 GLU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 79 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain F residue 35 GLU Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 119 ILE Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 252 ASP Chi-restraints excluded: chain H residue 256 VAL Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain H residue 309 LEU Chi-restraints excluded: chain H residue 350 LEU Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 277 VAL Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 259 ASP Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain G residue 354 ILE Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 76 MET Chi-restraints excluded: chain p residue 88 ASN Chi-restraints excluded: chain p residue 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 128 GLU Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain U residue 211 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 230 THR Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 309 LEU Chi-restraints excluded: chain U residue 323 GLU Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 62 ASN Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 311 SER Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 149 GLU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 217 ILE Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 66 LEU Chi-restraints excluded: chain j residue 76 MET Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain i residue 64 LEU Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain i residue 91 SER Chi-restraints excluded: chain i residue 141 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain d residue 67 VAL Chi-restraints excluded: chain d residue 127 ILE Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 217 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 248 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 297 THR Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain f residue 323 GLU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 189 VAL Chi-restraints excluded: chain g residue 195 THR Chi-restraints excluded: chain g residue 219 ILE Chi-restraints excluded: chain g residue 258 ILE Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 294 SER Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 311 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 87 GLN Chi-restraints excluded: chain e residue 108 GLU Chi-restraints excluded: chain e residue 146 PHE Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 186 SER Chi-restraints excluded: chain e residue 218 ARG Chi-restraints excluded: chain e residue 295 ASP Chi-restraints excluded: chain e residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 566 optimal weight: 0.2980 chunk 911 optimal weight: 0.1980 chunk 556 optimal weight: 0.5980 chunk 432 optimal weight: 3.9990 chunk 633 optimal weight: 9.9990 chunk 956 optimal weight: 0.6980 chunk 880 optimal weight: 0.9980 chunk 761 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 588 optimal weight: 6.9990 chunk 466 optimal weight: 0.3980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN C 87 GLN D 73 ASN B 62 ASN ** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 66 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 87 GLN L 70 GLN K 46 GLN F 8 ASN I 73 ASN ** G 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 66 HIS ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 87 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 77418 Z= 0.116 Angle : 0.455 10.693 104268 Z= 0.248 Chirality : 0.042 0.184 12342 Planarity : 0.003 0.039 13056 Dihedral : 4.047 58.887 10262 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.11 % Allowed : 27.72 % Favored : 70.17 % 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: -0.25 (0.08), residues: 9648 helix: 2.20 (0.10), residues: 2736 sheet: -0.29 (0.11), residues: 1884 loop : -1.54 (0.08), residues: 5028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.003 0.000 HIS R 250 PHE 0.013 0.001 PHE g 12 TYR 0.029 0.001 TYR Q 60 ARG 0.004 0.000 ARG G 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19296 Ramachandran restraints generated. 9648 Oldfield, 0 Emsley, 9648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 778 time to evaluate : 6.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 126 ASP cc_start: 0.8426 (t0) cc_final: 0.8120 (t0) REVERT: a 136 TYR cc_start: 0.8526 (p90) cc_final: 0.8256 (p90) REVERT: a 140 ASP cc_start: 0.8334 (t0) cc_final: 0.8126 (t0) REVERT: C 152 LEU cc_start: 0.8190 (mt) cc_final: 0.7935 (mm) REVERT: D 152 LEU cc_start: 0.5999 (OUTLIER) cc_final: 0.4954 (mp) REVERT: D 196 LYS cc_start: 0.6467 (tptm) cc_final: 0.6197 (mmtp) REVERT: D 352 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7502 (mt) REVERT: B 36 LYS cc_start: 0.6668 (pttm) cc_final: 0.6432 (pttt) REVERT: B 150 ASP cc_start: 0.4815 (t70) cc_final: 0.4583 (t70) REVERT: B 182 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5171 (t80) REVERT: n 23 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8759 (mp) REVERT: Y 138 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.6575 (t80) REVERT: Y 141 ILE cc_start: 0.7770 (tt) cc_final: 0.7538 (tt) REVERT: S 13 LYS cc_start: 0.8028 (pttt) cc_final: 0.7688 (ptpt) REVERT: S 152 LEU cc_start: 0.8367 (mt) cc_final: 0.7995 (mt) REVERT: S 252 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7709 (t0) REVERT: V 152 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5370 (mp) REVERT: V 196 LYS cc_start: 0.6668 (tptm) cc_final: 0.6251 (mmtp) REVERT: P 45 GLU cc_start: 0.5871 (mm-30) cc_final: 0.5660 (tp30) REVERT: P 66 MET cc_start: 0.4707 (pmm) cc_final: 0.3766 (ttm) REVERT: P 182 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.5662 (t80) REVERT: Z 65 TYR cc_start: 0.8613 (m-80) cc_final: 0.8363 (m-80) REVERT: Z 138 PHE cc_start: 0.8669 (OUTLIER) cc_final: 0.8402 (t80) REVERT: T 44 HIS cc_start: 0.6592 (t-90) cc_final: 0.6351 (t-90) REVERT: W 65 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7114 (mm) REVERT: W 284 GLU cc_start: 0.7397 (tt0) cc_final: 0.6970 (mm-30) REVERT: W 288 LYS cc_start: 0.7845 (mttp) cc_final: 0.7602 (mttp) REVERT: Q 92 PHE cc_start: 0.7772 (t80) cc_final: 0.7292 (t80) REVERT: K 136 TYR cc_start: 0.8585 (p90) cc_final: 0.8263 (p90) REVERT: K 140 ASP cc_start: 0.8354 (t0) cc_final: 0.8149 (t0) REVERT: F 71 MET cc_start: 0.8978 (tpp) cc_final: 0.8723 (mmp) REVERT: I 42 GLU cc_start: 0.7026 (pp20) cc_final: 0.6750 (pp20) REVERT: I 152 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5029 (mp) REVERT: I 196 LYS cc_start: 0.6501 (tptm) cc_final: 0.6213 (mmtp) REVERT: G 36 LYS cc_start: 0.6647 (pttm) cc_final: 0.6395 (pttt) REVERT: G 150 ASP cc_start: 0.4798 (t70) cc_final: 0.4540 (t70) REVERT: G 312 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7556 (mptt) REVERT: p 23 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8750 (mp) REVERT: c 138 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.6489 (t80) REVERT: U 13 LYS cc_start: 0.8010 (pttt) cc_final: 0.7652 (ptpt) REVERT: X 152 LEU cc_start: 0.6449 (OUTLIER) cc_final: 0.5364 (mp) REVERT: X 196 LYS cc_start: 0.6561 (tptm) cc_final: 0.6212 (mmtp) REVERT: X 284 GLU cc_start: 0.7199 (tt0) cc_final: 0.6963 (mm-30) REVERT: R 44 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6456 (m90) REVERT: R 96 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7418 (tptp) REVERT: R 182 TYR cc_start: 0.6036 (OUTLIER) cc_final: 0.5242 (t80) REVERT: R 218 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5541 (mtt180) REVERT: R 319 MET cc_start: 0.5965 (mtp) cc_final: 0.5658 (mtp) REVERT: h 65 TYR cc_start: 0.8631 (m-80) cc_final: 0.8389 (m-80) REVERT: h 138 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.8401 (t80) REVERT: f 44 HIS cc_start: 0.6663 (t-90) cc_final: 0.6404 (t-90) REVERT: g 65 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7036 (mm) REVERT: g 284 GLU cc_start: 0.7387 (tt0) cc_final: 0.6940 (mm-30) REVERT: g 288 LYS cc_start: 0.7859 (mttp) cc_final: 0.7615 (mttp) REVERT: g 352 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7607 (mt) REVERT: e 92 PHE cc_start: 0.7768 (t80) cc_final: 0.7296 (t80) outliers start: 179 outliers final: 127 residues processed: 930 average time/residue: 0.6807 time to fit residues: 1107.3137 Evaluate side-chains 833 residues out of total 8496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 685 time to evaluate : 6.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 VAL Chi-restraints excluded: chain b residue 116 LEU Chi-restraints excluded: chain b residue 133 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain a residue 141 ILE Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 221 ARG Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain D residue 352 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain S residue 86 ILE Chi-restraints excluded: chain S residue 88 THR Chi-restraints excluded: chain S residue 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain V residue 137 VAL Chi-restraints excluded: chain V residue 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 188 VAL Chi-restraints excluded: chain V residue 189 VAL Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain o residue 30 VAL Chi-restraints excluded: chain o residue 76 MET Chi-restraints excluded: chain o residue 133 VAL Chi-restraints excluded: chain Z residue 31 GLN Chi-restraints excluded: chain Z residue 138 PHE Chi-restraints excluded: chain l residue 79 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 160 VAL Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain T residue 309 LEU Chi-restraints excluded: chain T residue 350 LEU Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 287 GLU Chi-restraints excluded: chain W residue 307 SER Chi-restraints excluded: chain W residue 319 MET Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 146 PHE Chi-restraints excluded: chain Q residue 182 TYR Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain L residue 30 VAL Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 160 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 219 ILE Chi-restraints excluded: chain I residue 51 VAL Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 153 VAL Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 258 ILE Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain I residue 311 SER Chi-restraints excluded: chain I residue 319 MET Chi-restraints excluded: chain G residue 12 PHE Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 258 ILE Chi-restraints excluded: chain G residue 312 LYS Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain U residue 86 ILE Chi-restraints excluded: chain U residue 88 THR Chi-restraints excluded: chain U residue 153 VAL Chi-restraints excluded: chain U residue 160 VAL Chi-restraints excluded: chain X residue 137 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain X residue 188 VAL Chi-restraints excluded: chain X residue 189 VAL Chi-restraints excluded: chain X residue 258 ILE Chi-restraints excluded: chain X residue 307 SER Chi-restraints excluded: chain X residue 314 VAL Chi-restraints excluded: chain X residue 319 MET Chi-restraints excluded: chain R residue 12 PHE Chi-restraints excluded: chain R residue 44 HIS Chi-restraints excluded: chain R residue 93 LEU Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 182 TYR Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 218 ARG Chi-restraints excluded: chain j residue 30 VAL Chi-restraints excluded: chain j residue 54 THR Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain h residue 31 GLN Chi-restraints excluded: chain h residue 138 PHE Chi-restraints excluded: chain i residue 79 ILE Chi-restraints excluded: chain d residue 64 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain f residue 88 THR Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 170 LEU Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 309 LEU Chi-restraints excluded: chain g residue 12 PHE Chi-restraints excluded: chain g residue 51 VAL Chi-restraints excluded: chain g residue 65 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 188 VAL Chi-restraints excluded: chain g residue 287 GLU Chi-restraints excluded: chain g residue 307 SER Chi-restraints excluded: chain g residue 319 MET Chi-restraints excluded: chain g residue 352 ILE Chi-restraints excluded: chain e residue 12 PHE Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 93 LEU Chi-restraints excluded: chain e residue 146 PHE Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 345 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 604 optimal weight: 20.0000 chunk 811 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 702 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 762 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 783 optimal weight: 0.0170 chunk 96 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 overall best weight: 4.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN A 8 ASN D 73 ASN M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN N 8 ASN L 70 GLN K 46 GLN F 8 ASN I 57 ASN I 73 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN d 8 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.101099 restraints weight = 128744.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100342 restraints weight = 288007.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.101132 restraints weight = 249685.125| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 77418 Z= 0.276 Angle : 0.543 10.181 104268 Z= 0.293 Chirality : 0.044 0.178 12342 Planarity : 0.003 0.037 13056 Dihedral : 4.419 59.672 10262 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.54 % Allowed : 27.58 % Favored : 69.88 % 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 (0.08), residues: 9648 helix: 2.00 (0.10), residues: 2652 sheet: -0.49 (0.11), residues: 1956 loop : -1.59 (0.08), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP l 119 HIS 0.005 0.001 HIS W 250 PHE 0.021 0.001 PHE H 92 TYR 0.033 0.002 TYR Q 60 ARG 0.009 0.000 ARG G 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16894.24 seconds wall clock time: 293 minutes 57.54 seconds (17637.54 seconds total)