Starting phenix.real_space_refine on Sat Jan 25 05:09:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_42961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_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/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_42961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_42961.map" model { file = "/net/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_42961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v3z_42961/01_2025/8v3z_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): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 32.97, per 1000 atoms: 0.43 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: 13.66 Conformation dependent library (CDL) restraints added in 7.1 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: 7.74 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: 31.94 Time building geometry restraints manager: 16.16 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: 0.02 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: 2.220 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: 0.080 Extract box with map and model: 2.200 Check model and map are aligned: 0.440 Set scattering table: 0.530 Process input model: 130.240 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.810 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 20 poor density : 1033 time to evaluate : 8.827 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: 0.7382 time to fit residues: 1328.7211 Evaluate side-chains 737 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 729 time to evaluate : 6.942 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.132315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.111860 restraints weight = 127094.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112444 restraints weight = 298629.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111914 restraints weight = 175184.958| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 to be fit. rotamer outliers: 183 poor density : 798 time to evaluate : 6.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 68 SER cc_start: 0.7951 (t) cc_final: 0.7708 (p) REVERT: a 136 TYR cc_start: 0.8218 (p90) cc_final: 0.7886 (p90) REVERT: a 140 ASP cc_start: 0.8252 (t0) cc_final: 0.8029 (t0) REVERT: C 252 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7575 (m-30) REVERT: D 152 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.5955 (mp) REVERT: D 196 LYS cc_start: 0.7225 (tptm) cc_final: 0.6837 (mmtp) REVERT: B 46 LYS cc_start: 0.6101 (tmtt) cc_final: 0.5139 (tptt) REVERT: B 194 MET cc_start: 0.2610 (ttp) cc_final: 0.2375 (ttm) REVERT: n 23 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8875 (mp) REVERT: n 145 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8705 (pp) REVERT: Y 138 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.6728 (t80) REVERT: M 71 MET cc_start: 0.9108 (tpp) cc_final: 0.8829 (mmt) REVERT: S 13 LYS cc_start: 0.7924 (pttt) cc_final: 0.7686 (ptpt) REVERT: S 217 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8277 (mp) REVERT: V 152 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.5872 (mp) REVERT: V 196 LYS cc_start: 0.7173 (tptm) cc_final: 0.6680 (mmtp) REVERT: P 66 MET cc_start: 0.4466 (pmm) cc_final: 0.3150 (ttm) REVERT: P 105 LYS cc_start: 0.6197 (mmtt) cc_final: 0.5981 (mmmt) REVERT: P 149 GLU cc_start: 0.5921 (pm20) cc_final: 0.5195 (mm-30) REVERT: P 295 ASP cc_start: 0.5855 (t70) cc_final: 0.5554 (t70) REVERT: o 1 MET cc_start: 0.5352 (OUTLIER) cc_final: 0.5017 (mtp) REVERT: l 34 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8302 (mtm) REVERT: l 68 SER cc_start: 0.7958 (t) cc_final: 0.7751 (p) REVERT: T 30 MET cc_start: 0.7871 (ttm) cc_final: 0.7497 (ttm) REVERT: T 74 LYS cc_start: 0.8141 (ttpp) cc_final: 0.7831 (ttpp) REVERT: T 103 MET cc_start: 0.6423 (ttm) cc_final: 0.5789 (ttt) REVERT: W 87 GLN cc_start: 0.6941 (mp10) cc_final: 0.6541 (mm-40) REVERT: W 152 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6048 (mp) REVERT: W 196 LYS cc_start: 0.6844 (tptm) cc_final: 0.6371 (mmtm) REVERT: Q 295 ASP cc_start: 0.5698 (t70) cc_final: 0.5392 (t70) REVERT: K 68 SER cc_start: 0.7948 (t) cc_final: 0.7704 (p) REVERT: K 136 TYR cc_start: 0.8241 (p90) cc_final: 0.8029 (p90) REVERT: K 140 ASP cc_start: 0.8275 (t0) cc_final: 0.8050 (t0) REVERT: F 71 MET cc_start: 0.8952 (tpp) cc_final: 0.8604 (mmt) REVERT: H 152 LEU cc_start: 0.8527 (mt) cc_final: 0.8255 (tt) REVERT: H 252 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7577 (m-30) REVERT: I 152 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.5967 (mp) REVERT: I 196 LYS cc_start: 0.7223 (tptm) cc_final: 0.6793 (mmtp) REVERT: G 46 LYS cc_start: 0.6120 (tmtt) cc_final: 0.5154 (tptt) REVERT: G 211 ILE cc_start: 0.6328 (tp) cc_final: 0.6055 (tt) REVERT: p 23 ILE cc_start: 0.9136 (OUTLIER) cc_final: 0.8878 (mp) REVERT: p 145 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8666 (pp) REVERT: c 138 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.6686 (t80) REVERT: O 71 MET cc_start: 0.9139 (tpp) cc_final: 0.8880 (mmt) REVERT: U 13 LYS cc_start: 0.7930 (pttt) cc_final: 0.7685 (ptpt) REVERT: U 217 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (mp) REVERT: X 87 GLN cc_start: 0.6003 (mm-40) cc_final: 0.5414 (tp40) REVERT: X 152 LEU cc_start: 0.6793 (OUTLIER) cc_final: 0.5904 (mp) REVERT: X 196 LYS cc_start: 0.7155 (tptm) cc_final: 0.6688 (mmtp) REVERT: R 103 MET cc_start: 0.6570 (tpt) cc_final: 0.6258 (tpt) REVERT: R 149 GLU cc_start: 0.5600 (pm20) cc_final: 0.5258 (mm-30) REVERT: R 295 ASP cc_start: 0.5924 (t70) cc_final: 0.5627 (t70) REVERT: j 1 MET cc_start: 0.5435 (OUTLIER) cc_final: 0.5087 (mtp) REVERT: f 15 LEU cc_start: 0.7998 (tt) cc_final: 0.7760 (mt) REVERT: f 74 LYS cc_start: 0.8176 (ttpp) cc_final: 0.7826 (ttpp) REVERT: f 103 MET cc_start: 0.6405 (ttm) cc_final: 0.5816 (ttt) REVERT: f 217 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8251 (mm) REVERT: g 152 LEU cc_start: 0.6760 (OUTLIER) cc_final: 0.5992 (mp) REVERT: g 196 LYS cc_start: 0.6768 (tptm) cc_final: 0.6325 (mmtm) REVERT: g 352 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8116 (mt) REVERT: e 295 ASP cc_start: 0.5635 (t70) cc_final: 0.5320 (t70) outliers start: 183 outliers final: 71 residues processed: 946 average time/residue: 0.6729 time to fit residues: 1103.6789 Evaluate side-chains 785 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 693 time to evaluate : 6.857 ------------------------------------------------------------------------------- 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 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 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 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 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 U residue 217 ILE 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 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 786 optimal weight: 20.0000 chunk 182 optimal weight: 5.9990 chunk 869 optimal weight: 7.9990 chunk 695 optimal weight: 6.9990 chunk 810 optimal weight: 5.9990 chunk 939 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 641 optimal weight: 6.9990 chunk 519 optimal weight: 1.9990 chunk 637 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110297 restraints weight = 127132.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.108718 restraints weight = 304196.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.106010 restraints weight = 163052.446| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 77418 Z= 0.318 Angle : 0.566 8.558 104268 Z= 0.309 Chirality : 0.045 0.174 12342 Planarity : 0.003 0.040 13056 Dihedral : 4.607 40.385 10262 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.86 % Allowed : 22.53 % Favored : 73.61 % 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: -0.32 (0.08), residues: 9648 helix: 2.00 (0.10), residues: 2652 sheet: -0.36 (0.11), residues: 2070 loop : -1.45 (0.08), residues: 4926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 119 HIS 0.006 0.001 HIS N 66 PHE 0.025 0.002 PHE I 12 TYR 0.020 0.002 TYR O 99 ARG 0.007 0.001 ARG G 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 1017 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 328 poor density : 689 time to evaluate : 7.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 138 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7326 (t80) REVERT: a 17 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (tp) REVERT: a 68 SER cc_start: 0.7984 (t) cc_final: 0.7681 (p) REVERT: a 136 TYR cc_start: 0.8350 (p90) cc_final: 0.8002 (p90) REVERT: a 140 ASP cc_start: 0.8333 (t0) cc_final: 0.8110 (t0) REVERT: C 252 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7836 (t0) REVERT: D 196 LYS cc_start: 0.7133 (tptm) cc_final: 0.6701 (mmtp) REVERT: B 295 ASP cc_start: 0.6349 (t70) cc_final: 0.5940 (t70) REVERT: n 23 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8937 (mp) REVERT: n 98 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8337 (mt) REVERT: n 145 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8674 (pp) REVERT: Y 138 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.6784 (t80) REVERT: M 71 MET cc_start: 0.9134 (tpp) cc_final: 0.8928 (mmt) REVERT: S 119 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8441 (mt) REVERT: S 217 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8377 (mp) REVERT: S 265 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8714 (t) REVERT: V 196 LYS cc_start: 0.7171 (tptm) cc_final: 0.6544 (mmtp) REVERT: V 352 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.7969 (mt) REVERT: P 66 MET cc_start: 0.4977 (pmm) cc_final: 0.3616 (ttm) REVERT: P 182 TYR cc_start: 0.6007 (OUTLIER) cc_final: 0.5177 (t80) REVERT: P 218 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5809 (mtt-85) REVERT: P 295 ASP cc_start: 0.6252 (t70) cc_final: 0.6020 (t70) REVERT: o 1 MET cc_start: 0.5742 (OUTLIER) cc_final: 0.5258 (mtp) REVERT: Z 77 GLU cc_start: 0.7115 (pm20) cc_final: 0.6804 (mp0) REVERT: Z 138 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8182 (t80) REVERT: l 68 SER cc_start: 0.8033 (t) cc_final: 0.7754 (p) REVERT: l 136 TYR cc_start: 0.8321 (p90) cc_final: 0.7931 (p90) REVERT: T 103 MET cc_start: 0.6646 (ttm) cc_final: 0.6144 (ttt) REVERT: W 97 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: W 196 LYS cc_start: 0.6757 (tptm) cc_final: 0.6311 (mmtm) REVERT: Q 295 ASP cc_start: 0.6383 (t70) cc_final: 0.6003 (t70) REVERT: J 138 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.7328 (t80) REVERT: K 17 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8926 (tp) REVERT: K 68 SER cc_start: 0.7975 (t) cc_final: 0.7681 (p) REVERT: K 136 TYR cc_start: 0.8445 (p90) cc_final: 0.8095 (p90) REVERT: K 140 ASP cc_start: 0.8357 (t0) cc_final: 0.8135 (t0) REVERT: H 252 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7861 (t0) REVERT: I 196 LYS cc_start: 0.7071 (tptm) cc_final: 0.6649 (mmtp) REVERT: G 295 ASP cc_start: 0.6340 (t70) cc_final: 0.5930 (t70) REVERT: p 23 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8922 (mp) REVERT: p 145 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8658 (pp) REVERT: c 138 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.6782 (t80) REVERT: m 34 MET cc_start: 0.8723 (mtm) cc_final: 0.8491 (mtm) REVERT: U 119 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8473 (mt) REVERT: U 152 LEU cc_start: 0.8430 (mt) cc_final: 0.8074 (mt) REVERT: U 217 ILE cc_start: 0.8627 (OUTLIER) cc_final: 0.8381 (mp) REVERT: X 196 LYS cc_start: 0.7254 (tptm) cc_final: 0.6640 (mmtp) REVERT: R 66 MET cc_start: 0.4650 (pmm) cc_final: 0.3128 (ttm) REVERT: R 103 MET cc_start: 0.6522 (tpt) cc_final: 0.6235 (tpt) REVERT: R 150 ASP cc_start: 0.4285 (t0) cc_final: 0.4076 (t70) REVERT: R 295 ASP cc_start: 0.6329 (t70) cc_final: 0.6091 (t70) REVERT: j 1 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4882 (mtp) REVERT: h 54 MET cc_start: 0.9283 (mmt) cc_final: 0.9018 (mmt) REVERT: h 77 GLU cc_start: 0.7132 (pm20) cc_final: 0.6819 (mp0) REVERT: h 138 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8216 (t80) REVERT: f 15 LEU cc_start: 0.8181 (tt) cc_final: 0.7920 (mt) REVERT: f 103 MET cc_start: 0.6602 (ttm) cc_final: 0.6119 (ttm) REVERT: f 217 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8375 (mm) REVERT: g 12 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7960 (p90) REVERT: g 40 LEU cc_start: 0.7625 (tp) cc_final: 0.7397 (tp) REVERT: g 97 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: g 196 LYS cc_start: 0.6695 (tptm) cc_final: 0.6266 (mmtm) REVERT: g 352 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8226 (mt) REVERT: e 295 ASP cc_start: 0.6206 (t70) cc_final: 0.5819 (t70) outliers start: 328 outliers final: 187 residues processed: 987 average time/residue: 0.6547 time to fit residues: 1132.0803 Evaluate side-chains 854 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 637 time to evaluate : 6.943 ------------------------------------------------------------------------------- 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 E residue 141 ILE Chi-restraints excluded: chain a residue 17 LEU 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 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 153 VAL 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 287 GLU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 311 SER 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 160 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 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 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 248 ILE Chi-restraints excluded: chain S residue 252 ASP Chi-restraints excluded: chain S residue 265 VAL Chi-restraints excluded: chain V residue 12 PHE Chi-restraints excluded: chain V residue 40 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 150 ASP 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 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 179 SER Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 218 ARG 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 133 VAL Chi-restraints excluded: chain o residue 144 ASN 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 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 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 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 189 VAL Chi-restraints excluded: chain W residue 195 THR Chi-restraints excluded: chain W residue 291 LEU 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 Q residue 354 ILE 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 J residue 141 ILE Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 50 ASP 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 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 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 153 VAL 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 287 GLU 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 145 LEU Chi-restraints excluded: chain c residue 138 PHE Chi-restraints excluded: chain m residue 79 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 160 VAL Chi-restraints excluded: chain U residue 217 ILE Chi-restraints excluded: chain U residue 248 ILE Chi-restraints excluded: chain U residue 252 ASP Chi-restraints excluded: chain X residue 12 PHE Chi-restraints excluded: chain X residue 40 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 150 ASP 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 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 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 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 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 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 189 VAL Chi-restraints excluded: chain g residue 195 THR 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 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 288 optimal weight: 40.0000 chunk 789 optimal weight: 6.9990 chunk 810 optimal weight: 5.9990 chunk 867 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 378 optimal weight: 9.9990 chunk 869 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 564 optimal weight: 9.9990 chunk 620 optimal weight: 8.9990 chunk 720 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 70 GLN a 46 GLN D 73 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN W 73 ASN L 70 GLN K 46 GLN I 73 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN g 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.123858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101708 restraints weight = 128826.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.100796 restraints weight = 268141.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101746 restraints weight = 227357.717| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 77418 Z= 0.299 Angle : 0.543 8.528 104268 Z= 0.297 Chirality : 0.045 0.175 12342 Planarity : 0.003 0.038 13056 Dihedral : 4.621 45.082 10262 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.28 % Allowed : 23.15 % Favored : 72.56 % 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: -0.45 (0.08), residues: 9648 helix: 1.92 (0.10), residues: 2652 sheet: -0.45 (0.11), residues: 1974 loop : -1.53 (0.08), residues: 5022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 119 HIS 0.006 0.001 HIS P 44 PHE 0.022 0.001 PHE I 12 TYR 0.019 0.002 TYR O 99 ARG 0.006 0.000 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 1052 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 364 poor density : 688 time to evaluate : 6.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1 MET cc_start: 0.5599 (OUTLIER) cc_final: 0.5137 (mtp) REVERT: E 138 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7373 (t80) REVERT: a 68 SER cc_start: 0.7885 (t) cc_final: 0.7614 (p) REVERT: a 136 TYR cc_start: 0.8382 (p90) cc_final: 0.8056 (p90) REVERT: a 140 ASP cc_start: 0.8429 (t0) cc_final: 0.8222 (t0) REVERT: C 252 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7831 (t0) REVERT: D 196 LYS cc_start: 0.7241 (tptm) cc_final: 0.6833 (mmtp) REVERT: B 218 ARG cc_start: 0.6794 (OUTLIER) cc_final: 0.6542 (mtt-85) REVERT: B 295 ASP cc_start: 0.6489 (t70) cc_final: 0.6006 (t70) REVERT: n 23 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8909 (mp) REVERT: n 98 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8343 (mt) REVERT: n 145 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8618 (pp) REVERT: Y 138 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.6691 (t80) REVERT: k 75 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8951 (pt) REVERT: S 119 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8430 (mt) REVERT: S 217 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8355 (mp) REVERT: S 265 VAL cc_start: 0.9056 (OUTLIER) cc_final: 0.8703 (t) REVERT: V 152 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.6119 (mp) REVERT: V 196 LYS cc_start: 0.7366 (tptm) cc_final: 0.6704 (mmtp) REVERT: V 352 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.7927 (mt) REVERT: P 66 MET cc_start: 0.4887 (pmm) cc_final: 0.3702 (ttm) REVERT: P 182 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.5217 (t80) REVERT: P 218 ARG cc_start: 0.6136 (OUTLIER) cc_final: 0.5858 (mtt-85) REVERT: o 1 MET cc_start: 0.5736 (OUTLIER) cc_final: 0.5271 (mtp) REVERT: Z 77 GLU cc_start: 0.6932 (pm20) cc_final: 0.6727 (mp0) REVERT: l 68 SER cc_start: 0.7972 (t) cc_final: 0.7721 (p) REVERT: l 136 TYR cc_start: 0.8370 (p90) cc_final: 0.8024 (p90) REVERT: T 103 MET cc_start: 0.6701 (ttm) cc_final: 0.6291 (ttm) REVERT: W 97 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: W 196 LYS cc_start: 0.6852 (tptm) cc_final: 0.6444 (mmtm) REVERT: Q 218 ARG cc_start: 0.6542 (OUTLIER) cc_final: 0.6222 (mtt-85) REVERT: Q 295 ASP cc_start: 0.6329 (t70) cc_final: 0.5953 (t70) REVERT: J 138 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7343 (t80) REVERT: K 68 SER cc_start: 0.7921 (t) cc_final: 0.7622 (p) REVERT: K 136 TYR cc_start: 0.8438 (p90) cc_final: 0.8125 (p90) REVERT: K 140 ASP cc_start: 0.8448 (t0) cc_final: 0.8237 (t0) REVERT: H 252 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7830 (t0) REVERT: I 152 LEU cc_start: 0.7030 (OUTLIER) cc_final: 0.5816 (mp) REVERT: I 196 LYS cc_start: 0.7159 (tptm) cc_final: 0.6820 (mmtp) REVERT: G 295 ASP cc_start: 0.6448 (t70) cc_final: 0.5927 (t70) REVERT: p 1 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.5473 (mtp) REVERT: p 23 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8910 (mp) REVERT: p 98 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8359 (mt) REVERT: p 145 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8606 (pp) REVERT: c 138 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.6821 (t80) REVERT: m 34 MET cc_start: 0.8768 (mtm) cc_final: 0.8513 (mtm) REVERT: m 75 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.8959 (pt) REVERT: U 119 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8434 (mt) REVERT: U 152 LEU cc_start: 0.8430 (mt) cc_final: 0.8144 (mt) REVERT: U 217 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8353 (mp) REVERT: X 152 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.5974 (mp) REVERT: X 196 LYS cc_start: 0.7364 (tptm) cc_final: 0.6660 (mmtp) REVERT: R 166 ARG cc_start: 0.6231 (tpt170) cc_final: 0.5939 (tpt170) REVERT: R 213 GLU cc_start: 0.6049 (OUTLIER) cc_final: 0.5188 (tt0) REVERT: j 1 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5192 (mtp) REVERT: h 54 MET cc_start: 0.9257 (mmt) cc_final: 0.8978 (mmt) REVERT: h 77 GLU cc_start: 0.6981 (pm20) cc_final: 0.6766 (mp0) REVERT: i 136 TYR cc_start: 0.8374 (p90) cc_final: 0.8055 (p90) REVERT: f 15 LEU cc_start: 0.8231 (tt) cc_final: 0.7925 (mt) REVERT: f 103 MET cc_start: 0.6744 (ttm) cc_final: 0.6435 (ttm) REVERT: g 97 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6568 (mt-10) REVERT: g 196 LYS cc_start: 0.6838 (tptm) cc_final: 0.6437 (mmtm) REVERT: g 352 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8179 (mt) REVERT: e 218 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.6190 (mtt-85) REVERT: e 295 ASP cc_start: 0.6301 (t70) cc_final: 0.5925 (t70) outliers start: 364 outliers final: 238 residues processed: 1013 average time/residue: 0.6363 time to fit residues: 1137.6300 Evaluate side-chains 910 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 274 poor density : 636 time to evaluate : 6.852 ------------------------------------------------------------------------------- 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 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 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 15 LEU 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 150 ASP 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 208 LEU 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 53 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 ARG 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 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 k residue 50 ASP Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain S residue 49 ILE 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 256 VAL Chi-restraints excluded: chain S residue 265 VAL 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 62 ASN Chi-restraints excluded: chain V residue 65 LEU 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 232 GLU 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 53 LEU Chi-restraints excluded: chain P residue 88 THR 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 218 ARG Chi-restraints excluded: chain P residue 249 ILE Chi-restraints excluded: chain o residue 1 MET 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 Z residue 31 GLN 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 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 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 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 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 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 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 119 ILE 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 309 LEU Chi-restraints excluded: chain H residue 323 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 152 LEU Chi-restraints excluded: chain I residue 153 VAL 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 208 LEU 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 160 VAL Chi-restraints excluded: chain G residue 186 SER 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 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 50 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain U residue 49 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 217 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 256 VAL 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 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 232 GLU Chi-restraints excluded: chain X residue 248 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 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 249 ILE Chi-restraints excluded: chain j residue 1 MET 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 h residue 31 GLN 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 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 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 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 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 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 345 MET 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 573 optimal weight: 30.0000 chunk 225 optimal weight: 6.9990 chunk 291 optimal weight: 8.9990 chunk 921 optimal weight: 20.0000 chunk 380 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 463 optimal weight: 9.9990 chunk 769 optimal weight: 8.9990 chunk 246 optimal weight: 6.9990 chunk 334 optimal weight: 10.0000 chunk 506 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 A 8 ASN C 271 ASN D 73 ASN M 8 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN N 8 ASN W 73 ASN L 70 GLN J 72 HIS K 46 GLN F 8 ASN I 73 ASN O 8 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.099672 restraints weight = 129267.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.095250 restraints weight = 126245.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095447 restraints weight = 201067.608| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2001 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= 0.403 Angle : 0.604 7.673 104268 Z= 0.329 Chirality : 0.046 0.205 12342 Planarity : 0.004 0.048 13056 Dihedral : 4.922 49.862 10262 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.08 % Allowed : 23.23 % Favored : 71.68 % 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: -0.76 (0.08), residues: 9648 helix: 1.64 (0.10), residues: 2646 sheet: -0.79 (0.11), residues: 2016 loop : -1.62 (0.08), residues: 4986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 119 HIS 0.006 0.002 HIS W 250 PHE 0.028 0.002 PHE I 12 TYR 0.021 0.002 TYR O 99 ARG 0.006 0.001 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 1067 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 432 poor density : 635 time to evaluate : 6.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 1 MET cc_start: 0.5701 (OUTLIER) cc_final: 0.5196 (mtp) REVERT: b 145 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8786 (pp) REVERT: E 138 PHE cc_start: 0.8336 (OUTLIER) cc_final: 0.7327 (t80) REVERT: a 68 SER cc_start: 0.8009 (t) cc_final: 0.7698 (p) REVERT: a 75 ILE cc_start: 0.9268 (OUTLIER) cc_final: 0.8946 (pt) REVERT: a 136 TYR cc_start: 0.8370 (p90) cc_final: 0.8113 (p90) REVERT: C 252 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7905 (t0) REVERT: D 152 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.5645 (mp) REVERT: D 196 LYS cc_start: 0.7104 (tptm) cc_final: 0.6571 (tppt) REVERT: B 108 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: B 182 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5755 (t80) REVERT: B 295 ASP cc_start: 0.6642 (t70) cc_final: 0.6184 (t70) REVERT: n 23 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8884 (mp) REVERT: n 98 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8346 (mt) REVERT: n 145 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8578 (pp) REVERT: Y 138 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.6733 (t80) REVERT: k 75 ILE cc_start: 0.9243 (OUTLIER) cc_final: 0.8946 (pt) REVERT: S 119 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8384 (mt) REVERT: S 217 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8339 (mp) REVERT: S 258 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7171 (tt) REVERT: V 152 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.5457 (mp) REVERT: V 196 LYS cc_start: 0.7153 (tptm) cc_final: 0.6422 (mmtp) REVERT: V 202 ARG cc_start: 0.7730 (ttt90) cc_final: 0.7465 (mtt90) REVERT: V 352 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.7962 (mt) REVERT: P 66 MET cc_start: 0.5144 (pmm) cc_final: 0.3819 (ttm) REVERT: P 108 GLU cc_start: 0.6543 (OUTLIER) cc_final: 0.6071 (tm-30) REVERT: P 149 GLU cc_start: 0.5767 (OUTLIER) cc_final: 0.5376 (mm-30) REVERT: P 182 TYR cc_start: 0.6051 (OUTLIER) cc_final: 0.5448 (t80) REVERT: P 218 ARG cc_start: 0.5908 (OUTLIER) cc_final: 0.5552 (mtt-85) REVERT: Z 138 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8141 (t80) REVERT: l 68 SER cc_start: 0.8110 (t) cc_final: 0.7822 (p) REVERT: l 75 ILE cc_start: 0.9250 (OUTLIER) cc_final: 0.8866 (pt) REVERT: T 103 MET cc_start: 0.7008 (ttm) cc_final: 0.6669 (ttm) REVERT: W 87 GLN cc_start: 0.7547 (mp10) cc_final: 0.6381 (tp-100) REVERT: W 97 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6929 (mt-10) REVERT: W 150 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: W 196 LYS cc_start: 0.6650 (tptm) cc_final: 0.6209 (mmtm) REVERT: Q 149 GLU cc_start: 0.6043 (OUTLIER) cc_final: 0.5220 (mm-30) REVERT: Q 182 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.5546 (t80) REVERT: Q 218 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.5835 (mtt-85) REVERT: Q 295 ASP cc_start: 0.6730 (t70) cc_final: 0.6074 (t70) REVERT: L 1 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.4786 (mtp) REVERT: L 145 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8779 (pp) REVERT: J 138 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7328 (t80) REVERT: K 17 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8949 (tp) REVERT: K 68 SER cc_start: 0.8005 (t) cc_final: 0.7698 (p) REVERT: K 75 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8944 (pt) REVERT: K 136 TYR cc_start: 0.8405 (p90) cc_final: 0.8131 (p90) REVERT: F 71 MET cc_start: 0.9049 (tpp) cc_final: 0.8830 (mmt) REVERT: H 152 LEU cc_start: 0.8536 (mt) cc_final: 0.8302 (mt) REVERT: H 217 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8271 (mm) REVERT: H 252 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7878 (t0) REVERT: I 196 LYS cc_start: 0.6942 (tptm) cc_final: 0.6575 (mmtp) REVERT: G 36 LYS cc_start: 0.7406 (pttt) cc_final: 0.5884 (mptt) REVERT: G 108 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: G 182 TYR cc_start: 0.5875 (OUTLIER) cc_final: 0.5575 (t80) REVERT: G 211 ILE cc_start: 0.6619 (tp) cc_final: 0.6392 (tt) REVERT: p 23 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8873 (mp) REVERT: p 98 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8368 (mt) REVERT: p 145 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8568 (pp) REVERT: c 138 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.6774 (t80) REVERT: m 75 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8948 (pt) REVERT: U 119 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8372 (mt) REVERT: U 152 LEU cc_start: 0.8465 (mt) cc_final: 0.8107 (mt) REVERT: U 217 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8344 (mp) REVERT: U 258 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.7193 (tt) REVERT: X 152 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.5424 (mp) REVERT: X 196 LYS cc_start: 0.7120 (tptm) cc_final: 0.6388 (mmtp) REVERT: R 149 GLU cc_start: 0.5563 (OUTLIER) cc_final: 0.5183 (mm-30) REVERT: R 182 TYR cc_start: 0.5983 (OUTLIER) cc_final: 0.5623 (t80) REVERT: R 218 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5658 (mtt180) REVERT: h 138 PHE cc_start: 0.8518 (OUTLIER) cc_final: 0.8216 (t80) REVERT: i 75 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8857 (pt) REVERT: f 103 MET cc_start: 0.6987 (ttm) cc_final: 0.6714 (ttm) REVERT: g 97 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6892 (mt-10) REVERT: g 150 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: g 196 LYS cc_start: 0.6632 (tptm) cc_final: 0.6298 (mmtm) REVERT: g 352 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8117 (mt) REVERT: e 149 GLU cc_start: 0.6053 (OUTLIER) cc_final: 0.5206 (mm-30) REVERT: e 218 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5770 (mtt-85) REVERT: e 295 ASP cc_start: 0.6623 (t70) cc_final: 0.6026 (t70) outliers start: 432 outliers final: 301 residues processed: 1030 average time/residue: 0.6411 time to fit residues: 1170.1955 Evaluate side-chains 964 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 358 poor density : 606 time to evaluate : 6.840 ------------------------------------------------------------------------------- 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 123 ASN 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 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 15 LEU 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 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 153 VAL 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 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 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 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 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 75 ILE Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain S residue 49 ILE 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 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 62 ASN 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 232 GLU Chi-restraints excluded: chain V residue 248 ILE Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 277 VAL 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 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 218 ARG Chi-restraints excluded: chain P residue 243 VAL 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 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 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 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 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 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 258 ILE Chi-restraints excluded: chain W residue 277 VAL 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 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 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 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 123 ASN 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 138 PHE Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain K residue 17 LEU 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 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 211 ILE 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 256 VAL 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 I residue 12 PHE Chi-restraints excluded: chain I residue 150 ASP Chi-restraints excluded: chain I residue 153 VAL 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 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 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 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 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 81 ARG Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 137 ASP Chi-restraints excluded: chain O residue 64 LEU Chi-restraints excluded: chain U residue 49 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 211 ILE Chi-restraints excluded: chain U residue 217 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 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 232 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 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 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 133 VAL Chi-restraints excluded: chain j residue 144 ASN 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 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 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 277 VAL 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 87 GLN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 149 GLU Chi-restraints excluded: chain e residue 177 SER 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 249 ILE 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 21 optimal weight: 0.0980 chunk 254 optimal weight: 0.9990 chunk 247 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 952 optimal weight: 5.9990 chunk 432 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 748 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 664 optimal weight: 7.9990 chunk 158 optimal weight: 10.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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 P 68 ASN 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 d 8 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101299 restraints weight = 128241.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.100276 restraints weight = 266945.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.101116 restraints weight = 241710.130| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1992 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= 0.202 Angle : 0.497 9.619 104268 Z= 0.272 Chirality : 0.043 0.260 12342 Planarity : 0.003 0.037 13056 Dihedral : 4.485 52.217 10262 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 4.10 % Allowed : 24.71 % Favored : 71.20 % 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: -0.51 (0.08), residues: 9648 helix: 1.92 (0.10), residues: 2724 sheet: -0.55 (0.11), residues: 1956 loop : -1.62 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 119 HIS 0.003 0.001 HIS W 250 PHE 0.016 0.001 PHE I 12 TYR 0.017 0.001 TYR I 60 ARG 0.005 0.000 ARG B 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 1033 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 348 poor density : 685 time to evaluate : 7.155 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: 0.8719 (OUTLIER) cc_final: 0.8513 (mt) REVERT: b 116 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9052 (tp) REVERT: E 138 PHE cc_start: 0.8299 (OUTLIER) cc_final: 0.7348 (t80) REVERT: a 68 SER cc_start: 0.7905 (t) cc_final: 0.7625 (p) REVERT: a 136 TYR cc_start: 0.8338 (p90) cc_final: 0.8081 (p90) REVERT: C 252 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7504 (m-30) REVERT: D 152 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.5765 (mp) REVERT: D 196 LYS cc_start: 0.7152 (tptm) cc_final: 0.6749 (mmtp) REVERT: B 182 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5271 (t80) REVERT: B 218 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6829 (mtt-85) REVERT: n 23 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8788 (mp) REVERT: n 98 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8315 (mt) REVERT: n 145 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8603 (pp) REVERT: Y 138 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.6703 (t80) REVERT: M 35 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8135 (mm-30) REVERT: S 119 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8414 (mt) REVERT: S 217 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8319 (mp) REVERT: V 152 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.5850 (mp) REVERT: V 196 LYS cc_start: 0.7394 (tptm) cc_final: 0.6644 (mmtp) REVERT: V 202 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7244 (mtt90) REVERT: P 28 ILE cc_start: 0.7845 (OUTLIER) cc_final: 0.7490 (mm) REVERT: P 66 MET cc_start: 0.4808 (pmm) cc_final: 0.3883 (ttm) REVERT: P 182 TYR cc_start: 0.5836 (OUTLIER) cc_final: 0.5285 (t80) REVERT: P 218 ARG cc_start: 0.6076 (OUTLIER) cc_final: 0.5836 (mtt-85) REVERT: Z 138 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8242 (t80) REVERT: l 68 SER cc_start: 0.8031 (t) cc_final: 0.7826 (p) REVERT: T 103 MET cc_start: 0.6473 (ttm) cc_final: 0.6014 (ttt) REVERT: W 97 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6637 (mt-10) REVERT: W 196 LYS cc_start: 0.6740 (tptm) cc_final: 0.6470 (mmtm) REVERT: Q 44 HIS cc_start: 0.6193 (OUTLIER) cc_final: 0.5881 (m90) REVERT: Q 149 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5560 (mm-30) REVERT: Q 218 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6119 (mtt-85) REVERT: L 98 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8506 (mt) REVERT: J 138 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7361 (t80) REVERT: K 68 SER cc_start: 0.7825 (t) cc_final: 0.7542 (p) REVERT: K 136 TYR cc_start: 0.8411 (p90) cc_final: 0.8161 (p90) REVERT: F 71 MET cc_start: 0.9014 (tpp) cc_final: 0.8796 (mmt) REVERT: H 252 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: I 152 LEU cc_start: 0.6805 (OUTLIER) cc_final: 0.5762 (mp) REVERT: I 196 LYS cc_start: 0.7077 (tptm) cc_final: 0.6779 (mmtp) REVERT: G 182 TYR cc_start: 0.5833 (OUTLIER) cc_final: 0.5313 (t80) REVERT: G 218 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.6763 (mtt-85) REVERT: p 1 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.5097 (mtp) REVERT: p 23 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8787 (mp) REVERT: p 98 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8377 (mt) REVERT: p 145 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8567 (pp) REVERT: c 138 PHE cc_start: 0.8383 (OUTLIER) cc_final: 0.6594 (t80) REVERT: U 119 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8414 (mt) REVERT: U 217 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8289 (mp) REVERT: U 252 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7818 (t0) REVERT: X 152 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.5840 (mp) REVERT: X 196 LYS cc_start: 0.7419 (tptm) cc_final: 0.6625 (mmtp) REVERT: R 66 MET cc_start: 0.4685 (pmm) cc_final: 0.3754 (ttm) REVERT: R 108 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5989 (tm-30) REVERT: R 182 TYR cc_start: 0.5762 (OUTLIER) cc_final: 0.5277 (t80) REVERT: R 218 ARG cc_start: 0.6394 (OUTLIER) cc_final: 0.5879 (mtt180) REVERT: h 138 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8250 (t80) REVERT: g 65 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7005 (mm) REVERT: g 196 LYS cc_start: 0.6741 (tptm) cc_final: 0.6468 (mmtm) REVERT: g 352 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8033 (mt) REVERT: e 182 TYR cc_start: 0.5936 (OUTLIER) cc_final: 0.5438 (t80) REVERT: e 218 ARG cc_start: 0.6505 (OUTLIER) cc_final: 0.6035 (mtt180) outliers start: 348 outliers final: 229 residues processed: 999 average time/residue: 0.6484 time to fit residues: 1143.1163 Evaluate side-chains 913 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 275 poor density : 638 time to evaluate : 6.904 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain b residue 66 LEU 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 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 128 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 139 LEU 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 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 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 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 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 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 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 345 MET 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 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 138 PHE Chi-restraints excluded: chain k residue 50 ASP Chi-restraints excluded: chain k residue 91 SER 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 217 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 248 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 62 ASN Chi-restraints excluded: chain V residue 65 LEU 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 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 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 182 TYR Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain P residue 345 MET 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 144 ASN 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 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 160 VAL Chi-restraints excluded: chain T residue 219 ILE Chi-restraints excluded: chain T residue 252 ASP Chi-restraints excluded: chain W residue 12 PHE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 97 GLU Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 185 LEU 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 44 HIS 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 186 SER Chi-restraints excluded: chain Q residue 218 ARG Chi-restraints excluded: chain Q residue 352 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 98 LEU 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 128 GLU Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 139 LEU 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 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 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 309 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 165 SER 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 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 182 TYR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 218 ARG 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 98 LEU Chi-restraints excluded: chain p residue 143 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 79 ILE Chi-restraints excluded: chain m residue 91 SER 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 160 VAL Chi-restraints excluded: chain U residue 217 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 152 LEU Chi-restraints excluded: chain X residue 153 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 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 160 VAL Chi-restraints excluded: chain R residue 179 SER Chi-restraints excluded: chain R residue 182 TYR 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 144 ASN 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 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 219 ILE Chi-restraints excluded: chain f residue 252 ASP Chi-restraints excluded: chain f residue 256 VAL 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 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 146 PHE Chi-restraints excluded: chain e residue 177 SER Chi-restraints excluded: chain e residue 182 TYR Chi-restraints excluded: chain e residue 218 ARG 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 185 optimal weight: 8.9990 chunk 559 optimal weight: 4.9990 chunk 826 optimal weight: 5.9990 chunk 645 optimal weight: 10.0000 chunk 859 optimal weight: 7.9990 chunk 869 optimal weight: 1.9990 chunk 462 optimal weight: 20.0000 chunk 510 optimal weight: 10.0000 chunk 420 optimal weight: 6.9990 chunk 596 optimal weight: 9.9990 chunk 900 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 B 140 HIS ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN L 70 GLN K 46 GLN I 73 ASN G 140 HIS ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN d 8 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.100007 restraints weight = 128883.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099149 restraints weight = 282749.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099726 restraints weight = 247650.557| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 77418 Z= 0.323 Angle : 0.556 9.133 104268 Z= 0.303 Chirality : 0.045 0.314 12342 Planarity : 0.003 0.038 13056 Dihedral : 4.701 54.579 10262 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.83 % Allowed : 24.51 % Favored : 70.67 % 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: -0.68 (0.08), residues: 9648 helix: 1.77 (0.10), residues: 2652 sheet: -0.64 (0.11), residues: 1956 loop : -1.67 (0.08), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 119 HIS 0.005 0.001 HIS W 250 PHE 0.023 0.002 PHE I 12 TYR 0.019 0.002 TYR O 99 ARG 0.006 0.000 ARG R 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 1037 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 410 poor density : 627 time to evaluate : 7.307 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: 0.8732 (OUTLIER) cc_final: 0.8469 (mt) REVERT: E 138 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7375 (t80) REVERT: a 68 SER cc_start: 0.7962 (t) cc_final: 0.7661 (p) REVERT: a 136 TYR cc_start: 0.8371 (p90) cc_final: 0.8109 (p90) REVERT: C 252 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7814 (t0) REVERT: D 152 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.5953 (mp) REVERT: D 196 LYS cc_start: 0.7132 (tptm) cc_final: 0.6775 (mmtp) REVERT: B 108 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.6291 (tm-30) REVERT: B 182 TYR cc_start: 0.6175 (OUTLIER) cc_final: 0.5355 (t80) REVERT: B 218 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6856 (mtt-85) REVERT: n 23 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8810 (mp) REVERT: n 98 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8374 (mt) REVERT: n 145 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8545 (pp) REVERT: Y 138 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.6814 (t80) REVERT: k 75 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8936 (pt) REVERT: M 35 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8157 (mm-30) REVERT: S 119 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8415 (mt) REVERT: S 258 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7079 (tt) REVERT: V 152 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.5859 (mp) REVERT: V 196 LYS cc_start: 0.7417 (tptm) cc_final: 0.6634 (mmtp) REVERT: V 202 ARG cc_start: 0.7442 (ttt90) cc_final: 0.7178 (ttt90) REVERT: V 352 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.7985 (mt) REVERT: P 28 ILE cc_start: 0.7807 (OUTLIER) cc_final: 0.7467 (mm) REVERT: P 66 MET cc_start: 0.4836 (pmm) cc_final: 0.3841 (ttm) REVERT: P 103 MET cc_start: 0.7373 (tpt) cc_final: 0.7015 (tpt) REVERT: P 182 TYR cc_start: 0.5841 (OUTLIER) cc_final: 0.5275 (t80) REVERT: P 218 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5792 (mtt-85) REVERT: Z 138 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8204 (t80) REVERT: l 68 SER cc_start: 0.8083 (t) cc_final: 0.7854 (p) REVERT: T 103 MET cc_start: 0.6641 (ttm) cc_final: 0.6325 (ttm) REVERT: W 87 GLN cc_start: 0.7175 (mp10) cc_final: 0.6271 (tp-100) REVERT: W 97 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6740 (mt-10) REVERT: W 150 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.7097 (m-30) REVERT: W 196 LYS cc_start: 0.6804 (tptm) cc_final: 0.6514 (mmtm) REVERT: Q 28 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7348 (mm) REVERT: Q 44 HIS cc_start: 0.6255 (OUTLIER) cc_final: 0.5846 (m90) REVERT: Q 108 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.6587 (tm-30) REVERT: Q 149 GLU cc_start: 0.6092 (OUTLIER) cc_final: 0.5599 (mm-30) REVERT: Q 182 TYR cc_start: 0.5933 (OUTLIER) cc_final: 0.5398 (t80) REVERT: Q 218 ARG cc_start: 0.6455 (OUTLIER) cc_final: 0.6011 (mtt-85) REVERT: Q 295 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5573 (t70) REVERT: L 98 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8490 (mt) REVERT: J 138 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7327 (t80) REVERT: K 68 SER cc_start: 0.7956 (t) cc_final: 0.7649 (p) REVERT: K 136 TYR cc_start: 0.8427 (p90) cc_final: 0.8154 (p90) REVERT: F 71 MET cc_start: 0.9020 (tpp) cc_final: 0.8798 (mmt) REVERT: H 60 TYR cc_start: 0.8152 (m-10) cc_final: 0.7832 (m-10) REVERT: H 252 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7812 (t0) REVERT: I 152 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.5992 (mp) REVERT: I 196 LYS cc_start: 0.7108 (tptm) cc_final: 0.6773 (mmtp) REVERT: G 108 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6259 (tm-30) REVERT: G 182 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.5331 (t80) REVERT: G 218 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6776 (mtt-85) REVERT: p 1 MET cc_start: 0.5554 (OUTLIER) cc_final: 0.5077 (mtp) REVERT: p 23 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8804 (mp) REVERT: p 98 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8373 (mt) REVERT: p 145 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8531 (pp) REVERT: c 138 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.6744 (t80) REVERT: O 35 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: U 119 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8423 (mt) REVERT: U 217 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8365 (mm) REVERT: U 258 ILE cc_start: 0.7405 (OUTLIER) cc_final: 0.7091 (tt) REVERT: X 152 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.5849 (mp) REVERT: X 196 LYS cc_start: 0.7408 (tptm) cc_final: 0.6633 (mmtp) REVERT: R 66 MET cc_start: 0.4403 (pmm) cc_final: 0.3603 (ttm) REVERT: R 108 GLU cc_start: 0.6418 (OUTLIER) cc_final: 0.6029 (tm-30) REVERT: R 182 TYR cc_start: 0.5989 (OUTLIER) cc_final: 0.5427 (t80) REVERT: R 218 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5878 (mtt180) REVERT: h 138 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8182 (t80) REVERT: g 97 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6640 (mt-10) REVERT: g 196 LYS cc_start: 0.6804 (tptm) cc_final: 0.6512 (mmtm) REVERT: g 352 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8179 (mt) REVERT: e 28 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7433 (mm) REVERT: e 108 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6405 (tm-30) REVERT: e 149 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5552 (mm-30) REVERT: e 182 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5446 (t80) REVERT: e 218 ARG cc_start: 0.6599 (OUTLIER) cc_final: 0.6068 (mtt-85) outliers start: 410 outliers final: 305 residues processed: 994 average time/residue: 0.6361 time to fit residues: 1120.8862 Evaluate side-chains 969 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 363 poor density : 606 time to evaluate : 6.836 ------------------------------------------------------------------------------- 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 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 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 64 LEU 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 152 LEU 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 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 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 248 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 44 HIS 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 160 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 ARG 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 71 SER 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 75 ILE Chi-restraints excluded: chain k residue 91 SER Chi-restraints excluded: chain k residue 137 ASP 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 219 ILE Chi-restraints excluded: chain S residue 248 ILE 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 62 ASN Chi-restraints excluded: chain V residue 65 LEU 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 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 208 LEU 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 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain P residue 218 ARG 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 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 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 160 VAL Chi-restraints excluded: chain T residue 211 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 297 THR 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 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 291 LEU 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 44 HIS 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 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 295 ASP Chi-restraints excluded: chain Q residue 352 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 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 123 ASN 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 79 ILE Chi-restraints excluded: chain K residue 91 SER Chi-restraints excluded: chain K residue 141 ILE Chi-restraints excluded: chain F residue 64 LEU 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 165 SER Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 181 THR 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 323 GLU Chi-restraints excluded: chain I residue 12 PHE Chi-restraints excluded: chain I residue 51 VAL 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 189 VAL Chi-restraints excluded: chain I residue 195 THR 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 44 HIS 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 160 VAL Chi-restraints excluded: chain G residue 182 TYR Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain G residue 218 ARG 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 54 THR Chi-restraints excluded: chain p residue 71 SER 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 79 ILE Chi-restraints excluded: chain m residue 81 ARG Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain m residue 137 ASP 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 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 217 ILE Chi-restraints excluded: chain U residue 219 ILE Chi-restraints excluded: chain U residue 248 ILE 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 137 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 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 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 93 LEU Chi-restraints excluded: chain R residue 108 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 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 133 VAL Chi-restraints excluded: chain j residue 134 VAL Chi-restraints excluded: chain j residue 144 ASN 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 119 ILE Chi-restraints excluded: chain f residue 153 VAL Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 203 VAL Chi-restraints excluded: chain f residue 211 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 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 97 GLU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 185 LEU 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 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 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 93 LEU 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 345 MET 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 901 optimal weight: 7.9990 chunk 863 optimal weight: 5.9990 chunk 686 optimal weight: 2.9990 chunk 510 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 438 optimal weight: 3.9990 chunk 856 optimal weight: 6.9990 chunk 402 optimal weight: 0.9990 chunk 252 optimal weight: 0.8980 chunk 742 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102776 restraints weight = 128544.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102679 restraints weight = 274414.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103050 restraints weight = 238288.511| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 77418 Z= 0.183 Angle : 0.488 9.158 104268 Z= 0.266 Chirality : 0.043 0.190 12342 Planarity : 0.003 0.037 13056 Dihedral : 4.403 56.656 10262 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.15 % Allowed : 25.31 % Favored : 70.54 % 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: 1.98 (0.10), residues: 2724 sheet: -0.50 (0.11), residues: 1956 loop : -1.61 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 119 HIS 0.003 0.001 HIS Q 250 PHE 0.015 0.001 PHE I 12 TYR 0.019 0.001 TYR e 60 ARG 0.007 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 1018 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 353 poor density : 665 time to evaluate : 6.960 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: 0.8689 (OUTLIER) cc_final: 0.8480 (mt) REVERT: E 138 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7316 (t80) REVERT: a 68 SER cc_start: 0.7827 (t) cc_final: 0.7603 (p) REVERT: a 136 TYR cc_start: 0.8335 (p90) cc_final: 0.8079 (p90) REVERT: C 252 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: D 152 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.5870 (mp) REVERT: D 196 LYS cc_start: 0.7049 (tptm) cc_final: 0.6763 (mmtp) REVERT: B 108 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: B 182 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 218 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6784 (mtt-85) REVERT: n 23 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8795 (mp) REVERT: n 98 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8363 (mt) REVERT: n 145 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8678 (pp) REVERT: Y 138 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.6698 (t80) REVERT: S 119 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8434 (mt) REVERT: S 258 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6960 (tt) REVERT: V 152 LEU cc_start: 0.7200 (OUTLIER) cc_final: 0.5954 (mp) REVERT: V 196 LYS cc_start: 0.7297 (tptm) cc_final: 0.6673 (mmtp) REVERT: V 352 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.7881 (mt) REVERT: P 28 ILE cc_start: 0.7670 (OUTLIER) cc_final: 0.7333 (mm) REVERT: P 66 MET cc_start: 0.4457 (pmm) cc_final: 0.3604 (ttm) REVERT: P 103 MET cc_start: 0.7199 (tpt) cc_final: 0.6899 (tpt) REVERT: P 108 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5861 (tm-30) REVERT: P 182 TYR cc_start: 0.5794 (OUTLIER) cc_final: 0.5228 (t80) REVERT: P 218 ARG cc_start: 0.6080 (OUTLIER) cc_final: 0.5862 (mtt180) REVERT: Z 138 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.8203 (t80) REVERT: T 103 MET cc_start: 0.6321 (ttm) cc_final: 0.6097 (ttt) REVERT: W 87 GLN cc_start: 0.7108 (mp10) cc_final: 0.6743 (mm-40) REVERT: W 196 LYS cc_start: 0.6757 (tptm) cc_final: 0.6531 (mmtm) REVERT: Q 44 HIS cc_start: 0.6088 (OUTLIER) cc_final: 0.5819 (m90) REVERT: Q 108 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.5813 (tm-30) REVERT: Q 149 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5573 (mm-30) REVERT: Q 218 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6066 (mtt-85) REVERT: L 126 ASP cc_start: 0.8163 (t0) cc_final: 0.7940 (t0) REVERT: J 138 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7326 (t80) REVERT: K 68 SER cc_start: 0.7832 (t) cc_final: 0.7593 (p) REVERT: K 136 TYR cc_start: 0.8426 (p90) cc_final: 0.8180 (p90) REVERT: F 71 MET cc_start: 0.8984 (tpp) cc_final: 0.8744 (mmt) REVERT: H 252 ASP cc_start: 0.8032 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: I 152 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.5881 (mp) REVERT: I 196 LYS cc_start: 0.7062 (tptm) cc_final: 0.6787 (mmtp) REVERT: G 27 ILE cc_start: 0.8645 (mm) cc_final: 0.8220 (mt) REVERT: G 218 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6721 (mtt-85) REVERT: p 1 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5173 (mtp) REVERT: p 23 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8786 (mp) REVERT: p 98 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8388 (mt) REVERT: p 145 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8657 (pp) REVERT: c 138 PHE cc_start: 0.8302 (OUTLIER) cc_final: 0.6483 (t80) REVERT: m 75 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8971 (pt) REVERT: O 35 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8127 (mm-30) REVERT: U 119 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8442 (mt) REVERT: U 258 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.7100 (tt) REVERT: X 152 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.5888 (mp) REVERT: X 196 LYS cc_start: 0.7340 (tptm) cc_final: 0.6614 (mmtp) REVERT: R 108 GLU cc_start: 0.6382 (OUTLIER) cc_final: 0.6017 (tm-30) REVERT: R 182 TYR cc_start: 0.5888 (OUTLIER) cc_final: 0.5233 (t80) REVERT: R 218 ARG cc_start: 0.6345 (OUTLIER) cc_final: 0.5816 (mtt180) REVERT: h 138 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.8214 (t80) REVERT: g 97 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6546 (mt-10) REVERT: g 196 LYS cc_start: 0.6756 (tptm) cc_final: 0.6526 (mmtm) REVERT: g 352 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8006 (mt) REVERT: e 28 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7298 (mm) REVERT: e 108 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: e 149 GLU cc_start: 0.5968 (OUTLIER) cc_final: 0.5562 (mm-30) REVERT: e 182 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5481 (t80) REVERT: e 218 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.6068 (mtt-85) outliers start: 353 outliers final: 263 residues processed: 975 average time/residue: 0.6433 time to fit residues: 1106.0506 Evaluate side-chains 952 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 640 time to evaluate : 6.948 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain b residue 66 LEU Chi-restraints excluded: chain b residue 76 MET 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 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 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 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 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 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 189 VAL Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 221 ARG 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 319 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 53 LEU 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 218 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 354 ILE 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 54 THR 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 138 PHE Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain k residue 50 ASP 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 219 ILE Chi-restraints excluded: chain S residue 248 ILE 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 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 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 208 LEU 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 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 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain P residue 345 MET Chi-restraints excluded: chain o residue 1 MET 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 o residue 134 VAL 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 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 160 VAL 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 256 VAL Chi-restraints excluded: chain T residue 297 THR 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 137 VAL 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 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 44 HIS 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 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 218 ARG Chi-restraints excluded: chain Q residue 243 VAL 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 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 128 GLU 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 64 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 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 309 LEU Chi-restraints excluded: chain H residue 323 GLU 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 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 248 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 15 LEU Chi-restraints excluded: chain G residue 44 HIS 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 218 ARG 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 54 THR 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 50 ASP Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 79 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 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 230 THR Chi-restraints excluded: chain U residue 248 ILE 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 137 VAL Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 153 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 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 108 GLU Chi-restraints excluded: chain R residue 182 TYR 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 134 VAL 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 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 170 LEU Chi-restraints excluded: chain f residue 211 ILE Chi-restraints excluded: chain f residue 219 ILE Chi-restraints excluded: chain f residue 252 ASP 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 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 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 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 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 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 153 optimal weight: 10.0000 chunk 894 optimal weight: 0.0060 chunk 619 optimal weight: 20.0000 chunk 425 optimal weight: 20.0000 chunk 586 optimal weight: 9.9990 chunk 826 optimal weight: 1.9990 chunk 798 optimal weight: 7.9990 chunk 476 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 319 optimal weight: 0.0980 chunk 853 optimal weight: 5.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- 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 ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN o 70 GLN L 70 GLN K 46 GLN I 73 ASN G 62 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.124005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.101752 restraints weight = 128476.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.097819 restraints weight = 137565.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.098140 restraints weight = 155326.714| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2178 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= 0.195 Angle : 0.492 10.461 104268 Z= 0.268 Chirality : 0.043 0.166 12342 Planarity : 0.003 0.038 13056 Dihedral : 4.353 59.327 10262 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.26 % Allowed : 25.33 % Favored : 70.41 % 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: -0.42 (0.08), residues: 9648 helix: 2.04 (0.10), residues: 2724 sheet: -0.48 (0.11), residues: 1956 loop : -1.59 (0.08), residues: 4968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 119 HIS 0.003 0.001 HIS W 250 PHE 0.017 0.001 PHE I 12 TYR 0.023 0.001 TYR e 60 ARG 0.008 0.000 ARG B 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 1021 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 362 poor density : 659 time to evaluate : 7.082 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: 0.8693 (OUTLIER) cc_final: 0.8458 (mt) REVERT: E 138 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7318 (t80) REVERT: a 68 SER cc_start: 0.7869 (t) cc_final: 0.7627 (p) REVERT: a 136 TYR cc_start: 0.8326 (p90) cc_final: 0.8072 (p90) REVERT: A 35 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: C 152 LEU cc_start: 0.8488 (mm) cc_final: 0.8282 (mt) REVERT: C 252 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7439 (m-30) REVERT: D 152 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5552 (mp) REVERT: D 196 LYS cc_start: 0.6768 (tptm) cc_final: 0.6482 (mmtp) REVERT: B 108 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6327 (tm-30) REVERT: B 182 TYR cc_start: 0.6075 (OUTLIER) cc_final: 0.5085 (t80) REVERT: B 218 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6640 (mtt-85) REVERT: n 23 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8797 (mp) REVERT: n 98 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8320 (mt) REVERT: n 145 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8667 (pp) REVERT: Y 138 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.6735 (t80) REVERT: S 119 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8359 (mt) REVERT: S 258 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7141 (tt) REVERT: V 152 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.5633 (mp) REVERT: V 196 LYS cc_start: 0.6953 (tptm) cc_final: 0.6342 (mmtp) REVERT: V 352 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.7852 (mt) REVERT: P 28 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7730 (mm) REVERT: P 103 MET cc_start: 0.7045 (tpt) cc_final: 0.6837 (tpt) REVERT: P 108 GLU cc_start: 0.6429 (OUTLIER) cc_final: 0.6023 (tm-30) REVERT: P 182 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5474 (t80) REVERT: P 218 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5562 (mtt-85) REVERT: Z 138 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8245 (t80) REVERT: W 87 GLN cc_start: 0.7287 (mp10) cc_final: 0.6659 (mm-40) REVERT: W 196 LYS cc_start: 0.6539 (tptm) cc_final: 0.6307 (mmtm) REVERT: W 221 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7587 (tpt170) REVERT: Q 44 HIS cc_start: 0.6434 (OUTLIER) cc_final: 0.5958 (m90) REVERT: Q 108 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5957 (tm-30) REVERT: Q 218 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5731 (mtt-85) REVERT: L 98 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8447 (mt) REVERT: J 138 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.7326 (t80) REVERT: K 17 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8952 (tp) REVERT: K 68 SER cc_start: 0.7888 (t) cc_final: 0.7647 (p) REVERT: K 136 TYR cc_start: 0.8406 (p90) cc_final: 0.8140 (p90) REVERT: F 71 MET cc_start: 0.9005 (tpp) cc_final: 0.8773 (mmt) REVERT: H 252 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7445 (m-30) REVERT: I 152 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.5426 (mp) REVERT: I 196 LYS cc_start: 0.6749 (tptm) cc_final: 0.6462 (mmtp) REVERT: G 27 ILE cc_start: 0.8552 (mm) cc_final: 0.8259 (mt) REVERT: G 108 GLU cc_start: 0.6675 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: G 218 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6624 (mtp85) REVERT: p 1 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5353 (mtp) REVERT: p 23 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8779 (mp) REVERT: p 98 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8374 (mt) REVERT: p 145 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8636 (pp) REVERT: c 138 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.6516 (t80) REVERT: m 75 ILE cc_start: 0.9242 (OUTLIER) cc_final: 0.8972 (pt) REVERT: U 103 MET cc_start: 0.7575 (tpp) cc_final: 0.7203 (ttm) REVERT: U 119 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8379 (mt) REVERT: U 258 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7141 (tt) REVERT: X 152 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.5555 (mp) REVERT: X 196 LYS cc_start: 0.7007 (tptm) cc_final: 0.6283 (mmtp) REVERT: R 108 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6134 (tm-30) REVERT: R 182 TYR cc_start: 0.6061 (OUTLIER) cc_final: 0.5449 (t80) REVERT: R 218 ARG cc_start: 0.6225 (OUTLIER) cc_final: 0.5620 (mtt180) REVERT: h 138 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8245 (t80) REVERT: g 97 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: g 196 LYS cc_start: 0.6566 (tptm) cc_final: 0.6318 (mmtm) REVERT: g 352 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.7899 (mt) REVERT: e 28 ILE cc_start: 0.7928 (OUTLIER) cc_final: 0.7659 (mm) REVERT: e 108 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5842 (tm-30) REVERT: e 149 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.5191 (mm-30) REVERT: e 218 ARG cc_start: 0.6063 (OUTLIER) cc_final: 0.5684 (mtt-85) outliers start: 362 outliers final: 285 residues processed: 976 average time/residue: 0.6500 time to fit residues: 1125.0563 Evaluate side-chains 978 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 336 poor density : 642 time to evaluate : 7.031 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 221 ARG 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 319 MET Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 44 HIS 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 160 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 354 ILE 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 54 THR 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 138 PHE Chi-restraints excluded: chain Y residue 141 ILE Chi-restraints excluded: chain k residue 91 SER 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 219 ILE Chi-restraints excluded: chain S residue 248 ILE 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 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 189 VAL Chi-restraints excluded: chain V residue 195 THR Chi-restraints excluded: chain V residue 208 LEU 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 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 186 SER Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain P residue 345 MET Chi-restraints excluded: chain o residue 1 MET 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 o residue 134 VAL 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 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 170 LEU Chi-restraints excluded: chain T residue 211 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 297 THR 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 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 221 ARG Chi-restraints excluded: chain W residue 258 ILE 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 44 HIS 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 108 GLU Chi-restraints excluded: chain Q residue 146 PHE 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 123 ASN 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 17 LEU 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 F residue 64 LEU 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 160 VAL Chi-restraints excluded: chain H residue 165 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 323 GLU 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 189 VAL Chi-restraints excluded: chain I residue 195 THR Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 248 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 15 LEU Chi-restraints excluded: chain G residue 44 HIS 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 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 218 ARG 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 30 VAL Chi-restraints excluded: chain p residue 52 LEU Chi-restraints excluded: chain p residue 54 THR Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 98 LEU 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 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER Chi-restraints excluded: chain O residue 64 LEU 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 119 ILE 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 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 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 189 VAL Chi-restraints excluded: chain X residue 195 THR Chi-restraints excluded: chain X residue 208 LEU 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 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 108 GLU 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 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 134 VAL Chi-restraints excluded: chain j residue 143 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 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 153 VAL Chi-restraints excluded: chain f residue 160 VAL Chi-restraints excluded: chain f residue 211 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 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 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 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 87 GLN Chi-restraints excluded: chain e residue 88 THR Chi-restraints excluded: chain e residue 93 LEU 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 218 ARG Chi-restraints excluded: chain e residue 295 ASP Chi-restraints excluded: chain e residue 345 MET 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 547 optimal weight: 6.9990 chunk 340 optimal weight: 0.0770 chunk 683 optimal weight: 1.9990 chunk 447 optimal weight: 0.5980 chunk 779 optimal weight: 7.9990 chunk 810 optimal weight: 9.9990 chunk 918 optimal weight: 0.9990 chunk 830 optimal weight: 20.0000 chunk 895 optimal weight: 7.9990 chunk 819 optimal weight: 4.9990 chunk 405 optimal weight: 8.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- 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 68 ASN ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN T 87 GLN L 70 GLN K 46 GLN F 8 ASN I 73 ASN G 68 ASN ** U 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 87 GLN d 8 ASN f 87 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103389 restraints weight = 127845.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.102252 restraints weight = 271229.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102894 restraints weight = 237022.820| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 77418 Z= 0.140 Angle : 0.461 10.464 104268 Z= 0.251 Chirality : 0.042 0.159 12342 Planarity : 0.003 0.039 13056 Dihedral : 4.127 59.626 10262 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.32 % Allowed : 26.33 % Favored : 70.35 % 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: -0.20 (0.08), residues: 9648 helix: 2.23 (0.10), residues: 2730 sheet: -0.28 (0.11), residues: 1944 loop : -1.50 (0.08), residues: 4974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.003 0.001 HIS Q 250 PHE 0.021 0.001 PHE H 92 TYR 0.029 0.001 TYR e 60 ARG 0.006 0.000 ARG B 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 992 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 710 time to evaluate : 7.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 126 ASP cc_start: 0.8060 (t0) cc_final: 0.7836 (t0) REVERT: E 138 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7276 (t80) REVERT: a 136 TYR cc_start: 0.8346 (p90) cc_final: 0.8072 (p90) REVERT: D 152 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.5831 (mp) REVERT: D 196 LYS cc_start: 0.6903 (tptm) cc_final: 0.6685 (mmtp) REVERT: B 218 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6820 (mtt-85) REVERT: n 23 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8766 (mp) REVERT: n 145 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8684 (pp) REVERT: Y 138 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.6771 (t80) REVERT: S 258 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7052 (tt) REVERT: V 152 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.5908 (mp) REVERT: V 196 LYS cc_start: 0.7269 (tptm) cc_final: 0.6745 (mmtp) REVERT: V 352 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.7831 (mt) REVERT: P 103 MET cc_start: 0.6976 (tpt) cc_final: 0.6684 (tpt) REVERT: P 182 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.5192 (t80) REVERT: P 218 ARG cc_start: 0.6039 (OUTLIER) cc_final: 0.5790 (mtt-85) REVERT: Z 138 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8197 (t80) REVERT: W 87 GLN cc_start: 0.7099 (mp10) cc_final: 0.6617 (mm-40) REVERT: W 221 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7501 (tpt170) REVERT: Q 44 HIS cc_start: 0.6032 (OUTLIER) cc_final: 0.5776 (m90) REVERT: L 98 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8464 (mt) REVERT: J 138 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7290 (t80) REVERT: K 136 TYR cc_start: 0.8437 (p90) cc_final: 0.8166 (p90) REVERT: F 71 MET cc_start: 0.8945 (tpp) cc_final: 0.8722 (mmt) REVERT: I 152 LEU cc_start: 0.6821 (OUTLIER) cc_final: 0.5836 (mp) REVERT: I 196 LYS cc_start: 0.6914 (tptm) cc_final: 0.6712 (mmtp) REVERT: G 103 MET cc_start: 0.7103 (tpt) cc_final: 0.6875 (tpt) REVERT: p 1 MET cc_start: 0.5694 (OUTLIER) cc_final: 0.5316 (mtp) REVERT: p 23 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8767 (mp) REVERT: p 145 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8685 (pp) REVERT: c 138 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.6613 (t80) REVERT: m 75 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8944 (pt) REVERT: U 103 MET cc_start: 0.7285 (tpp) cc_final: 0.7045 (ttt) REVERT: X 59 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.5842 (tt0) REVERT: X 152 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.5881 (mp) REVERT: X 196 LYS cc_start: 0.7221 (tptm) cc_final: 0.6745 (mmtp) REVERT: R 182 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.5072 (t80) REVERT: R 218 ARG cc_start: 0.6313 (OUTLIER) cc_final: 0.5844 (mtt180) REVERT: h 138 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8238 (t80) REVERT: g 352 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.7983 (mt) REVERT: e 149 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5505 (mm-30) REVERT: e 218 ARG cc_start: 0.6423 (OUTLIER) cc_final: 0.6031 (mtt-85) outliers start: 282 outliers final: 209 residues processed: 950 average time/residue: 0.6912 time to fit residues: 1147.7178 Evaluate side-chains 890 residues out of total 8496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 239 poor density : 651 time to evaluate : 6.965 ------------------------------------------------------------------------------- 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 76 MET Chi-restraints excluded: chain b residue 101 THR 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 141 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 165 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 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 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 189 VAL Chi-restraints excluded: chain D residue 221 ARG 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 319 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 44 HIS 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 182 TYR Chi-restraints excluded: chain B residue 218 ARG Chi-restraints excluded: chain B residue 258 ILE Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain n residue 23 ILE Chi-restraints excluded: chain n residue 30 VAL Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 71 SER Chi-restraints excluded: chain n residue 143 LEU Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain Y residue 138 PHE Chi-restraints excluded: chain k residue 91 SER 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 160 VAL Chi-restraints excluded: chain S residue 211 ILE Chi-restraints excluded: chain S residue 219 ILE Chi-restraints excluded: chain S residue 258 ILE Chi-restraints excluded: chain S residue 309 LEU 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 152 LEU Chi-restraints excluded: chain V residue 153 VAL Chi-restraints excluded: chain V residue 258 ILE Chi-restraints excluded: chain V residue 314 VAL Chi-restraints excluded: chain V residue 352 ILE Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 160 VAL Chi-restraints excluded: chain P residue 182 TYR Chi-restraints excluded: chain P residue 218 ARG Chi-restraints excluded: chain P residue 345 MET Chi-restraints excluded: chain o residue 1 MET 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 o residue 134 VAL 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 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 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 256 VAL 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 137 VAL Chi-restraints excluded: chain W residue 188 VAL Chi-restraints excluded: chain W residue 189 VAL Chi-restraints excluded: chain W residue 219 ILE Chi-restraints excluded: chain W residue 221 ARG Chi-restraints excluded: chain W residue 258 ILE 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 44 HIS Chi-restraints excluded: chain Q residue 88 THR Chi-restraints excluded: chain Q residue 146 PHE 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 243 VAL 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 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 J residue 115 THR Chi-restraints excluded: chain J residue 138 PHE Chi-restraints excluded: chain J residue 141 ILE 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 165 SER Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain H residue 248 ILE Chi-restraints excluded: chain H residue 323 GLU 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 189 VAL Chi-restraints excluded: chain I residue 221 ARG 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 44 HIS 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 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 p residue 1 MET Chi-restraints excluded: chain p residue 23 ILE Chi-restraints excluded: chain p residue 30 VAL Chi-restraints excluded: chain p residue 54 THR Chi-restraints excluded: chain p residue 71 SER Chi-restraints excluded: chain p residue 88 ASN 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 75 ILE Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain m residue 91 SER 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 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 X residue 12 PHE Chi-restraints excluded: chain X residue 59 GLU Chi-restraints excluded: chain X residue 65 LEU 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 208 LEU 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 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 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 134 VAL Chi-restraints excluded: chain j residue 143 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 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 g residue 51 VAL Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 189 VAL 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 87 GLN 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 218 ARG Chi-restraints excluded: chain e residue 295 ASP Chi-restraints excluded: chain e residue 345 MET 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 808 optimal weight: 0.9980 chunk 944 optimal weight: 6.9990 chunk 534 optimal weight: 10.0000 chunk 297 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 428 optimal weight: 4.9990 chunk 338 optimal weight: 10.0000 chunk 448 optimal weight: 30.0000 chunk 510 optimal weight: 8.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- 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 ** R 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 8 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101352 restraints weight = 128877.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.100768 restraints weight = 287443.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.101457 restraints weight = 247261.907| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 77418 Z= 0.327 Angle : 0.561 9.929 104268 Z= 0.305 Chirality : 0.045 0.167 12342 Planarity : 0.003 0.038 13056 Dihedral : 4.593 59.397 10262 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.84 % Allowed : 26.13 % Favored : 70.03 % 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: -0.55 (0.08), residues: 9648 helix: 1.89 (0.10), residues: 2646 sheet: -0.54 (0.11), residues: 1968 loop : -1.59 (0.08), residues: 5034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP m 119 HIS 0.005 0.001 HIS W 250 PHE 0.025 0.002 PHE g 12 TYR 0.033 0.002 TYR e 60 ARG 0.006 0.000 ARG l 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21518.92 seconds wall clock time: 375 minutes 44.95 seconds (22544.95 seconds total)