Starting phenix.real_space_refine on Mon Jun 23 17:32:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.map" model { file = "/net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yb6_39110/06_2025/8yb6_39110.cif" } resolution = 3.06 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= -0.000 sd= 0.080 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 60 5.49 5 S 115 5.16 5 C 17387 2.51 5 N 4884 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27758 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2768 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2166 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 20, 'TRANS': 246} Chain: "C" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 1303 Classifications: {'RNA': 61} Modifications used: {'5*END': 1, 'rna2p_pur': 17, 'rna2p_pyr': 9, 'rna3p_pur': 18, 'rna3p_pyr': 17} Link IDs: {'rna2p': 25, 'rna3p': 35} Chain: "D" Number of atoms: 2897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2897 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 13, 'TRANS': 358} Chain: "E" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2882 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 13, 'TRANS': 356} Chain: "F" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2911 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 13, 'TRANS': 360} Chain: "G" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "H" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2935 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 13, 'TRANS': 363} Chain: "I" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2072 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 12, 'TRANS': 255} Chain breaks: 2 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3531 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 28, 'TRANS': 414} Chain: "K" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1356 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 8, 'TRANS': 156} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2101 SG CYS A 298 41.464 47.449 71.635 1.00 53.53 S ATOM 2122 SG CYS A 301 40.017 49.331 68.641 1.00 54.72 S ATOM 2338 SG CYS A 329 43.654 49.799 69.543 1.00 62.09 S ATOM 2363 SG CYS A 332 40.965 51.236 71.750 1.00 63.65 S ATOM 23999 SG CYS J 215 61.978 39.812 166.800 1.00 87.93 S ATOM 24019 SG CYS J 218 62.860 42.864 164.829 1.00 84.22 S ATOM 24738 SG CYS J 311 59.725 40.770 163.884 1.00 91.10 S ATOM 24756 SG CYS J 314 62.965 39.363 163.113 1.00 94.58 S Time building chain proxies: 15.69, per 1000 atoms: 0.57 Number of scatterers: 27758 At special positions: 0 Unit cell: (113.9, 139.4, 196.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 115 16.00 P 60 15.00 O 5310 8.00 N 4884 7.00 C 17387 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: 6.00 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 301 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 329 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 332 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 298 " pdb=" ZN J 601 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 311 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 215 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 314 " pdb="ZN ZN J 601 " - pdb=" SG CYS J 218 " Number of angles added : 12 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6268 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 31 sheets defined 38.1% alpha, 16.7% beta 6 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 8.88 Creating SS restraints... Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.512A pdb=" N GLY A 42 " --> pdb=" O SER A 38 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 removed outlier: 4.089A pdb=" N LYS A 62 " --> pdb=" O SER A 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 65 " --> pdb=" O PRO A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.610A pdb=" N ALA A 156 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.613A pdb=" N ALA A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 329 through 340 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.836A pdb=" N ARG A 377 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 42 through 48 removed outlier: 3.681A pdb=" N GLU B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.628A pdb=" N CYS B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 91 through 96' Processing helix chain 'B' and resid 166 through 183 removed outlier: 3.961A pdb=" N LYS B 178 " --> pdb=" O TRP B 174 " (cutoff:3.500A) Proline residue: B 180 - end of helix Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.881A pdb=" N LYS B 246 " --> pdb=" O LYS B 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.635A pdb=" N ARG D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 4.218A pdb=" N ALA D 54 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.525A pdb=" N LEU D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.792A pdb=" N TRP D 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS D 79 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LYS D 80 " --> pdb=" O CYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 removed outlier: 4.115A pdb=" N LYS D 87 " --> pdb=" O GLU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 106 No H-bonds generated for 'chain 'D' and resid 104 through 106' Processing helix chain 'D' and resid 107 through 116 removed outlier: 3.716A pdb=" N LEU D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 136 removed outlier: 3.547A pdb=" N VAL D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 131 " --> pdb=" O GLN D 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 146 Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.717A pdb=" N ALA D 191 " --> pdb=" O TYR D 188 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA D 192 " --> pdb=" O PHE D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 Processing helix chain 'D' and resid 233 through 250 removed outlier: 3.583A pdb=" N LYS D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 3.776A pdb=" N VAL D 285 " --> pdb=" O ASN D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 315 Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 349 through 362 Processing helix chain 'E' and resid 38 through 48 Processing helix chain 'E' and resid 50 through 54 removed outlier: 4.290A pdb=" N ALA E 54 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 removed outlier: 3.577A pdb=" N LEU E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 77 through 88 removed outlier: 5.860A pdb=" N GLU E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE E 84 " --> pdb=" O LYS E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 116 removed outlier: 4.025A pdb=" N ASP E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG E 113 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 114 " --> pdb=" O ASP E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 256 through 261 Processing helix chain 'E' and resid 279 through 286 removed outlier: 4.409A pdb=" N ASN E 282 " --> pdb=" O SER E 279 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE E 284 " --> pdb=" O ALA E 281 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL E 285 " --> pdb=" O ASN E 282 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG E 286 " --> pdb=" O ALA E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 329 through 332 Processing helix chain 'E' and resid 349 through 361 Processing helix chain 'F' and resid 38 through 48 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 74 through 89 removed outlier: 4.306A pdb=" N TRP F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 117 removed outlier: 3.811A pdb=" N LYS F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ASP F 110 " --> pdb=" O ASP F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 136 Processing helix chain 'F' and resid 139 through 146 Processing helix chain 'F' and resid 223 through 230 Processing helix chain 'F' and resid 233 through 249 removed outlier: 3.508A pdb=" N HIS F 239 " --> pdb=" O ASN F 235 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 249 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 286 removed outlier: 3.583A pdb=" N PHE F 284 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL F 285 " --> pdb=" O ASN F 282 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG F 286 " --> pdb=" O ALA F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 315 removed outlier: 3.514A pdb=" N GLN F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 332 Processing helix chain 'F' and resid 349 through 362 Processing helix chain 'F' and resid 365 through 370 removed outlier: 3.658A pdb=" N GLN F 370 " --> pdb=" O TRP F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 48 Processing helix chain 'G' and resid 49 through 56 removed outlier: 5.248A pdb=" N ALA G 54 " --> pdb=" O ASP G 51 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU G 56 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 72 Processing helix chain 'G' and resid 76 through 89 removed outlier: 3.936A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 96 removed outlier: 3.547A pdb=" N ASP G 95 " --> pdb=" O ASN G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 106 No H-bonds generated for 'chain 'G' and resid 104 through 106' Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 122 through 135 removed outlier: 3.510A pdb=" N GLN G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 146 Processing helix chain 'G' and resid 223 through 231 Processing helix chain 'G' and resid 233 through 250 removed outlier: 3.528A pdb=" N LYS G 250 " --> pdb=" O LEU G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 285 removed outlier: 3.616A pdb=" N VAL G 285 " --> pdb=" O ASN G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 314 removed outlier: 3.528A pdb=" N GLN G 299 " --> pdb=" O ASP G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 Processing helix chain 'G' and resid 349 through 363 Processing helix chain 'G' and resid 368 through 372 removed outlier: 3.782A pdb=" N LYS G 371 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 52 through 56 removed outlier: 3.534A pdb=" N LEU H 56 " --> pdb=" O LYS H 53 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 Processing helix chain 'H' and resid 77 through 89 removed outlier: 3.665A pdb=" N GLY H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 116 Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 223 through 230 Processing helix chain 'H' and resid 233 through 250 Processing helix chain 'H' and resid 280 through 285 removed outlier: 3.652A pdb=" N VAL H 285 " --> pdb=" O ASN H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 315 Processing helix chain 'H' and resid 329 through 332 Processing helix chain 'H' and resid 349 through 363 Processing helix chain 'H' and resid 365 through 370 removed outlier: 3.643A pdb=" N GLN H 370 " --> pdb=" O TRP H 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 47 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 139 through 144 Processing helix chain 'I' and resid 223 through 231 Processing helix chain 'I' and resid 233 through 248 Processing helix chain 'I' and resid 281 through 286 removed outlier: 3.622A pdb=" N VAL I 285 " --> pdb=" O ASN I 282 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 286 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 315 Processing helix chain 'I' and resid 328 through 332 Processing helix chain 'I' and resid 339 through 343 Processing helix chain 'I' and resid 349 through 362 removed outlier: 3.603A pdb=" N GLY I 362 " --> pdb=" O LEU I 358 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 110 Processing helix chain 'J' and resid 120 through 143 removed outlier: 3.541A pdb=" N ARG J 124 " --> pdb=" O ASN J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 163 removed outlier: 3.636A pdb=" N ASN J 163 " --> pdb=" O TRP J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 167 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 217 through 225 Processing helix chain 'J' and resid 255 through 263 removed outlier: 3.606A pdb=" N ALA J 261 " --> pdb=" O ALA J 257 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN J 262 " --> pdb=" O GLY J 258 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN J 263 " --> pdb=" O MET J 259 " (cutoff:3.500A) Processing helix chain 'J' and resid 287 through 292 Processing helix chain 'J' and resid 418 through 426 Processing helix chain 'J' and resid 427 through 438 removed outlier: 3.777A pdb=" N LYS J 438 " --> pdb=" O ALA J 434 " (cutoff:3.500A) Processing helix chain 'J' and resid 450 through 465 removed outlier: 3.809A pdb=" N ALA J 454 " --> pdb=" O THR J 450 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE J 456 " --> pdb=" O GLN J 452 " (cutoff:3.500A) Proline residue: J 458 - end of helix removed outlier: 3.502A pdb=" N ASN J 462 " --> pdb=" O PRO J 458 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 474 removed outlier: 3.933A pdb=" N GLU J 473 " --> pdb=" O GLY J 469 " (cutoff:3.500A) Processing helix chain 'J' and resid 478 through 483 Processing helix chain 'J' and resid 486 through 498 removed outlier: 3.669A pdb=" N THR J 491 " --> pdb=" O GLY J 487 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS J 492 " --> pdb=" O GLU J 488 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER J 496 " --> pdb=" O LYS J 492 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 514 removed outlier: 3.819A pdb=" N ARG J 506 " --> pdb=" O THR J 502 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER J 514 " --> pdb=" O GLY J 510 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 14 Processing helix chain 'K' and resid 16 through 25 Processing helix chain 'K' and resid 34 through 52 Proline residue: K 47 - end of helix Processing helix chain 'K' and resid 57 through 71 Processing helix chain 'K' and resid 80 through 90 Processing helix chain 'K' and resid 96 through 107 removed outlier: 3.544A pdb=" N ARG K 100 " --> pdb=" O LYS K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 111 Processing helix chain 'K' and resid 113 through 115 No H-bonds generated for 'chain 'K' and resid 113 through 115' Processing helix chain 'K' and resid 116 through 130 removed outlier: 3.549A pdb=" N LEU K 120 " --> pdb=" O MET K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'K' and resid 149 through 165 removed outlier: 4.057A pdb=" N LYS K 153 " --> pdb=" O GLN K 149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 17 removed outlier: 6.855A pdb=" N THR A 7 " --> pdb=" O GLN A 142 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN A 142 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 9 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 140 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ARG A 11 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU A 138 " --> pdb=" O ARG A 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N GLU A 13 " --> pdb=" O SER A 136 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N SER A 136 " --> pdb=" O GLU A 13 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA A 15 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N THR A 124 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL A 85 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LEU A 126 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N HIS A 83 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG A 128 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP A 81 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU A 130 " --> pdb=" O TRP A 79 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TRP A 79 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU A 132 " --> pdb=" O ILE A 77 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ILE A 77 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP A 134 " --> pdb=" O PRO A 75 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET A 68 " --> pdb=" O ASP A 213 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ARG A 74 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 12.218A pdb=" N ILE A 207 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ARG A 241 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU A 243 " --> pdb=" O ASP A 232 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 74 removed outlier: 4.039A pdb=" N TYR B 3 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LEU B 8 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 186 through 207 removed outlier: 6.650A pdb=" N VAL B 235 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N CYS B 189 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLU B 233 " --> pdb=" O CYS B 189 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU B 191 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU B 231 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN B 193 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ALA B 229 " --> pdb=" O GLN B 193 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY B 195 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 227 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 197 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU B 225 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLY B 199 " --> pdb=" O ASN B 223 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ASN B 223 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LYS B 201 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LYS B 221 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLU B 203 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLU B 219 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LYS B 205 " --> pdb=" O TRP B 217 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TRP B 217 " --> pdb=" O LYS B 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA7, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 26 through 29 removed outlier: 3.782A pdb=" N CYS D 27 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N SER D 35 " --> pdb=" O SER D 178 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLY D 268 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.706A pdb=" N VAL D 101 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 326 through 327 removed outlier: 6.297A pdb=" N TRP D 326 " --> pdb=" O ILE D 347 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 26 through 29 removed outlier: 3.792A pdb=" N VAL E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N SER E 35 " --> pdb=" O SER E 178 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE E 177 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY E 268 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL E 271 " --> pdb=" O PHE E 325 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE E 323 " --> pdb=" O PHE E 273 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N GLY E 324 " --> pdb=" O ARG E 345 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE E 347 " --> pdb=" O GLY E 324 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N TRP E 326 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'E' and resid 185 through 187 Processing sheet with id=AB6, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 29 removed outlier: 3.781A pdb=" N VAL F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER F 35 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE F 177 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 268 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE F 323 " --> pdb=" O PHE F 273 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLY F 324 " --> pdb=" O ARG F 345 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 347 " --> pdb=" O GLY F 324 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TRP F 326 " --> pdb=" O ILE F 347 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'F' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 26 through 29 removed outlier: 3.538A pdb=" N VAL G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER G 35 " --> pdb=" O SER G 178 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE G 323 " --> pdb=" O PHE G 273 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AC4, first strand: chain 'H' and resid 26 through 29 removed outlier: 3.647A pdb=" N CYS H 27 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER H 35 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 177 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY H 268 " --> pdb=" O ILE H 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE H 323 " --> pdb=" O PHE H 273 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N GLY H 324 " --> pdb=" O ARG H 345 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ILE H 347 " --> pdb=" O GLY H 324 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP H 326 " --> pdb=" O ILE H 347 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 58 through 61 removed outlier: 3.529A pdb=" N THR H 61 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL H 101 " --> pdb=" O THR H 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 185 through 187 Processing sheet with id=AC7, first strand: chain 'I' and resid 26 through 29 removed outlier: 3.815A pdb=" N VAL I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N SER I 35 " --> pdb=" O SER I 178 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE I 177 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE I 323 " --> pdb=" O PHE I 273 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 185 through 187 Processing sheet with id=AC9, first strand: chain 'J' and resid 99 through 102 Processing sheet with id=AD1, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AD2, first strand: chain 'J' and resid 248 through 252 removed outlier: 4.477A pdb=" N LYS J 389 " --> pdb=" O HIS J 252 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP J 398 " --> pdb=" O SER J 402 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER J 402 " --> pdb=" O ASP J 398 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 305 through 306 Processing sheet with id=AD4, first strand: chain 'K' and resid 74 through 75 removed outlier: 5.622A pdb=" N GLU K 74 " --> pdb=" O LEU K 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 1030 hydrogen bonds defined for protein. 2856 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 8.90 Time building geometry restraints manager: 7.20 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: 8258 1.34 - 1.46: 4996 1.46 - 1.57: 14958 1.57 - 1.69: 120 1.69 - 1.81: 171 Bond restraints: 28503 Sorted by residual: bond pdb=" N PRO J 331 " pdb=" CD PRO J 331 " ideal model delta sigma weight residual 1.473 1.516 -0.043 1.40e-02 5.10e+03 9.62e+00 bond pdb=" C SER E 12 " pdb=" N PRO E 13 " ideal model delta sigma weight residual 1.334 1.369 -0.035 2.34e-02 1.83e+03 2.28e+00 bond pdb=" C SER F 12 " pdb=" N PRO F 13 " ideal model delta sigma weight residual 1.334 1.365 -0.031 2.34e-02 1.83e+03 1.74e+00 bond pdb=" O5' U C 20 " pdb=" C5' U C 20 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.67e+00 bond pdb=" O5' U C 32 " pdb=" C5' U C 32 " ideal model delta sigma weight residual 1.420 1.439 -0.019 1.50e-02 4.44e+03 1.65e+00 ... (remaining 28498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 38175 2.00 - 3.99: 614 3.99 - 5.99: 80 5.99 - 7.98: 18 7.98 - 9.98: 2 Bond angle restraints: 38889 Sorted by residual: angle pdb=" C THR D 123 " pdb=" N GLU D 124 " pdb=" CA GLU D 124 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 angle pdb=" C GLN F 319 " pdb=" N SER F 320 " pdb=" CA SER F 320 " ideal model delta sigma weight residual 122.83 126.47 -3.64 1.08e+00 8.57e-01 1.14e+01 angle pdb=" C THR A 31 " pdb=" N ALA A 32 " pdb=" CA ALA A 32 " ideal model delta sigma weight residual 121.54 115.45 6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C ASP I 317 " pdb=" N GLU I 318 " pdb=" CA GLU I 318 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" N GLY A 42 " pdb=" CA GLY A 42 " pdb=" C GLY A 42 " ideal model delta sigma weight residual 113.18 105.67 7.51 2.37e+00 1.78e-01 1.01e+01 ... (remaining 38884 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 16131 34.77 - 69.54: 993 69.54 - 104.31: 80 104.31 - 139.08: 1 139.08 - 173.85: 3 Dihedral angle restraints: 17208 sinusoidal: 7483 harmonic: 9725 Sorted by residual: dihedral pdb=" O4' U C 42 " pdb=" C1' U C 42 " pdb=" N1 U C 42 " pdb=" C2 U C 42 " ideal model delta sinusoidal sigma weight residual 200.00 34.90 165.10 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' U C 32 " pdb=" C1' U C 32 " pdb=" N1 U C 32 " pdb=" C2 U C 32 " ideal model delta sinusoidal sigma weight residual 200.00 47.39 152.61 1 1.50e+01 4.44e-03 8.05e+01 dihedral pdb=" O4' U C 2 " pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C2 U C 2 " ideal model delta sinusoidal sigma weight residual -128.00 45.85 -173.85 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 17205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 3009 0.041 - 0.082: 945 0.082 - 0.123: 281 0.123 - 0.164: 47 0.164 - 0.204: 1 Chirality restraints: 4283 Sorted by residual: chirality pdb=" C1' G C 14 " pdb=" O4' G C 14 " pdb=" C2' G C 14 " pdb=" N9 G C 14 " both_signs ideal model delta sigma weight residual False 2.46 2.25 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C2' U C 20 " pdb=" C3' U C 20 " pdb=" O2' U C 20 " pdb=" C1' U C 20 " both_signs ideal model delta sigma weight residual False -2.75 -2.59 -0.16 2.00e-01 2.50e+01 6.63e-01 chirality pdb=" CB VAL H 129 " pdb=" CA VAL H 129 " pdb=" CG1 VAL H 129 " pdb=" CG2 VAL H 129 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.59e-01 ... (remaining 4280 not shown) Planarity restraints: 4830 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 144 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO A 145 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 398 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.62e+00 pdb=" CG ASP J 398 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASP J 398 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP J 398 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 361 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ILE E 361 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE E 361 " -0.015 2.00e-02 2.50e+03 pdb=" N GLY E 362 " -0.014 2.00e-02 2.50e+03 ... (remaining 4827 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 4697 2.77 - 3.30: 24552 3.30 - 3.83: 45788 3.83 - 4.37: 52539 4.37 - 4.90: 92745 Nonbonded interactions: 220321 Sorted by model distance: nonbonded pdb=" ND1 HIS B 135 " pdb=" OP1 U C 55 " model vdw 2.234 3.120 nonbonded pdb=" O ALA H 247 " pdb=" CG2 THR H 251 " model vdw 2.237 3.460 nonbonded pdb=" O LEU D 149 " pdb=" OG1 THR D 165 " model vdw 2.256 3.040 nonbonded pdb=" O LEU J 226 " pdb=" OG1 THR J 230 " model vdw 2.270 3.040 nonbonded pdb=" O CYS J 138 " pdb=" OG1 THR J 142 " model vdw 2.274 3.040 ... (remaining 220316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 1 through 370) selection = chain 'E' selection = (chain 'F' and resid 1 through 370) selection = (chain 'G' and resid 1 through 370) selection = (chain 'H' and resid 1 through 370) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 67.740 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28511 Z= 0.161 Angle : 0.627 9.981 38901 Z= 0.332 Chirality : 0.044 0.204 4283 Planarity : 0.005 0.060 4830 Dihedral : 20.077 173.850 10940 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.14 % Allowed : 35.80 % Favored : 64.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 3337 helix: -0.49 (0.15), residues: 1165 sheet: 0.19 (0.22), residues: 555 loop : -1.80 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP J 159 HIS 0.005 0.001 HIS F 6 PHE 0.016 0.001 PHE F 260 TYR 0.020 0.001 TYR E 360 ARG 0.008 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.18729 ( 1015) hydrogen bonds : angle 6.40923 ( 2890) metal coordination : bond 0.00472 ( 8) metal coordination : angle 2.96261 ( 12) covalent geometry : bond 0.00347 (28503) covalent geometry : angle 0.62488 (38889) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 284 average time/residue: 0.3979 time to fit residues: 178.8624 Evaluate side-chains 279 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 277 time to evaluate : 3.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain G residue 233 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 285 optimal weight: 8.9990 chunk 256 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 87 optimal weight: 30.0000 chunk 172 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 306 optimal weight: 0.4980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 225 GLN ** H 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.128438 restraints weight = 36410.854| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.38 r_work: 0.3333 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28511 Z= 0.153 Angle : 0.546 8.318 38901 Z= 0.285 Chirality : 0.041 0.196 4283 Planarity : 0.004 0.050 4830 Dihedral : 12.812 177.051 4563 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.65 % Allowed : 32.36 % Favored : 63.98 % 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: -0.92 (0.15), residues: 3337 helix: 0.28 (0.16), residues: 1161 sheet: 0.32 (0.22), residues: 537 loop : -1.61 (0.15), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 156 HIS 0.004 0.001 HIS F 6 PHE 0.014 0.001 PHE G 219 TYR 0.013 0.001 TYR D 337 ARG 0.007 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 1015) hydrogen bonds : angle 4.80393 ( 2890) metal coordination : bond 0.00488 ( 8) metal coordination : angle 2.86151 ( 12) covalent geometry : bond 0.00348 (28503) covalent geometry : angle 0.54375 (38889) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 298 time to evaluate : 3.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 TYR cc_start: 0.6883 (m-80) cc_final: 0.6639 (m-80) REVERT: A 232 ASP cc_start: 0.7932 (p0) cc_final: 0.7705 (p0) REVERT: D 222 ASP cc_start: 0.8623 (t70) cc_final: 0.8372 (t0) REVERT: E 1 MET cc_start: 0.7620 (ttp) cc_final: 0.7377 (ttp) REVERT: F 148 MET cc_start: 0.5005 (tpt) cc_final: 0.4770 (tpt) REVERT: G 4 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8370 (mm-30) REVERT: G 148 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: G 233 ASP cc_start: 0.5912 (m-30) cc_final: 0.5684 (m-30) REVERT: G 337 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6742 (m-10) REVERT: G 352 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: H 4 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7915 (mm-30) REVERT: H 47 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8045 (ptt-90) REVERT: H 209 MET cc_start: 0.8809 (mtt) cc_final: 0.8580 (mtm) REVERT: I 298 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: J 230 THR cc_start: 0.8609 (m) cc_final: 0.8168 (p) REVERT: J 262 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: J 363 ARG cc_start: 0.7849 (ptt-90) cc_final: 0.7609 (ptt-90) REVERT: K 92 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7255 (mt) outliers start: 103 outliers final: 50 residues processed: 378 average time/residue: 0.4007 time to fit residues: 239.4570 Evaluate side-chains 334 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 275 time to evaluate : 3.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain F residue 149 LEU Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 4 GLU Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain K residue 17 GLU Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 101 optimal weight: 5.9990 chunk 328 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 322 optimal weight: 6.9990 chunk 220 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 225 GLN E 229 ASN F 82 GLN F 135 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 131 ASN I 172 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.124095 restraints weight = 36908.504| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.42 r_work: 0.3274 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 28511 Z= 0.308 Angle : 0.663 8.944 38901 Z= 0.346 Chirality : 0.046 0.248 4283 Planarity : 0.005 0.057 4830 Dihedral : 12.831 169.494 4559 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 5.14 % Allowed : 31.90 % Favored : 62.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3337 helix: 0.12 (0.15), residues: 1162 sheet: 0.13 (0.22), residues: 535 loop : -1.73 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 156 HIS 0.007 0.001 HIS F 6 PHE 0.021 0.002 PHE G 219 TYR 0.024 0.002 TYR F 316 ARG 0.005 0.001 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.05420 ( 1015) hydrogen bonds : angle 4.95073 ( 2890) metal coordination : bond 0.00762 ( 8) metal coordination : angle 3.91224 ( 12) covalent geometry : bond 0.00728 (28503) covalent geometry : angle 0.66003 (38889) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 288 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 240 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7690 (t70) REVERT: D 222 ASP cc_start: 0.8769 (t70) cc_final: 0.8539 (t0) REVERT: E 1 MET cc_start: 0.7609 (ttp) cc_final: 0.7353 (ttp) REVERT: E 19 ASP cc_start: 0.8402 (t70) cc_final: 0.8170 (t70) REVERT: E 76 GLU cc_start: 0.3407 (OUTLIER) cc_final: 0.2496 (pm20) REVERT: E 254 SER cc_start: 0.8646 (p) cc_final: 0.8363 (p) REVERT: F 82 GLN cc_start: 0.4970 (OUTLIER) cc_final: 0.4217 (mp-120) REVERT: F 148 MET cc_start: 0.5516 (tpt) cc_final: 0.5272 (tpt) REVERT: F 159 LYS cc_start: 0.5203 (OUTLIER) cc_final: 0.4941 (tppt) REVERT: F 337 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: G 148 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8216 (tmm) REVERT: G 337 TYR cc_start: 0.7350 (OUTLIER) cc_final: 0.6956 (m-10) REVERT: G 352 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: H 4 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: H 47 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8180 (ptt-90) REVERT: H 156 LYS cc_start: 0.3075 (OUTLIER) cc_final: 0.2496 (mtmt) REVERT: I 298 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: J 262 GLN cc_start: 0.7429 (OUTLIER) cc_final: 0.6664 (mp10) REVERT: J 319 GLU cc_start: 0.5975 (tm-30) cc_final: 0.5686 (tm-30) REVERT: K 92 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7339 (mt) REVERT: K 96 LYS cc_start: 0.7560 (mmtp) cc_final: 0.7302 (mmmm) outliers start: 145 outliers final: 83 residues processed: 404 average time/residue: 0.4058 time to fit residues: 254.9747 Evaluate side-chains 371 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 274 time to evaluate : 2.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 179 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 159 LYS Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 337 TYR Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 354 VAL Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 250 LYS Chi-restraints excluded: chain H residue 279 SER Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 254 SER Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 346 THR Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 113 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 321 optimal weight: 2.9990 chunk 319 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 188 optimal weight: 0.0970 chunk 157 optimal weight: 0.2980 chunk 116 optimal weight: 6.9990 chunk 318 optimal weight: 1.9990 chunk 65 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 295 optimal weight: 7.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN E 17 ASN E 86 ASN ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 ASN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.172371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127282 restraints weight = 36921.903| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.41 r_work: 0.3324 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28511 Z= 0.135 Angle : 0.535 8.607 38901 Z= 0.278 Chirality : 0.041 0.211 4283 Planarity : 0.004 0.050 4830 Dihedral : 12.668 169.537 4559 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 3.72 % Allowed : 33.11 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.15), residues: 3337 helix: 0.54 (0.16), residues: 1159 sheet: 0.22 (0.22), residues: 545 loop : -1.66 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 156 HIS 0.006 0.001 HIS I 204 PHE 0.014 0.001 PHE F 260 TYR 0.012 0.001 TYR F 316 ARG 0.010 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1015) hydrogen bonds : angle 4.54456 ( 2890) metal coordination : bond 0.00417 ( 8) metal coordination : angle 2.78227 ( 12) covalent geometry : bond 0.00306 (28503) covalent geometry : angle 0.53236 (38889) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 295 time to evaluate : 2.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6703 (ptt180) REVERT: A 232 ASP cc_start: 0.8176 (p0) cc_final: 0.7863 (p0) REVERT: D 165 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7895 (t) REVERT: D 222 ASP cc_start: 0.8641 (t70) cc_final: 0.8388 (t0) REVERT: E 1 MET cc_start: 0.7539 (ttp) cc_final: 0.7257 (ttp) REVERT: E 76 GLU cc_start: 0.3344 (OUTLIER) cc_final: 0.2415 (pm20) REVERT: F 103 MET cc_start: 0.7265 (ptm) cc_final: 0.7029 (ppp) REVERT: F 131 ASN cc_start: 0.7310 (OUTLIER) cc_final: 0.7074 (t0) REVERT: F 148 MET cc_start: 0.5565 (tpt) cc_final: 0.5345 (tpt) REVERT: G 148 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8182 (tmm) REVERT: G 337 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: G 352 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: H 4 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7877 (mm-30) REVERT: H 209 MET cc_start: 0.8795 (mtt) cc_final: 0.8576 (mtm) REVERT: J 230 THR cc_start: 0.8664 (m) cc_final: 0.8136 (p) REVERT: J 259 MET cc_start: 0.6570 (tpp) cc_final: 0.5994 (ttp) REVERT: J 262 GLN cc_start: 0.7451 (OUTLIER) cc_final: 0.6697 (mp10) REVERT: J 319 GLU cc_start: 0.5865 (tm-30) cc_final: 0.5582 (tm-30) REVERT: J 445 LYS cc_start: 0.7167 (tttt) cc_final: 0.6412 (tttt) REVERT: K 92 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7295 (mt) outliers start: 105 outliers final: 63 residues processed: 378 average time/residue: 0.4188 time to fit residues: 250.2229 Evaluate side-chains 353 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 280 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 128 GLN Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 174 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 261 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 251 optimal weight: 8.9990 chunk 67 optimal weight: 6.9990 chunk 290 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 246 optimal weight: 0.0570 chunk 66 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.172514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127039 restraints weight = 36570.617| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.43 r_work: 0.3315 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28511 Z= 0.146 Angle : 0.535 8.693 38901 Z= 0.277 Chirality : 0.041 0.201 4283 Planarity : 0.004 0.046 4830 Dihedral : 12.599 167.031 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.50 % Allowed : 32.22 % Favored : 63.28 % 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: -0.69 (0.15), residues: 3337 helix: 0.69 (0.16), residues: 1158 sheet: 0.28 (0.22), residues: 545 loop : -1.61 (0.15), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 156 HIS 0.004 0.001 HIS I 204 PHE 0.012 0.001 PHE G 219 TYR 0.012 0.001 TYR F 337 ARG 0.006 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 1015) hydrogen bonds : angle 4.43847 ( 2890) metal coordination : bond 0.00719 ( 8) metal coordination : angle 3.76020 ( 12) covalent geometry : bond 0.00338 (28503) covalent geometry : angle 0.53100 (38889) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 289 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.6766 (ptt180) REVERT: A 232 ASP cc_start: 0.8181 (p0) cc_final: 0.7860 (p0) REVERT: D 165 THR cc_start: 0.8406 (OUTLIER) cc_final: 0.7863 (t) REVERT: D 222 ASP cc_start: 0.8667 (t70) cc_final: 0.8400 (t0) REVERT: E 1 MET cc_start: 0.7581 (ttp) cc_final: 0.7306 (ttp) REVERT: E 76 GLU cc_start: 0.3341 (OUTLIER) cc_final: 0.2401 (pm20) REVERT: F 82 GLN cc_start: 0.4769 (OUTLIER) cc_final: 0.3888 (mp-120) REVERT: F 131 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7062 (t0) REVERT: F 148 MET cc_start: 0.5677 (tpt) cc_final: 0.5405 (tpt) REVERT: G 148 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8214 (tmm) REVERT: G 337 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6914 (m-10) REVERT: G 352 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: H 4 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: H 47 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8006 (ptt-90) REVERT: H 60 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8288 (ttp-110) REVERT: H 102 PHE cc_start: 0.8202 (t80) cc_final: 0.7712 (t80) REVERT: H 209 MET cc_start: 0.8828 (mtt) cc_final: 0.8622 (mtm) REVERT: H 295 ASP cc_start: 0.8405 (m-30) cc_final: 0.8161 (m-30) REVERT: J 230 THR cc_start: 0.8683 (m) cc_final: 0.8165 (p) REVERT: J 259 MET cc_start: 0.6543 (tpp) cc_final: 0.6048 (ttp) REVERT: J 262 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: J 319 GLU cc_start: 0.5881 (tm-30) cc_final: 0.5585 (tm-30) REVERT: J 445 LYS cc_start: 0.7223 (tttt) cc_final: 0.6591 (tttt) REVERT: K 92 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7388 (mt) REVERT: K 161 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7781 (mp) outliers start: 127 outliers final: 75 residues processed: 393 average time/residue: 0.4392 time to fit residues: 272.6604 Evaluate side-chains 371 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 283 time to evaluate : 2.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 181 ILE Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 98 optimal weight: 9.9990 chunk 212 optimal weight: 0.5980 chunk 58 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 286 optimal weight: 20.0000 chunk 215 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 131 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 ASN F 70 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.172248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.127030 restraints weight = 36752.914| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.46 r_work: 0.3316 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 28511 Z= 0.158 Angle : 0.538 8.907 38901 Z= 0.278 Chirality : 0.041 0.201 4283 Planarity : 0.004 0.043 4830 Dihedral : 12.568 166.813 4559 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.71 % Allowed : 32.05 % Favored : 63.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3337 helix: 0.73 (0.16), residues: 1157 sheet: 0.29 (0.22), residues: 545 loop : -1.60 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 156 HIS 0.005 0.001 HIS F 6 PHE 0.013 0.001 PHE G 219 TYR 0.013 0.001 TYR F 316 ARG 0.008 0.000 ARG J 363 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 1015) hydrogen bonds : angle 4.42444 ( 2890) metal coordination : bond 0.00537 ( 8) metal coordination : angle 3.58290 ( 12) covalent geometry : bond 0.00366 (28503) covalent geometry : angle 0.53489 (38889) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 292 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6984 (OUTLIER) cc_final: 0.6710 (ptt180) REVERT: A 232 ASP cc_start: 0.8205 (p0) cc_final: 0.7872 (p0) REVERT: D 56 LEU cc_start: 0.7113 (OUTLIER) cc_final: 0.6685 (tp) REVERT: D 102 PHE cc_start: 0.8127 (t80) cc_final: 0.7927 (t80) REVERT: D 165 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.7849 (t) REVERT: D 222 ASP cc_start: 0.8723 (t70) cc_final: 0.8410 (t0) REVERT: E 1 MET cc_start: 0.7461 (ttp) cc_final: 0.7195 (ttp) REVERT: E 76 GLU cc_start: 0.3321 (OUTLIER) cc_final: 0.2394 (pm20) REVERT: F 131 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6985 (t0) REVERT: F 148 MET cc_start: 0.5812 (tpt) cc_final: 0.5402 (tpt) REVERT: F 171 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9097 (tp) REVERT: G 148 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8237 (tmm) REVERT: G 337 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: G 352 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6467 (mp0) REVERT: H 4 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7878 (mm-30) REVERT: H 47 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: H 102 PHE cc_start: 0.8134 (t80) cc_final: 0.7801 (t80) REVERT: H 156 LYS cc_start: 0.3468 (OUTLIER) cc_final: 0.2870 (mtmt) REVERT: H 209 MET cc_start: 0.8824 (mtt) cc_final: 0.8615 (mtm) REVERT: H 295 ASP cc_start: 0.8404 (m-30) cc_final: 0.8152 (m-30) REVERT: J 230 THR cc_start: 0.8685 (m) cc_final: 0.8170 (p) REVERT: J 259 MET cc_start: 0.6558 (tpp) cc_final: 0.6068 (ttp) REVERT: J 262 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.6674 (mp10) REVERT: J 319 GLU cc_start: 0.5915 (tm-30) cc_final: 0.5605 (tm-30) REVERT: J 445 LYS cc_start: 0.7267 (tttt) cc_final: 0.6713 (tttt) REVERT: K 92 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7384 (mt) REVERT: K 161 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7778 (mp) outliers start: 133 outliers final: 92 residues processed: 402 average time/residue: 0.4068 time to fit residues: 257.3563 Evaluate side-chains 388 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 281 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 120 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 279 optimal weight: 8.9990 chunk 67 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 276 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 105 optimal weight: 0.0870 chunk 313 optimal weight: 10.0000 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 GLN F 82 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.171903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126425 restraints weight = 36501.398| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.47 r_work: 0.3314 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28511 Z= 0.164 Angle : 0.545 8.925 38901 Z= 0.282 Chirality : 0.042 0.202 4283 Planarity : 0.004 0.042 4830 Dihedral : 12.552 166.980 4559 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 4.82 % Allowed : 31.73 % Favored : 63.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3337 helix: 0.74 (0.16), residues: 1157 sheet: 0.29 (0.22), residues: 545 loop : -1.59 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 159 HIS 0.005 0.001 HIS F 6 PHE 0.013 0.001 PHE G 219 TYR 0.013 0.001 TYR F 316 ARG 0.004 0.000 ARG H 62 Details of bonding type rmsd hydrogen bonds : bond 0.03917 ( 1015) hydrogen bonds : angle 4.41315 ( 2890) metal coordination : bond 0.00495 ( 8) metal coordination : angle 3.42433 ( 12) covalent geometry : bond 0.00383 (28503) covalent geometry : angle 0.54180 (38889) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 289 time to evaluate : 2.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6599 (ptt180) REVERT: A 232 ASP cc_start: 0.8254 (p0) cc_final: 0.7912 (p0) REVERT: D 56 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6741 (tp) REVERT: D 165 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.7823 (t) REVERT: D 222 ASP cc_start: 0.8716 (t70) cc_final: 0.8402 (t0) REVERT: E 1 MET cc_start: 0.7457 (ttp) cc_final: 0.7188 (ttp) REVERT: E 76 GLU cc_start: 0.3269 (OUTLIER) cc_final: 0.2380 (pm20) REVERT: F 82 GLN cc_start: 0.4718 (OUTLIER) cc_final: 0.3821 (mp-120) REVERT: F 148 MET cc_start: 0.5875 (tpt) cc_final: 0.5299 (tpt) REVERT: F 171 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9112 (tp) REVERT: G 148 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: G 337 TYR cc_start: 0.7215 (OUTLIER) cc_final: 0.6912 (m-10) REVERT: G 352 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: H 4 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7835 (mm-30) REVERT: H 47 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8038 (ptt-90) REVERT: H 102 PHE cc_start: 0.8089 (t80) cc_final: 0.7747 (t80) REVERT: H 156 LYS cc_start: 0.3490 (OUTLIER) cc_final: 0.2968 (mtmt) REVERT: H 209 MET cc_start: 0.8834 (mtt) cc_final: 0.8615 (mtm) REVERT: H 295 ASP cc_start: 0.8368 (m-30) cc_final: 0.8125 (m-30) REVERT: J 230 THR cc_start: 0.8703 (m) cc_final: 0.8177 (p) REVERT: J 259 MET cc_start: 0.6520 (tpp) cc_final: 0.6137 (ttp) REVERT: J 262 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: J 319 GLU cc_start: 0.5971 (tm-30) cc_final: 0.5658 (tm-30) REVERT: J 418 ASN cc_start: 0.7166 (p0) cc_final: 0.6755 (p0) REVERT: J 445 LYS cc_start: 0.7282 (tttt) cc_final: 0.6789 (tttt) REVERT: K 92 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7335 (mt) REVERT: K 161 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7725 (mp) outliers start: 136 outliers final: 106 residues processed: 400 average time/residue: 0.3972 time to fit residues: 250.0801 Evaluate side-chains 402 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 281 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 158 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 347 ILE Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain G residue 365 LYS Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 19 ASP Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 241 ILE Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 335 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 222 optimal weight: 20.0000 chunk 183 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 173 optimal weight: 0.8980 chunk 116 optimal weight: 20.0000 chunk 27 optimal weight: 0.4980 chunk 202 optimal weight: 0.8980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 70 GLN ** F 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.173190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127423 restraints weight = 36518.842| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.69 r_work: 0.3322 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28511 Z= 0.128 Angle : 0.522 8.768 38901 Z= 0.270 Chirality : 0.041 0.191 4283 Planarity : 0.004 0.042 4830 Dihedral : 12.509 166.744 4559 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.57 % Allowed : 32.05 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3337 helix: 0.84 (0.16), residues: 1159 sheet: 0.37 (0.22), residues: 537 loop : -1.55 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 159 HIS 0.005 0.001 HIS G 204 PHE 0.013 0.001 PHE F 260 TYR 0.011 0.001 TYR A 283 ARG 0.008 0.000 ARG J 363 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 1015) hydrogen bonds : angle 4.32187 ( 2890) metal coordination : bond 0.00413 ( 8) metal coordination : angle 3.18088 ( 12) covalent geometry : bond 0.00291 (28503) covalent geometry : angle 0.51948 (38889) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 302 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6564 (ptt180) REVERT: A 232 ASP cc_start: 0.8144 (p0) cc_final: 0.7803 (p0) REVERT: B 203 GLU cc_start: 0.7500 (tt0) cc_final: 0.7238 (mt-10) REVERT: B 212 GLN cc_start: 0.4501 (OUTLIER) cc_final: 0.4232 (tm-30) REVERT: D 56 LEU cc_start: 0.6962 (OUTLIER) cc_final: 0.6584 (tp) REVERT: D 165 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7759 (t) REVERT: D 222 ASP cc_start: 0.8625 (t70) cc_final: 0.8272 (t0) REVERT: D 312 ARG cc_start: 0.6612 (mmm160) cc_final: 0.6337 (mmm160) REVERT: E 1 MET cc_start: 0.7403 (ttp) cc_final: 0.7108 (ttp) REVERT: E 76 GLU cc_start: 0.3149 (OUTLIER) cc_final: 0.2320 (pm20) REVERT: E 127 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6698 (tm-30) REVERT: E 161 LYS cc_start: 0.6831 (mmmt) cc_final: 0.5882 (ptmm) REVERT: F 131 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6983 (t0) REVERT: F 148 MET cc_start: 0.5943 (tpt) cc_final: 0.5275 (tpt) REVERT: G 337 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.6855 (m-10) REVERT: G 352 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: H 4 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8011 (mm-30) REVERT: H 47 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7974 (ptt-90) REVERT: H 156 LYS cc_start: 0.3385 (OUTLIER) cc_final: 0.2908 (mtmt) REVERT: H 209 MET cc_start: 0.8811 (mtt) cc_final: 0.8582 (mtm) REVERT: H 295 ASP cc_start: 0.8230 (m-30) cc_final: 0.7958 (m-30) REVERT: J 230 THR cc_start: 0.8609 (m) cc_final: 0.8076 (p) REVERT: J 259 MET cc_start: 0.6391 (tpp) cc_final: 0.6041 (ttp) REVERT: J 262 GLN cc_start: 0.7273 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: J 319 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5593 (tm-30) REVERT: J 328 GLU cc_start: 0.6341 (pp20) cc_final: 0.6021 (pp20) REVERT: J 418 ASN cc_start: 0.7030 (p0) cc_final: 0.6638 (p0) REVERT: J 445 LYS cc_start: 0.7262 (tttt) cc_final: 0.6807 (tttt) REVERT: K 54 ARG cc_start: 0.8867 (mmm160) cc_final: 0.8657 (mmm-85) REVERT: K 92 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7315 (mt) REVERT: K 124 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.7559 (mtt) REVERT: K 161 ILE cc_start: 0.7926 (OUTLIER) cc_final: 0.7676 (mp) outliers start: 129 outliers final: 91 residues processed: 409 average time/residue: 0.4112 time to fit residues: 262.8153 Evaluate side-chains 393 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 113 ASN Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 212 GLN Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 240 THR Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 17 ASN Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 332 ARG Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 SER Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 279 SER Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 450 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 50 GLN Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 161 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 83 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 216 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 173 optimal weight: 0.2980 chunk 320 optimal weight: 0.9990 chunk 194 optimal weight: 9.9990 chunk 274 optimal weight: 0.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 17 ASN F 70 GLN F 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.175224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129809 restraints weight = 36579.712| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.61 r_work: 0.3360 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28511 Z= 0.100 Angle : 0.513 9.417 38901 Z= 0.263 Chirality : 0.040 0.171 4283 Planarity : 0.003 0.043 4830 Dihedral : 12.431 165.791 4559 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.69 % Allowed : 33.00 % Favored : 63.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 3337 helix: 0.96 (0.16), residues: 1173 sheet: 0.50 (0.22), residues: 533 loop : -1.51 (0.16), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 159 HIS 0.004 0.001 HIS G 204 PHE 0.012 0.001 PHE I 244 TYR 0.011 0.001 TYR B 29 ARG 0.007 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.03213 ( 1015) hydrogen bonds : angle 4.16258 ( 2890) metal coordination : bond 0.00332 ( 8) metal coordination : angle 2.96175 ( 12) covalent geometry : bond 0.00222 (28503) covalent geometry : angle 0.51028 (38889) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 295 time to evaluate : 2.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6993 (OUTLIER) cc_final: 0.6732 (ptt180) REVERT: A 232 ASP cc_start: 0.8002 (p0) cc_final: 0.7754 (p0) REVERT: B 203 GLU cc_start: 0.7465 (tt0) cc_final: 0.7200 (mt-10) REVERT: D 222 ASP cc_start: 0.8601 (t70) cc_final: 0.8253 (t0) REVERT: D 312 ARG cc_start: 0.6634 (mmm160) cc_final: 0.6421 (mmm160) REVERT: E 1 MET cc_start: 0.7530 (ttp) cc_final: 0.7258 (ttp) REVERT: E 76 GLU cc_start: 0.3204 (OUTLIER) cc_final: 0.2366 (pm20) REVERT: F 82 GLN cc_start: 0.4696 (OUTLIER) cc_final: 0.3866 (mp-120) REVERT: F 131 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.7083 (t0) REVERT: F 148 MET cc_start: 0.5833 (tpt) cc_final: 0.5438 (tpt) REVERT: G 337 TYR cc_start: 0.7115 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: G 352 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: H 4 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: H 47 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7927 (ptt-90) REVERT: H 209 MET cc_start: 0.8778 (mtt) cc_final: 0.8561 (mtm) REVERT: J 230 THR cc_start: 0.8616 (m) cc_final: 0.8138 (p) REVERT: J 259 MET cc_start: 0.6374 (tpp) cc_final: 0.6103 (ttp) REVERT: J 262 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6988 (mp10) REVERT: J 319 GLU cc_start: 0.5919 (tm-30) cc_final: 0.5607 (tm-30) REVERT: J 328 GLU cc_start: 0.6312 (pp20) cc_final: 0.6015 (pp20) REVERT: J 418 ASN cc_start: 0.7051 (p0) cc_final: 0.6664 (p0) REVERT: J 445 LYS cc_start: 0.7367 (tttt) cc_final: 0.6916 (tttt) REVERT: K 92 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7279 (mt) REVERT: K 124 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7466 (mtt) outliers start: 104 outliers final: 76 residues processed: 383 average time/residue: 0.4084 time to fit residues: 243.2208 Evaluate side-chains 371 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 284 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 268 ILE Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 18 ARG Chi-restraints excluded: chain F residue 82 GLN Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain I residue 294 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 183 optimal weight: 5.9990 chunk 299 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 2 optimal weight: 0.0870 chunk 144 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN F 17 ASN F 70 GLN I 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.173173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127387 restraints weight = 36514.304| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.66 r_work: 0.3325 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 28511 Z= 0.157 Angle : 0.541 9.187 38901 Z= 0.278 Chirality : 0.041 0.185 4283 Planarity : 0.004 0.048 4830 Dihedral : 12.425 166.184 4559 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 3.47 % Allowed : 33.32 % Favored : 63.20 % 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: -0.44 (0.15), residues: 3337 helix: 0.93 (0.16), residues: 1168 sheet: 0.43 (0.22), residues: 545 loop : -1.50 (0.16), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 159 HIS 0.005 0.001 HIS G 204 PHE 0.015 0.001 PHE F 260 TYR 0.016 0.001 TYR B 29 ARG 0.011 0.000 ARG H 60 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 1015) hydrogen bonds : angle 4.25111 ( 2890) metal coordination : bond 0.00452 ( 8) metal coordination : angle 3.12408 ( 12) covalent geometry : bond 0.00367 (28503) covalent geometry : angle 0.53857 (38889) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6674 Ramachandran restraints generated. 3337 Oldfield, 0 Emsley, 3337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 286 time to evaluate : 3.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.6893 (OUTLIER) cc_final: 0.6540 (ptt180) REVERT: A 232 ASP cc_start: 0.8085 (p0) cc_final: 0.7764 (p0) REVERT: D 67 LEU cc_start: 0.7864 (tp) cc_final: 0.6879 (mm) REVERT: D 78 TRP cc_start: 0.6909 (OUTLIER) cc_final: 0.5613 (t60) REVERT: D 165 THR cc_start: 0.8265 (p) cc_final: 0.7749 (t) REVERT: D 222 ASP cc_start: 0.8665 (t70) cc_final: 0.8289 (t0) REVERT: E 1 MET cc_start: 0.7424 (ttp) cc_final: 0.7162 (ttp) REVERT: E 76 GLU cc_start: 0.3052 (OUTLIER) cc_final: 0.2200 (pm20) REVERT: F 131 ASN cc_start: 0.7227 (OUTLIER) cc_final: 0.7022 (t0) REVERT: F 148 MET cc_start: 0.5982 (tpt) cc_final: 0.5526 (tpt) REVERT: G 337 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6827 (m-10) REVERT: G 352 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: H 4 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7922 (mm-30) REVERT: H 47 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.7942 (ptt-90) REVERT: H 156 LYS cc_start: 0.3299 (OUTLIER) cc_final: 0.2782 (mtmt) REVERT: H 295 ASP cc_start: 0.8280 (m-30) cc_final: 0.8004 (m-30) REVERT: J 230 THR cc_start: 0.8620 (m) cc_final: 0.8108 (p) REVERT: J 259 MET cc_start: 0.6374 (tpp) cc_final: 0.6109 (ttp) REVERT: J 262 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6935 (mp10) REVERT: J 319 GLU cc_start: 0.5917 (tm-30) cc_final: 0.5603 (tm-30) REVERT: J 418 ASN cc_start: 0.6971 (p0) cc_final: 0.6576 (p0) REVERT: J 445 LYS cc_start: 0.7348 (tttt) cc_final: 0.6920 (tttt) REVERT: K 92 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7245 (mt) REVERT: K 124 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.7552 (mtt) outliers start: 98 outliers final: 82 residues processed: 371 average time/residue: 0.4346 time to fit residues: 251.7227 Evaluate side-chains 374 residues out of total 2822 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 280 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 313 TYR Chi-restraints excluded: chain A residue 320 GLU Chi-restraints excluded: chain A residue 354 ASP Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 221 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain D residue 63 ARG Chi-restraints excluded: chain D residue 78 TRP Chi-restraints excluded: chain D residue 90 PHE Chi-restraints excluded: chain D residue 103 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 154 LYS Chi-restraints excluded: chain D residue 210 PHE Chi-restraints excluded: chain D residue 291 VAL Chi-restraints excluded: chain D residue 305 SER Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 323 ILE Chi-restraints excluded: chain D residue 350 LEU Chi-restraints excluded: chain D residue 364 PHE Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 339 HIS Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 17 ASN Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 45 SER Chi-restraints excluded: chain F residue 131 ASN Chi-restraints excluded: chain F residue 178 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 305 SER Chi-restraints excluded: chain F residue 364 PHE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 97 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 227 VAL Chi-restraints excluded: chain G residue 251 THR Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 337 TYR Chi-restraints excluded: chain G residue 341 LYS Chi-restraints excluded: chain G residue 352 GLU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 47 ARG Chi-restraints excluded: chain H residue 94 ASP Chi-restraints excluded: chain H residue 156 LYS Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 297 VAL Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 323 ILE Chi-restraints excluded: chain H residue 344 SER Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 167 VAL Chi-restraints excluded: chain I residue 186 ILE Chi-restraints excluded: chain I residue 205 ILE Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 275 ASN Chi-restraints excluded: chain I residue 293 GLU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 93 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain J residue 262 GLN Chi-restraints excluded: chain J residue 336 LEU Chi-restraints excluded: chain J residue 356 ILE Chi-restraints excluded: chain J residue 405 ILE Chi-restraints excluded: chain J residue 417 THR Chi-restraints excluded: chain J residue 484 THR Chi-restraints excluded: chain K residue 88 ILE Chi-restraints excluded: chain K residue 91 LYS Chi-restraints excluded: chain K residue 92 LEU Chi-restraints excluded: chain K residue 124 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 338 random chunks: chunk 287 optimal weight: 20.0000 chunk 20 optimal weight: 0.8980 chunk 265 optimal weight: 5.9990 chunk 238 optimal weight: 10.0000 chunk 314 optimal weight: 0.7980 chunk 172 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 272 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 70 GLN F 82 GLN G 17 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.175409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130870 restraints weight = 36609.871| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.38 r_work: 0.3369 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28511 Z= 0.099 Angle : 0.512 9.640 38901 Z= 0.262 Chirality : 0.040 0.169 4283 Planarity : 0.003 0.042 4830 Dihedral : 12.390 165.888 4559 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.08 % Allowed : 33.82 % Favored : 63.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.15), residues: 3337 helix: 1.05 (0.16), residues: 1174 sheet: 0.51 (0.22), residues: 531 loop : -1.49 (0.16), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 159 HIS 0.004 0.000 HIS G 204 PHE 0.012 0.001 PHE I 244 TYR 0.013 0.001 TYR E 316 ARG 0.010 0.000 ARG F 18 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 1015) hydrogen bonds : angle 4.10432 ( 2890) metal coordination : bond 0.00326 ( 8) metal coordination : angle 2.92472 ( 12) covalent geometry : bond 0.00217 (28503) covalent geometry : angle 0.50931 (38889) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18995.78 seconds wall clock time: 331 minutes 6.98 seconds (19866.98 seconds total)