Starting phenix.real_space_refine on Thu Mar 5 20:21:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trj_26098/03_2026/7trj_26098.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 16062 2.51 5 N 4372 2.21 5 O 4614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 152 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25190 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3210 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 395} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2571 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "G" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2203 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 1861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1861 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 11, 'TRANS': 224} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Restraints were copied for chains: B, C, F, H, J Time building chain proxies: 5.73, per 1000 atoms: 0.23 Number of scatterers: 25190 At special positions: 0 Unit cell: (141.95, 132.765, 166.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 142 16.00 O 4614 8.00 N 4372 7.00 C 16062 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: 1.97 Conformation dependent library (CDL) restraints added in 869.4 milliseconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 32 sheets defined 45.8% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 130 through 142 Processing helix chain 'A' and resid 161 through 175 Processing helix chain 'A' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.751A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA A 311 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'D' and resid 9 through 25 Processing helix chain 'D' and resid 30 through 48 Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET D 148 " --> pdb=" O LEU D 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 180 Processing helix chain 'D' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 Processing helix chain 'D' and resid 250 through 262 Processing helix chain 'D' and resid 270 through 274 removed outlier: 3.564A pdb=" N LYS D 273 " --> pdb=" O PRO D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU D 303 " --> pdb=" O GLY D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 334 No H-bonds generated for 'chain 'D' and resid 332 through 334' Processing helix chain 'D' and resid 335 through 344 Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS D 349 " --> pdb=" O PRO D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN E 194 " --> pdb=" O SER E 191 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 191 through 196' Processing helix chain 'E' and resid 204 through 216 Processing helix chain 'E' and resid 221 through 240 Processing helix chain 'E' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 270 through 286 Processing helix chain 'E' and resid 292 through 312 Processing helix chain 'E' and resid 312 through 324 Processing helix chain 'E' and resid 339 through 352 Processing helix chain 'E' and resid 368 through 380 removed outlier: 4.085A pdb=" N THR E 372 " --> pdb=" O GLU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 395 Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 420 through 430 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 459 through 464 Processing helix chain 'E' and resid 493 through 497 Processing helix chain 'E' and resid 508 through 510 No H-bonds generated for 'chain 'E' and resid 508 through 510' Processing helix chain 'E' and resid 511 through 519 removed outlier: 3.556A pdb=" N VAL E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS E 519 " --> pdb=" O VAL E 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 17 removed outlier: 4.204A pdb=" N ASP G 17 " --> pdb=" O GLN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.585A pdb=" N LYS G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 60 Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.868A pdb=" N SER G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU G 106 " --> pdb=" O ARG G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 116 Processing helix chain 'G' and resid 117 through 119 No H-bonds generated for 'chain 'G' and resid 117 through 119' Processing helix chain 'G' and resid 131 through 144 Processing helix chain 'G' and resid 160 through 170 Processing helix chain 'G' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL G 183 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 222 Processing helix chain 'G' and resid 231 through 235 removed outlier: 3.850A pdb=" N LYS G 234 " --> pdb=" O GLU G 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 removed outlier: 3.516A pdb=" N LYS G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 281 Processing helix chain 'G' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP G 298 " --> pdb=" O SER G 294 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 Processing helix chain 'I' and resid 34 through 35 No H-bonds generated for 'chain 'I' and resid 34 through 35' Processing helix chain 'I' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 93 Processing helix chain 'I' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU I 120 " --> pdb=" O GLU I 116 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 190 Processing helix chain 'I' and resid 209 through 218 Processing helix chain 'I' and resid 223 through 236 removed outlier: 5.366A pdb=" N ILE I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Proline residue: I 230 - end of helix Processing helix chain 'I' and resid 262 through 266 Processing helix chain 'I' and resid 315 through 334 Proline residue: I 327 - end of helix removed outlier: 3.741A pdb=" N ALA I 332 " --> pdb=" O LYS I 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 62 removed outlier: 3.726A pdb=" N ASP B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 68 removed outlier: 3.670A pdb=" N LEU B 67 " --> pdb=" O PRO B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 87 removed outlier: 3.523A pdb=" N TYR B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 109 removed outlier: 3.534A pdb=" N ILE B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 130 through 142 Processing helix chain 'B' and resid 161 through 175 Processing helix chain 'B' and resid 253 through 263 removed outlier: 3.699A pdb=" N ALA B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.752A pdb=" N PHE B 272 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.574A pdb=" N ALA B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.518A pdb=" N GLN C 72 " --> pdb=" O MET C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 128 through 153 removed outlier: 3.586A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 180 Processing helix chain 'C' and resid 199 through 209 removed outlier: 3.722A pdb=" N MET C 203 " --> pdb=" O GLN C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 250 through 262 Processing helix chain 'C' and resid 270 through 274 removed outlier: 3.565A pdb=" N LYS C 273 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 305 removed outlier: 3.813A pdb=" N LEU C 303 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.680A pdb=" N LEU C 320 " --> pdb=" O PRO C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 334 No H-bonds generated for 'chain 'C' and resid 332 through 334' Processing helix chain 'C' and resid 335 through 344 Processing helix chain 'C' and resid 345 through 349 removed outlier: 3.611A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 196 removed outlier: 3.827A pdb=" N GLN F 194 " --> pdb=" O SER F 191 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 195 " --> pdb=" O LEU F 192 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET F 196 " --> pdb=" O THR F 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 196' Processing helix chain 'F' and resid 204 through 216 Processing helix chain 'F' and resid 221 through 240 Processing helix chain 'F' and resid 247 through 267 removed outlier: 4.441A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 270 through 286 Processing helix chain 'F' and resid 292 through 312 Processing helix chain 'F' and resid 312 through 324 Processing helix chain 'F' and resid 339 through 352 Processing helix chain 'F' and resid 368 through 380 removed outlier: 4.086A pdb=" N THR F 372 " --> pdb=" O GLU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 395 Processing helix chain 'F' and resid 396 through 398 No H-bonds generated for 'chain 'F' and resid 396 through 398' Processing helix chain 'F' and resid 420 through 430 Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 459 through 464 Processing helix chain 'F' and resid 493 through 497 Processing helix chain 'F' and resid 508 through 510 No H-bonds generated for 'chain 'F' and resid 508 through 510' Processing helix chain 'F' and resid 511 through 519 removed outlier: 3.555A pdb=" N VAL F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS F 519 " --> pdb=" O VAL F 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 17 removed outlier: 4.205A pdb=" N ASP H 17 " --> pdb=" O GLN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 21 through 35 removed outlier: 3.584A pdb=" N LYS H 35 " --> pdb=" O LEU H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 60 Processing helix chain 'H' and resid 62 through 81 removed outlier: 3.867A pdb=" N SER H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 106 removed outlier: 3.626A pdb=" N LEU H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 116 Processing helix chain 'H' and resid 117 through 119 No H-bonds generated for 'chain 'H' and resid 117 through 119' Processing helix chain 'H' and resid 131 through 144 Processing helix chain 'H' and resid 160 through 170 Processing helix chain 'H' and resid 179 through 183 removed outlier: 4.047A pdb=" N VAL H 183 " --> pdb=" O ASP H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 222 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.849A pdb=" N LYS H 234 " --> pdb=" O GLU H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 removed outlier: 3.515A pdb=" N LYS H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 277 through 281 Processing helix chain 'H' and resid 294 through 304 removed outlier: 3.588A pdb=" N ASP H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 Processing helix chain 'J' and resid 34 through 35 No H-bonds generated for 'chain 'J' and resid 34 through 35' Processing helix chain 'J' and resid 36 through 44 removed outlier: 3.539A pdb=" N LEU J 40 " --> pdb=" O ILE J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 85 through 93 Processing helix chain 'J' and resid 114 through 124 removed outlier: 4.169A pdb=" N LEU J 120 " --> pdb=" O GLU J 116 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 190 Processing helix chain 'J' and resid 209 through 218 Processing helix chain 'J' and resid 223 through 236 removed outlier: 5.365A pdb=" N ILE J 229 " --> pdb=" O ARG J 225 " (cutoff:3.500A) Proline residue: J 230 - end of helix Processing helix chain 'J' and resid 262 through 266 Processing helix chain 'J' and resid 315 through 334 Proline residue: J 327 - end of helix removed outlier: 3.741A pdb=" N ALA J 332 " --> pdb=" O LYS J 328 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR A 91 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE A 123 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL A 93 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR A 152 " --> pdb=" O HIS A 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS A 248 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N CYS A 247 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N LYS A 186 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 249 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N MET A 181 " --> pdb=" O HIS A 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS A 290 " --> pdb=" O MET A 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET A 183 " --> pdb=" O HIS A 290 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR A 292 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE A 185 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 Processing sheet with id=AA3, first strand: chain 'A' and resid 212 through 217 removed outlier: 6.623A pdb=" N VAL A 212 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ASP A 206 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 238 " --> pdb=" O PHE I 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 223 through 227 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLN A 407 " --> pdb=" O LEU A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL A 378 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR A 395 " --> pdb=" O LEU A 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.785A pdb=" N ARG A 401 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU A 418 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL A 430 " --> pdb=" O ILE A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER D 326 " --> pdb=" O GLY D 329 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU D 265 " --> pdb=" O LEU D 323 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE D 325 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 267 " --> pdb=" O ILE D 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS D 268 " --> pdb=" O VAL D 232 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE D 234 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU D 163 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N ILE D 190 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR D 167 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR D 214 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 238 through 239 removed outlier: 3.761A pdb=" N THR D 238 " --> pdb=" O ARG D 246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 307 through 308 removed outlier: 6.279A pdb=" N SER D 307 " --> pdb=" O TYR E 385 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU E 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E 333 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL E 361 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 335 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR E 336 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N GLY E 404 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL E 401 " --> pdb=" O LEU E 435 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N CYS E 437 " --> pdb=" O VAL E 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU E 403 " --> pdb=" O CYS E 437 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL E 434 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE E 501 " --> pdb=" O VAL E 434 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL E 436 " --> pdb=" O ILE E 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'G' and resid 175 through 178 removed outlier: 6.459A pdb=" N VAL G 150 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N VAL G 178 " --> pdb=" O VAL G 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL G 152 " --> pdb=" O VAL G 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL G 193 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL G 229 " --> pdb=" O VAL G 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL G 195 " --> pdb=" O VAL G 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE G 226 " --> pdb=" O LEU G 283 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N PHE G 285 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL G 228 " --> pdb=" O PHE G 285 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 199 through 200 Processing sheet with id=AB7, first strand: chain 'I' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN I 4 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N LEU I 104 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL I 6 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER I 105 " --> pdb=" O HIS I 203 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N HIS I 203 " --> pdb=" O SER I 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA I 202 " --> pdb=" O LEU I 131 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU I 131 " --> pdb=" O ALA I 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU I 204 " --> pdb=" O ALA I 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA I 129 " --> pdb=" O LEU I 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 119 through 124 removed outlier: 6.673A pdb=" N THR B 91 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE B 123 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL B 93 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR B 152 " --> pdb=" O HIS B 248 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N HIS B 248 " --> pdb=" O TYR B 152 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N CYS B 247 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LYS B 186 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE B 249 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N MET B 181 " --> pdb=" O HIS B 288 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS B 290 " --> pdb=" O MET B 181 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET B 183 " --> pdb=" O HIS B 290 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N THR B 292 " --> pdb=" O MET B 183 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B 185 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 155 through 157 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 217 removed outlier: 6.624A pdb=" N VAL B 212 " --> pdb=" O ASP B 206 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ASP B 206 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 238 " --> pdb=" O PHE J 195 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 223 through 226 Processing sheet with id=AC3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.544A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 355 through 356 removed outlier: 6.423A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLN B 407 " --> pdb=" O LEU B 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 378 through 379 removed outlier: 6.339A pdb=" N VAL B 378 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N TYR B 395 " --> pdb=" O LEU B 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 401 through 402 removed outlier: 6.786A pdb=" N ARG B 401 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLU B 418 " --> pdb=" O VAL B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 430 through 431 removed outlier: 6.797A pdb=" N VAL B 430 " --> pdb=" O ILE B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 329 through 331 removed outlier: 3.732A pdb=" N SER C 326 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU C 265 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE C 325 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 267 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N CYS C 268 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE C 234 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 164 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE C 233 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N MET C 166 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLU C 163 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ILE C 190 " --> pdb=" O GLU C 163 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ALA C 192 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C 167 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 214 " --> pdb=" O ARG F 483 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 238 through 239 removed outlier: 3.762A pdb=" N THR C 238 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.321A pdb=" N SER C 307 " --> pdb=" O TYR F 385 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N LEU F 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE F 333 " --> pdb=" O VAL F 359 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL F 361 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL F 335 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR F 336 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLY F 404 " --> pdb=" O TYR F 336 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL F 401 " --> pdb=" O LEU F 435 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N CYS F 437 " --> pdb=" O VAL F 401 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LEU F 403 " --> pdb=" O CYS F 437 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 434 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N ILE F 501 " --> pdb=" O VAL F 434 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL F 436 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 407 through 408 Processing sheet with id=AD3, first strand: chain 'H' and resid 175 through 178 removed outlier: 6.458A pdb=" N VAL H 150 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL H 178 " --> pdb=" O VAL H 150 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL H 152 " --> pdb=" O VAL H 178 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N VAL H 193 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL H 229 " --> pdb=" O VAL H 193 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL H 195 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE H 226 " --> pdb=" O LEU H 283 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE H 285 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL H 228 " --> pdb=" O PHE H 285 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 199 through 200 Processing sheet with id=AD5, first strand: chain 'J' and resid 73 through 77 removed outlier: 6.546A pdb=" N GLN J 4 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU J 104 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL J 6 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER J 105 " --> pdb=" O HIS J 203 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS J 203 " --> pdb=" O SER J 105 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA J 202 " --> pdb=" O LEU J 131 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU J 131 " --> pdb=" O ALA J 202 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU J 204 " --> pdb=" O ALA J 129 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA J 129 " --> pdb=" O LEU J 204 " (cutoff:3.500A) 1086 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8288 1.35 - 1.47: 5617 1.47 - 1.59: 11533 1.59 - 1.71: 0 1.71 - 1.84: 216 Bond restraints: 25654 Sorted by residual: bond pdb=" CA ILE J 229 " pdb=" CB ILE J 229 " ideal model delta sigma weight residual 1.539 1.497 0.042 5.40e-03 3.43e+04 5.94e+01 bond pdb=" CA ILE I 229 " pdb=" CB ILE I 229 " ideal model delta sigma weight residual 1.539 1.498 0.041 5.40e-03 3.43e+04 5.80e+01 bond pdb=" CA SER F 510 " pdb=" C SER F 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.15e+00 bond pdb=" CA SER E 510 " pdb=" C SER E 510 " ideal model delta sigma weight residual 1.525 1.505 0.020 1.38e-02 5.25e+03 2.07e+00 bond pdb=" C VAL I 326 " pdb=" N PRO I 327 " ideal model delta sigma weight residual 1.334 1.355 -0.021 1.51e-02 4.39e+03 1.88e+00 ... (remaining 25649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 33920 2.26 - 4.51: 683 4.51 - 6.77: 125 6.77 - 9.03: 24 9.03 - 11.29: 20 Bond angle restraints: 34772 Sorted by residual: angle pdb=" CA LYS J 328 " pdb=" CB LYS J 328 " pdb=" CG LYS J 328 " ideal model delta sigma weight residual 114.10 125.16 -11.06 2.00e+00 2.50e-01 3.06e+01 angle pdb=" CA LYS I 328 " pdb=" CB LYS I 328 " pdb=" CG LYS I 328 " ideal model delta sigma weight residual 114.10 125.15 -11.05 2.00e+00 2.50e-01 3.05e+01 angle pdb=" N PHE B 56 " pdb=" CA PHE B 56 " pdb=" C PHE B 56 " ideal model delta sigma weight residual 110.70 102.65 8.05 1.55e+00 4.16e-01 2.69e+01 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 110.70 102.71 7.99 1.55e+00 4.16e-01 2.66e+01 angle pdb=" C LYS H 15 " pdb=" N GLU H 16 " pdb=" CA GLU H 16 " ideal model delta sigma weight residual 120.44 114.04 6.40 1.30e+00 5.92e-01 2.42e+01 ... (remaining 34767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 14009 17.41 - 34.83: 1033 34.83 - 52.24: 340 52.24 - 69.66: 170 69.66 - 87.07: 44 Dihedral angle restraints: 15596 sinusoidal: 6152 harmonic: 9444 Sorted by residual: dihedral pdb=" CA ASP A 139 " pdb=" CB ASP A 139 " pdb=" CG ASP A 139 " pdb=" OD1 ASP A 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.26 56.26 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 139 " pdb=" CB ASP B 139 " pdb=" CG ASP B 139 " pdb=" OD1 ASP B 139 " ideal model delta sinusoidal sigma weight residual -30.00 -86.22 56.22 1 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASP B 265 " pdb=" C ASP B 265 " pdb=" N TYR B 266 " pdb=" CA TYR B 266 " ideal model delta harmonic sigma weight residual 180.00 163.85 16.15 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 15593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3179 0.056 - 0.111: 751 0.111 - 0.167: 163 0.167 - 0.222: 5 0.222 - 0.278: 6 Chirality restraints: 4104 Sorted by residual: chirality pdb=" CA GLN J 325 " pdb=" N GLN J 325 " pdb=" C GLN J 325 " pdb=" CB GLN J 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA GLN I 325 " pdb=" N GLN I 325 " pdb=" C GLN I 325 " pdb=" CB GLN I 325 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LYS H 15 " pdb=" N LYS H 15 " pdb=" C LYS H 15 " pdb=" CB LYS H 15 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4101 not shown) Planarity restraints: 4414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 509 " -0.028 2.00e-02 2.50e+03 5.47e-02 2.99e+01 pdb=" C CYS E 509 " 0.095 2.00e-02 2.50e+03 pdb=" O CYS E 509 " -0.035 2.00e-02 2.50e+03 pdb=" N SER E 510 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 509 " 0.028 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C CYS F 509 " -0.094 2.00e-02 2.50e+03 pdb=" O CYS F 509 " 0.035 2.00e-02 2.50e+03 pdb=" N SER F 510 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 104 " -0.018 2.00e-02 2.50e+03 3.68e-02 1.36e+01 pdb=" C GLU B 104 " 0.064 2.00e-02 2.50e+03 pdb=" O GLU B 104 " -0.024 2.00e-02 2.50e+03 pdb=" N HIS B 105 " -0.022 2.00e-02 2.50e+03 ... (remaining 4411 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 398 2.64 - 3.21: 22662 3.21 - 3.77: 38435 3.77 - 4.34: 53319 4.34 - 4.90: 89533 Nonbonded interactions: 204347 Sorted by model distance: nonbonded pdb=" OD1 ASP A 271 " pdb=" NH2 ARG A 274 " model vdw 2.080 3.120 nonbonded pdb=" OD1 ASP B 271 " pdb=" NH2 ARG B 274 " model vdw 2.082 3.120 nonbonded pdb=" OG SER C 30 " pdb=" OE1 GLU C 33 " model vdw 2.142 3.040 nonbonded pdb=" OG SER D 30 " pdb=" OE1 GLU D 33 " model vdw 2.142 3.040 nonbonded pdb=" O TYR J 124 " pdb=" NH1 ARG J 299 " model vdw 2.180 3.120 ... (remaining 204342 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'C' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 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 0.044 25654 Z= 0.177 Angle : 0.843 11.287 34772 Z= 0.477 Chirality : 0.050 0.278 4104 Planarity : 0.005 0.055 4414 Dihedral : 16.162 87.072 9452 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.62 % Favored : 96.25 % Rotamer: Outliers : 6.92 % Allowed : 13.45 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3174 helix: 0.03 (0.14), residues: 1282 sheet: -1.82 (0.21), residues: 452 loop : -2.12 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG B 171 TYR 0.020 0.001 TYR B 306 PHE 0.020 0.001 PHE B 215 TRP 0.013 0.001 TRP C 51 HIS 0.011 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00329 (25654) covalent geometry : angle 0.84341 (34772) hydrogen bonds : bond 0.16283 ( 1086) hydrogen bonds : angle 6.00812 ( 3039) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 517 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8928 (mm) REVERT: D 47 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8726 (p) REVERT: E 169 THR cc_start: 0.8611 (OUTLIER) cc_final: 0.8352 (t) REVERT: E 250 ARG cc_start: 0.7610 (ptp90) cc_final: 0.7401 (ptt90) REVERT: E 510 SER cc_start: 0.8513 (OUTLIER) cc_final: 0.8282 (p) REVERT: G 83 TYR cc_start: 0.4340 (OUTLIER) cc_final: 0.3894 (m-80) REVERT: G 90 LYS cc_start: 0.3665 (OUTLIER) cc_final: 0.3387 (ttpp) REVERT: G 93 MET cc_start: 0.6185 (ttm) cc_final: 0.5448 (ptm) REVERT: G 103 ARG cc_start: 0.7708 (tpp80) cc_final: 0.7444 (mtt180) REVERT: G 149 SER cc_start: 0.7690 (OUTLIER) cc_final: 0.7413 (t) REVERT: G 245 ASP cc_start: 0.7706 (t0) cc_final: 0.7447 (t0) REVERT: I 50 GLU cc_start: 0.8399 (tp30) cc_final: 0.8194 (tp30) REVERT: I 75 ILE cc_start: 0.8890 (OUTLIER) cc_final: 0.8672 (mp) REVERT: I 116 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8378 (mm-30) REVERT: I 217 GLU cc_start: 0.8790 (tp30) cc_final: 0.8491 (tm-30) REVERT: I 227 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7829 (mt-10) REVERT: I 316 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8567 (tm) REVERT: B 98 LYS cc_start: 0.7687 (mttm) cc_final: 0.7404 (mttt) REVERT: B 150 LEU cc_start: 0.8681 (tp) cc_final: 0.8444 (tm) REVERT: B 166 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: B 355 ILE cc_start: 0.8302 (mt) cc_final: 0.7943 (mm) REVERT: B 401 ARG cc_start: 0.7127 (mtp-110) cc_final: 0.6707 (ptm160) REVERT: B 418 GLU cc_start: 0.8585 (tt0) cc_final: 0.8352 (tt0) REVERT: B 428 ARG cc_start: 0.7064 (mtm110) cc_final: 0.6693 (mmt180) REVERT: C 111 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7006 (ttmt) REVERT: F 173 TYR cc_start: 0.7362 (t80) cc_final: 0.6899 (t80) REVERT: F 251 ASP cc_start: 0.6412 (t70) cc_final: 0.6124 (t70) REVERT: H 14 MET cc_start: 0.8006 (mmm) cc_final: 0.7568 (tmt) REVERT: H 36 ARG cc_start: 0.5657 (mmt-90) cc_final: 0.5201 (mtm-85) REVERT: H 53 ILE cc_start: 0.8266 (pt) cc_final: 0.7980 (mt) REVERT: H 83 TYR cc_start: 0.4863 (OUTLIER) cc_final: 0.3908 (m-80) REVERT: H 92 ILE cc_start: 0.7887 (OUTLIER) cc_final: 0.7646 (pp) REVERT: H 95 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7355 (pt0) REVERT: H 103 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8050 (mtt180) REVERT: H 136 ARG cc_start: 0.7447 (tpt90) cc_final: 0.7119 (tmt170) REVERT: H 245 ASP cc_start: 0.8040 (t0) cc_final: 0.7625 (t0) REVERT: J 44 GLU cc_start: 0.8300 (tt0) cc_final: 0.8059 (pt0) REVERT: J 50 GLU cc_start: 0.7662 (tp30) cc_final: 0.7190 (tp30) REVERT: J 72 LYS cc_start: 0.8020 (mttp) cc_final: 0.7673 (tptp) REVERT: J 99 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7135 (p) REVERT: J 222 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7377 (t) REVERT: J 266 PHE cc_start: 0.7835 (m-80) cc_final: 0.7621 (m-10) REVERT: J 321 GLU cc_start: 0.8351 (tp30) cc_final: 0.8108 (tp30) outliers start: 192 outliers final: 43 residues processed: 658 average time/residue: 0.6792 time to fit residues: 509.2903 Evaluate side-chains 337 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 278 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 450 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 227 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 51 SER Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 90 LYS Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 111 LYS Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 92 ILE Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 222 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 177 ASN A 214 HIS A 219 GLN A 255 GLN A 286 GLN A 333 GLN A 337 HIS A 341 ASN A 359 ASN A 371 ASN A 376 ASN D 49 HIS D 80 ASN D 132 ASN D 188 HIS D 230 ASN E 194 GLN E 213 GLN E 448 GLN E 455 ASN E 464 GLN E 479 HIS G 48 ASN G 128 HIS G 243 GLN I 323 ASN B 72 ASN B 197 HIS B 219 GLN B 286 GLN B 359 ASN B 371 ASN B 376 ASN C 49 HIS C 80 ASN C 132 ASN C 162 ASN C 188 HIS C 230 ASN F 189 GLN F 213 GLN F 265 GLN F 371 HIS F 448 GLN F 455 ASN F 464 GLN H 48 ASN H 128 HIS H 222 GLN H 243 GLN J 323 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.078864 restraints weight = 44458.739| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.59 r_work: 0.3056 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 25654 Z= 0.234 Angle : 0.674 12.000 34772 Z= 0.343 Chirality : 0.048 0.285 4104 Planarity : 0.005 0.044 4414 Dihedral : 6.815 86.798 3574 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.91 % Allowed : 18.93 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3174 helix: 0.90 (0.15), residues: 1306 sheet: -1.13 (0.23), residues: 446 loop : -1.34 (0.15), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 428 TYR 0.016 0.002 TYR I 319 PHE 0.020 0.002 PHE C 177 TRP 0.013 0.001 TRP F 350 HIS 0.007 0.001 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00562 (25654) covalent geometry : angle 0.67384 (34772) hydrogen bonds : bond 0.04725 ( 1086) hydrogen bonds : angle 4.50271 ( 3039) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 274 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 50 ARG cc_start: 0.8264 (tpm170) cc_final: 0.7605 (tpt90) REVERT: D 59 GLU cc_start: 0.8713 (tp30) cc_final: 0.8486 (tp30) REVERT: D 171 SER cc_start: 0.8517 (OUTLIER) cc_final: 0.8092 (t) REVERT: E 173 TYR cc_start: 0.8343 (t80) cc_final: 0.8078 (t80) REVERT: E 240 TYR cc_start: 0.8734 (t80) cc_final: 0.8486 (t80) REVERT: E 283 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8158 (tm-30) REVERT: E 417 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7618 (tpm170) REVERT: E 510 SER cc_start: 0.8591 (OUTLIER) cc_final: 0.8296 (p) REVERT: G 10 PHE cc_start: 0.6469 (t80) cc_final: 0.6263 (t80) REVERT: G 14 MET cc_start: 0.7407 (tpp) cc_final: 0.7158 (mpp) REVERT: G 70 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7717 (tp30) REVERT: G 93 MET cc_start: 0.6481 (ttm) cc_final: 0.5918 (ptm) REVERT: G 120 LYS cc_start: 0.8444 (mttt) cc_final: 0.8151 (mmtt) REVERT: G 245 ASP cc_start: 0.8587 (t0) cc_final: 0.8064 (t0) REVERT: I 50 GLU cc_start: 0.8580 (tp30) cc_final: 0.8375 (tp30) REVERT: I 217 GLU cc_start: 0.9079 (tp30) cc_final: 0.8752 (tm-30) REVERT: I 227 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8101 (mt-10) REVERT: I 325 GLN cc_start: 0.9007 (mt0) cc_final: 0.8570 (mp10) REVERT: B 53 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6705 (p0) REVERT: B 126 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: B 161 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 166 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7435 (tp30) REVERT: B 355 ILE cc_start: 0.8173 (mt) cc_final: 0.7860 (mm) REVERT: B 401 ARG cc_start: 0.7093 (mtp-110) cc_final: 0.6863 (mtp-110) REVERT: B 418 GLU cc_start: 0.8652 (tt0) cc_final: 0.7766 (tp30) REVERT: B 428 ARG cc_start: 0.7521 (mtm110) cc_final: 0.6798 (mmt90) REVERT: C 172 ARG cc_start: 0.8157 (mmt180) cc_final: 0.7883 (mpt180) REVERT: C 319 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: F 250 ARG cc_start: 0.7440 (ptp90) cc_final: 0.7145 (mtm-85) REVERT: H 14 MET cc_start: 0.8125 (mmm) cc_final: 0.7494 (tmt) REVERT: H 27 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7236 (mp) REVERT: H 48 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7834 (p0) REVERT: H 95 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7501 (pt0) REVERT: H 245 ASP cc_start: 0.8648 (t0) cc_final: 0.8062 (t0) REVERT: H 284 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8178 (mp) REVERT: J 37 TRP cc_start: 0.7320 (t60) cc_final: 0.6955 (t60) REVERT: J 50 GLU cc_start: 0.7686 (tp30) cc_final: 0.7051 (tp30) REVERT: J 72 LYS cc_start: 0.7808 (mttp) cc_final: 0.7470 (ttpp) REVERT: J 194 ARG cc_start: 0.7598 (tpt90) cc_final: 0.7187 (tpt90) REVERT: J 222 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7442 (p) REVERT: J 227 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7972 (mt-10) REVERT: J 319 TYR cc_start: 0.8485 (t80) cc_final: 0.8192 (t80) REVERT: J 321 GLU cc_start: 0.8697 (tp30) cc_final: 0.8109 (tp30) outliers start: 164 outliers final: 73 residues processed: 407 average time/residue: 0.5818 time to fit residues: 275.7852 Evaluate side-chains 308 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 222 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 146 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 394 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 510 SER Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 154 GLU Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 222 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 305 ASP Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 27 ILE Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 222 THR Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 75 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 185 optimal weight: 3.9990 chunk 316 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 317 optimal weight: 7.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 371 HIS B 197 HIS B 337 HIS B 359 ASN C 110 HIS F 455 ASN H 48 ASN H 170 HIS J 172 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.109741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.078198 restraints weight = 44529.321| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.58 r_work: 0.3006 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25654 Z= 0.218 Angle : 0.610 12.211 34772 Z= 0.312 Chirality : 0.046 0.233 4104 Planarity : 0.004 0.046 4414 Dihedral : 5.952 79.854 3523 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 5.77 % Allowed : 19.36 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3174 helix: 1.26 (0.15), residues: 1290 sheet: -0.81 (0.24), residues: 462 loop : -0.96 (0.16), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 222 TYR 0.017 0.002 TYR J 94 PHE 0.020 0.002 PHE D 272 TRP 0.011 0.001 TRP D 51 HIS 0.013 0.001 HIS H 170 Details of bonding type rmsd covalent geometry : bond 0.00531 (25654) covalent geometry : angle 0.60972 (34772) hydrogen bonds : bond 0.04506 ( 1086) hydrogen bonds : angle 4.33024 ( 3039) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 228 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 171 SER cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (t) REVERT: E 196 MET cc_start: 0.9084 (mtt) cc_final: 0.8845 (mtt) REVERT: E 250 ARG cc_start: 0.8039 (ptp90) cc_final: 0.7527 (ptm-80) REVERT: E 417 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7689 (tpm170) REVERT: G 10 PHE cc_start: 0.6515 (t80) cc_final: 0.6241 (t80) REVERT: G 14 MET cc_start: 0.7555 (tpp) cc_final: 0.7340 (tpp) REVERT: G 70 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7699 (tp30) REVERT: G 120 LYS cc_start: 0.8489 (mttt) cc_final: 0.8194 (mmtp) REVERT: G 121 ASP cc_start: 0.8617 (t0) cc_final: 0.8372 (t70) REVERT: G 245 ASP cc_start: 0.8568 (t0) cc_final: 0.8051 (t0) REVERT: I 50 GLU cc_start: 0.8523 (tp30) cc_final: 0.8249 (tp30) REVERT: I 105 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7710 (p) REVERT: I 217 GLU cc_start: 0.9073 (tp30) cc_final: 0.8760 (tm-30) REVERT: I 227 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8165 (mt-10) REVERT: B 53 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.6813 (p0) REVERT: B 61 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7666 (mmtm) REVERT: B 126 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8218 (tp30) REVERT: B 161 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8447 (mp) REVERT: B 166 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: B 355 ILE cc_start: 0.8141 (mt) cc_final: 0.7860 (mm) REVERT: B 401 ARG cc_start: 0.7151 (mtp-110) cc_final: 0.6909 (mtp-110) REVERT: B 418 GLU cc_start: 0.8687 (tt0) cc_final: 0.7832 (tp30) REVERT: B 428 ARG cc_start: 0.7526 (mtm110) cc_final: 0.6672 (mmt90) REVERT: C 44 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8644 (tt0) REVERT: C 48 ASP cc_start: 0.8327 (m-30) cc_final: 0.8109 (m-30) REVERT: C 172 ARG cc_start: 0.8115 (mmt180) cc_final: 0.7888 (mpt180) REVERT: F 250 ARG cc_start: 0.7447 (ptp90) cc_final: 0.7181 (mtm-85) REVERT: H 14 MET cc_start: 0.8351 (mmm) cc_final: 0.7688 (tmt) REVERT: H 31 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6619 (mp) REVERT: H 95 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7585 (pt0) REVERT: H 198 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8824 (mt-10) REVERT: H 245 ASP cc_start: 0.8627 (t0) cc_final: 0.8068 (t0) REVERT: J 37 TRP cc_start: 0.7160 (t60) cc_final: 0.6852 (t60) REVERT: J 98 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7502 (mmtp) REVERT: J 325 GLN cc_start: 0.9257 (mt0) cc_final: 0.9006 (mt0) outliers start: 160 outliers final: 69 residues processed: 361 average time/residue: 0.5844 time to fit residues: 245.9070 Evaluate side-chains 289 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 208 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 286 SER Chi-restraints excluded: chain E residue 392 SER Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain I residue 222 THR Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 76 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 220 SER Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 190 optimal weight: 1.9990 chunk 301 optimal weight: 0.0060 chunk 114 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 371 HIS B 333 GLN B 359 ASN F 265 GLN F 371 HIS F 422 GLN F 455 ASN J 172 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.109597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.078175 restraints weight = 43919.121| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.61 r_work: 0.3063 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25654 Z= 0.136 Angle : 0.540 10.884 34772 Z= 0.278 Chirality : 0.044 0.223 4104 Planarity : 0.004 0.048 4414 Dihedral : 5.572 80.588 3518 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.72 % Allowed : 20.12 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.15), residues: 3174 helix: 1.51 (0.15), residues: 1302 sheet: -0.56 (0.24), residues: 462 loop : -0.69 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 428 TYR 0.016 0.001 TYR J 94 PHE 0.026 0.001 PHE H 33 TRP 0.006 0.001 TRP B 111 HIS 0.004 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00325 (25654) covalent geometry : angle 0.54045 (34772) hydrogen bonds : bond 0.03682 ( 1086) hydrogen bonds : angle 4.08942 ( 3039) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 228 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 305 MET cc_start: 0.8789 (mmm) cc_final: 0.8514 (mmp) REVERT: A 329 ASP cc_start: 0.9166 (OUTLIER) cc_final: 0.8938 (m-30) REVERT: D 50 ARG cc_start: 0.8262 (tpm170) cc_final: 0.7818 (tpm170) REVERT: D 171 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.8048 (t) REVERT: E 250 ARG cc_start: 0.7914 (ptp90) cc_final: 0.7416 (ptm-80) REVERT: E 331 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8461 (t0) REVERT: E 415 MET cc_start: 0.9147 (ttp) cc_final: 0.8867 (ttp) REVERT: E 417 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7510 (tpm170) REVERT: G 10 PHE cc_start: 0.6401 (t80) cc_final: 0.6109 (t80) REVERT: G 70 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7755 (mt-10) REVERT: G 120 LYS cc_start: 0.8496 (mttt) cc_final: 0.8150 (mmtt) REVERT: G 121 ASP cc_start: 0.8691 (t0) cc_final: 0.8451 (t70) REVERT: G 245 ASP cc_start: 0.8553 (t0) cc_final: 0.8068 (t0) REVERT: I 111 ASP cc_start: 0.8704 (p0) cc_final: 0.8486 (p0) REVERT: I 325 GLN cc_start: 0.8987 (mm-40) cc_final: 0.8524 (mm-40) REVERT: B 53 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.6996 (p0) REVERT: B 61 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7780 (mmtm) REVERT: B 126 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8267 (tp30) REVERT: B 145 ARG cc_start: 0.8300 (ptp-110) cc_final: 0.7274 (ptm-80) REVERT: B 147 ASP cc_start: 0.8930 (OUTLIER) cc_final: 0.8716 (OUTLIER) REVERT: B 161 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 166 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7447 (tp30) REVERT: B 329 ASP cc_start: 0.8694 (t0) cc_final: 0.8164 (t0) REVERT: B 355 ILE cc_start: 0.8152 (mt) cc_final: 0.7878 (mm) REVERT: B 358 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7953 (tp30) REVERT: B 384 HIS cc_start: 0.7864 (m-70) cc_final: 0.7498 (m-70) REVERT: B 401 ARG cc_start: 0.7186 (mtp-110) cc_final: 0.6977 (mtp-110) REVERT: B 418 GLU cc_start: 0.8649 (tt0) cc_final: 0.7785 (tp30) REVERT: C 48 ASP cc_start: 0.8340 (m-30) cc_final: 0.8104 (m-30) REVERT: C 172 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7832 (mpt180) REVERT: F 250 ARG cc_start: 0.7383 (ptp90) cc_final: 0.7120 (mtm-85) REVERT: H 8 GLU cc_start: 0.8403 (mp0) cc_final: 0.8114 (pm20) REVERT: H 14 MET cc_start: 0.8354 (mmm) cc_final: 0.7736 (tmt) REVERT: H 95 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: H 198 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8859 (mt-10) REVERT: H 245 ASP cc_start: 0.8587 (t0) cc_final: 0.8024 (t0) REVERT: J 37 TRP cc_start: 0.7082 (t60) cc_final: 0.6793 (t60) REVERT: J 98 LYS cc_start: 0.7847 (OUTLIER) cc_final: 0.7470 (mmtm) REVERT: J 194 ARG cc_start: 0.7655 (tpt90) cc_final: 0.7388 (tpt90) REVERT: J 319 TYR cc_start: 0.8578 (t80) cc_final: 0.8300 (t80) REVERT: J 325 GLN cc_start: 0.9239 (mt0) cc_final: 0.9009 (mt0) outliers start: 131 outliers final: 59 residues processed: 336 average time/residue: 0.5989 time to fit residues: 234.3243 Evaluate side-chains 287 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 216 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 334 CYS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 149 SER Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 113 optimal weight: 10.0000 chunk 276 optimal weight: 4.9990 chunk 312 optimal weight: 8.9990 chunk 162 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 224 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 371 HIS E 455 ASN B 333 GLN F 455 ASN J 172 ASN ** J 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.108192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.076799 restraints weight = 44070.411| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.59 r_work: 0.3048 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25654 Z= 0.177 Angle : 0.568 14.054 34772 Z= 0.291 Chirality : 0.045 0.212 4104 Planarity : 0.004 0.049 4414 Dihedral : 5.430 79.036 3511 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 4.40 % Allowed : 20.22 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.15), residues: 3174 helix: 1.57 (0.15), residues: 1302 sheet: -0.52 (0.24), residues: 462 loop : -0.57 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 95 TYR 0.020 0.001 TYR J 94 PHE 0.019 0.001 PHE J 214 TRP 0.007 0.001 TRP B 111 HIS 0.004 0.001 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00429 (25654) covalent geometry : angle 0.56816 (34772) hydrogen bonds : bond 0.03967 ( 1086) hydrogen bonds : angle 4.10673 ( 3039) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 237 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.9330 (ttt) cc_final: 0.9078 (ttp) REVERT: A 329 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8942 (m-30) REVERT: D 50 ARG cc_start: 0.8285 (tpm170) cc_final: 0.7840 (tpm170) REVERT: D 171 SER cc_start: 0.8470 (OUTLIER) cc_final: 0.8101 (t) REVERT: E 250 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7428 (ptt90) REVERT: E 417 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7576 (tpm170) REVERT: G 14 MET cc_start: 0.7651 (tpp) cc_final: 0.7305 (mmm) REVERT: G 70 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7745 (mt-10) REVERT: G 103 ARG cc_start: 0.8040 (tpp80) cc_final: 0.7668 (mtt-85) REVERT: G 120 LYS cc_start: 0.8512 (mttt) cc_final: 0.8217 (mmtp) REVERT: G 121 ASP cc_start: 0.8686 (t0) cc_final: 0.8468 (t70) REVERT: G 245 ASP cc_start: 0.8574 (t0) cc_final: 0.8106 (t0) REVERT: I 50 GLU cc_start: 0.8466 (tp30) cc_final: 0.8218 (tp30) REVERT: I 111 ASP cc_start: 0.8767 (p0) cc_final: 0.8556 (p0) REVERT: I 217 GLU cc_start: 0.9122 (tp30) cc_final: 0.8664 (tp30) REVERT: I 227 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8073 (mt-10) REVERT: I 307 GLU cc_start: 0.8109 (pt0) cc_final: 0.7578 (pp20) REVERT: I 325 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8705 (mm-40) REVERT: B 53 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.7109 (p0) REVERT: B 61 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7774 (mmtm) REVERT: B 126 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: B 161 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8426 (mp) REVERT: B 166 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7452 (tp30) REVERT: B 329 ASP cc_start: 0.8725 (t0) cc_final: 0.8124 (t0) REVERT: B 355 ILE cc_start: 0.8229 (mt) cc_final: 0.7948 (mm) REVERT: B 358 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7991 (tp30) REVERT: B 384 HIS cc_start: 0.7889 (m-70) cc_final: 0.7591 (m-70) REVERT: B 418 GLU cc_start: 0.8673 (tt0) cc_final: 0.7784 (tp30) REVERT: B 455 ASP cc_start: 0.3883 (OUTLIER) cc_final: 0.3679 (p0) REVERT: C 48 ASP cc_start: 0.8348 (m-30) cc_final: 0.8147 (m-30) REVERT: C 63 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7909 (ptp90) REVERT: F 250 ARG cc_start: 0.7388 (ptp90) cc_final: 0.7122 (mtm-85) REVERT: F 495 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8515 (pp20) REVERT: H 14 MET cc_start: 0.8460 (mmm) cc_final: 0.7890 (tmt) REVERT: H 95 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7868 (pt0) REVERT: H 198 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8855 (mt-10) REVERT: H 245 ASP cc_start: 0.8644 (t0) cc_final: 0.8103 (t0) REVERT: H 284 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8307 (mp) REVERT: J 37 TRP cc_start: 0.7261 (t60) cc_final: 0.6946 (t60) REVERT: J 44 GLU cc_start: 0.8654 (tp30) cc_final: 0.8059 (tp30) REVERT: J 50 GLU cc_start: 0.7126 (tp30) cc_final: 0.6561 (tp30) REVERT: J 98 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7615 (mmtp) REVERT: J 100 ASP cc_start: 0.8097 (m-30) cc_final: 0.7671 (m-30) REVERT: J 179 GLU cc_start: 0.7934 (pt0) cc_final: 0.7098 (pp20) REVERT: J 194 ARG cc_start: 0.7663 (tpt90) cc_final: 0.7353 (tpt90) outliers start: 122 outliers final: 72 residues processed: 340 average time/residue: 0.6162 time to fit residues: 242.8307 Evaluate side-chains 304 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 97 LEU Chi-restraints excluded: chain I residue 315 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 61 LYS Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 333 GLN Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 63 ARG Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 317 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 310 optimal weight: 7.9990 chunk 146 optimal weight: 0.9980 chunk 302 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 282 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN A 359 ASN E 189 GLN E 371 HIS F 371 HIS F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN ** J 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.107288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.075780 restraints weight = 44426.158| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.59 r_work: 0.3029 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25654 Z= 0.206 Angle : 0.589 12.704 34772 Z= 0.302 Chirality : 0.046 0.196 4104 Planarity : 0.004 0.049 4414 Dihedral : 5.473 78.681 3510 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.83 % Allowed : 20.55 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.15), residues: 3174 helix: 1.53 (0.15), residues: 1298 sheet: -0.46 (0.24), residues: 478 loop : -0.59 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 324 TYR 0.025 0.001 TYR J 94 PHE 0.020 0.002 PHE G 10 TRP 0.008 0.001 TRP B 111 HIS 0.007 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00503 (25654) covalent geometry : angle 0.58867 (34772) hydrogen bonds : bond 0.04126 ( 1086) hydrogen bonds : angle 4.14669 ( 3039) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 217 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.9331 (ttt) cc_final: 0.9075 (ttp) REVERT: A 329 ASP cc_start: 0.9144 (OUTLIER) cc_final: 0.8915 (m-30) REVERT: D 50 ARG cc_start: 0.8324 (tpm170) cc_final: 0.7914 (tpm170) REVERT: D 171 SER cc_start: 0.8468 (OUTLIER) cc_final: 0.8132 (t) REVERT: E 250 ARG cc_start: 0.7947 (ptp90) cc_final: 0.7428 (ptm-80) REVERT: E 417 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7605 (tpm170) REVERT: E 463 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8391 (mp) REVERT: G 14 MET cc_start: 0.7451 (tpp) cc_final: 0.7190 (mmm) REVERT: G 70 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7766 (mt-10) REVERT: G 120 LYS cc_start: 0.8532 (mttt) cc_final: 0.8229 (mmtp) REVERT: G 121 ASP cc_start: 0.8742 (t0) cc_final: 0.8525 (t70) REVERT: G 245 ASP cc_start: 0.8596 (t0) cc_final: 0.8175 (t0) REVERT: I 50 GLU cc_start: 0.8428 (tp30) cc_final: 0.8213 (tp30) REVERT: I 105 SER cc_start: 0.8394 (OUTLIER) cc_final: 0.7808 (p) REVERT: I 217 GLU cc_start: 0.9115 (tp30) cc_final: 0.8699 (tp30) REVERT: I 227 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8075 (mt-10) REVERT: I 307 GLU cc_start: 0.8101 (pt0) cc_final: 0.7656 (OUTLIER) REVERT: I 325 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8675 (mm-40) REVERT: B 53 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7295 (p0) REVERT: B 126 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8339 (tp30) REVERT: B 161 ILE cc_start: 0.8697 (OUTLIER) cc_final: 0.8443 (mp) REVERT: B 166 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7456 (tp30) REVERT: B 355 ILE cc_start: 0.8208 (mt) cc_final: 0.7942 (mm) REVERT: B 358 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7973 (tp30) REVERT: B 384 HIS cc_start: 0.7837 (m-70) cc_final: 0.7540 (m-70) REVERT: B 418 GLU cc_start: 0.8693 (tt0) cc_final: 0.7735 (tp30) REVERT: C 48 ASP cc_start: 0.8341 (m-30) cc_final: 0.8139 (m-30) REVERT: F 250 ARG cc_start: 0.7406 (ptp90) cc_final: 0.7155 (mtm-85) REVERT: F 294 GLU cc_start: 0.8272 (mp0) cc_final: 0.7573 (tp30) REVERT: F 470 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7826 (p-80) REVERT: F 495 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8564 (pp20) REVERT: H 95 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: H 120 LYS cc_start: 0.8261 (mttt) cc_final: 0.7837 (pttt) REVERT: H 198 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8826 (mt-10) REVERT: H 245 ASP cc_start: 0.8640 (t0) cc_final: 0.8104 (t0) REVERT: H 284 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8297 (mp) REVERT: J 37 TRP cc_start: 0.7251 (t60) cc_final: 0.6933 (t60) REVERT: J 98 LYS cc_start: 0.7750 (OUTLIER) cc_final: 0.7358 (mmtp) REVERT: J 100 ASP cc_start: 0.8044 (m-30) cc_final: 0.7685 (m-30) REVERT: J 194 ARG cc_start: 0.7628 (tpt90) cc_final: 0.7310 (tpt90) REVERT: J 216 MET cc_start: 0.7997 (mmm) cc_final: 0.7750 (mmt) REVERT: J 319 TYR cc_start: 0.8419 (t80) cc_final: 0.8142 (t80) outliers start: 134 outliers final: 76 residues processed: 332 average time/residue: 0.5703 time to fit residues: 221.0586 Evaluate side-chains 302 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 212 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 329 ASP Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 252 LEU Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 105 SER Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 226 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 261 SER Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 284 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 224 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 253 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 235 optimal weight: 0.2980 chunk 299 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 231 optimal weight: 0.0670 chunk 310 optimal weight: 10.0000 chunk 105 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 189 GLN E 281 ASN E 371 HIS ** B 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 371 HIS F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 323 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.109966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078662 restraints weight = 43858.831| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.60 r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25654 Z= 0.111 Angle : 0.527 12.198 34772 Z= 0.271 Chirality : 0.043 0.173 4104 Planarity : 0.004 0.049 4414 Dihedral : 5.184 77.761 3509 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.57 % Allowed : 21.70 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 3174 helix: 1.83 (0.15), residues: 1282 sheet: -0.30 (0.24), residues: 480 loop : -0.39 (0.17), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 324 TYR 0.023 0.001 TYR J 94 PHE 0.025 0.001 PHE G 10 TRP 0.006 0.001 TRP B 111 HIS 0.014 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00252 (25654) covalent geometry : angle 0.52651 (34772) hydrogen bonds : bond 0.03364 ( 1086) hydrogen bonds : angle 3.95178 ( 3039) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 230 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.9274 (ttt) cc_final: 0.9022 (ttp) REVERT: D 50 ARG cc_start: 0.8282 (tpm170) cc_final: 0.7909 (tpm170) REVERT: D 171 SER cc_start: 0.8471 (OUTLIER) cc_final: 0.8040 (t) REVERT: E 283 GLU cc_start: 0.8734 (tp30) cc_final: 0.8225 (tm-30) REVERT: E 331 ASP cc_start: 0.8748 (OUTLIER) cc_final: 0.8479 (t0) REVERT: E 415 MET cc_start: 0.9114 (ttp) cc_final: 0.8716 (ttm) REVERT: E 417 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7457 (tpm170) REVERT: G 14 MET cc_start: 0.7279 (tpp) cc_final: 0.7015 (mmm) REVERT: G 103 ARG cc_start: 0.8000 (tpp80) cc_final: 0.7622 (mtt-85) REVERT: G 120 LYS cc_start: 0.8528 (mttt) cc_final: 0.8274 (mmtp) REVERT: G 121 ASP cc_start: 0.8744 (t0) cc_final: 0.8502 (t70) REVERT: G 245 ASP cc_start: 0.8533 (t0) cc_final: 0.8085 (t0) REVERT: I 50 GLU cc_start: 0.8420 (tp30) cc_final: 0.8170 (tp30) REVERT: I 227 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8060 (mt-10) REVERT: I 307 GLU cc_start: 0.7993 (pt0) cc_final: 0.7737 (pp20) REVERT: I 325 GLN cc_start: 0.9091 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 53 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7368 (p0) REVERT: B 126 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8399 (tp30) REVERT: B 147 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8698 (OUTLIER) REVERT: B 166 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7440 (tp30) REVERT: B 329 ASP cc_start: 0.8746 (t0) cc_final: 0.8139 (t0) REVERT: B 355 ILE cc_start: 0.8227 (mt) cc_final: 0.7940 (mm) REVERT: B 358 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: B 384 HIS cc_start: 0.7755 (m-70) cc_final: 0.7446 (m-70) REVERT: B 418 GLU cc_start: 0.8689 (tt0) cc_final: 0.7750 (tp30) REVERT: C 48 ASP cc_start: 0.8305 (m-30) cc_final: 0.8073 (m-30) REVERT: C 128 GLN cc_start: 0.7634 (pm20) cc_final: 0.7363 (tp40) REVERT: C 139 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7877 (tm-30) REVERT: C 228 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8362 (mmt90) REVERT: F 250 ARG cc_start: 0.7368 (ptp90) cc_final: 0.7112 (mtm-85) REVERT: F 310 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8057 (mm-30) REVERT: F 495 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8487 (pp20) REVERT: H 93 MET cc_start: 0.5895 (mmm) cc_final: 0.5640 (tpt) REVERT: H 95 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7982 (pt0) REVERT: H 120 LYS cc_start: 0.8260 (mttt) cc_final: 0.7848 (pttt) REVERT: H 198 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8848 (mt-10) REVERT: H 245 ASP cc_start: 0.8624 (t0) cc_final: 0.8090 (t0) REVERT: J 37 TRP cc_start: 0.7302 (t60) cc_final: 0.6949 (t60) REVERT: J 98 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7257 (mmtm) REVERT: J 100 ASP cc_start: 0.7855 (m-30) cc_final: 0.7432 (m-30) REVERT: J 319 TYR cc_start: 0.8486 (t80) cc_final: 0.8095 (t80) REVERT: J 323 ASN cc_start: 0.8649 (OUTLIER) cc_final: 0.8373 (m110) outliers start: 99 outliers final: 54 residues processed: 319 average time/residue: 0.5865 time to fit residues: 218.4422 Evaluate side-chains 284 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 219 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 191 SER Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain I residue 108 LEU Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 171 SER Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 224 ILE Chi-restraints excluded: chain J residue 323 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 82 optimal weight: 0.8980 chunk 130 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 253 optimal weight: 2.9990 chunk 250 optimal weight: 0.9980 chunk 202 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 291 optimal weight: 0.9990 chunk 306 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 371 HIS B 255 GLN F 455 ASN ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.110289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.079063 restraints weight = 43926.952| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.60 r_work: 0.3091 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25654 Z= 0.110 Angle : 0.521 11.723 34772 Z= 0.268 Chirality : 0.043 0.175 4104 Planarity : 0.004 0.051 4414 Dihedral : 5.022 76.689 3505 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.17 % Allowed : 22.42 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 3174 helix: 1.87 (0.15), residues: 1284 sheet: -0.20 (0.24), residues: 484 loop : -0.28 (0.17), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 292 TYR 0.022 0.001 TYR J 94 PHE 0.022 0.001 PHE H 75 TRP 0.006 0.001 TRP B 111 HIS 0.003 0.001 HIS A 168 Details of bonding type rmsd covalent geometry : bond 0.00256 (25654) covalent geometry : angle 0.52092 (34772) hydrogen bonds : bond 0.03259 ( 1086) hydrogen bonds : angle 3.89971 ( 3039) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 225 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 MET cc_start: 0.9259 (ttt) cc_final: 0.9005 (ttp) REVERT: D 50 ARG cc_start: 0.8288 (tpm170) cc_final: 0.7933 (tpm170) REVERT: D 171 SER cc_start: 0.8378 (OUTLIER) cc_final: 0.7914 (t) REVERT: E 331 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8489 (t0) REVERT: E 415 MET cc_start: 0.9105 (ttp) cc_final: 0.8700 (ttm) REVERT: E 417 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7399 (tpm170) REVERT: G 14 MET cc_start: 0.7129 (tpp) cc_final: 0.6888 (mmm) REVERT: G 120 LYS cc_start: 0.8496 (mttt) cc_final: 0.8257 (mmtp) REVERT: G 121 ASP cc_start: 0.8731 (t0) cc_final: 0.8501 (t70) REVERT: G 245 ASP cc_start: 0.8473 (t0) cc_final: 0.8052 (t0) REVERT: I 50 GLU cc_start: 0.8401 (tp30) cc_final: 0.8132 (tp30) REVERT: I 227 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8050 (mt-10) REVERT: I 325 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8582 (mm-40) REVERT: B 53 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7367 (p0) REVERT: B 166 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7445 (tp30) REVERT: B 329 ASP cc_start: 0.8731 (t0) cc_final: 0.8128 (t0) REVERT: B 355 ILE cc_start: 0.8166 (mt) cc_final: 0.7874 (mm) REVERT: B 358 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7753 (tp30) REVERT: B 384 HIS cc_start: 0.7733 (m-70) cc_final: 0.7359 (m-70) REVERT: B 418 GLU cc_start: 0.8681 (tt0) cc_final: 0.7772 (tp30) REVERT: B 455 ASP cc_start: 0.3722 (OUTLIER) cc_final: 0.3411 (p0) REVERT: C 48 ASP cc_start: 0.8303 (m-30) cc_final: 0.8074 (m-30) REVERT: C 139 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7788 (tm-30) REVERT: C 228 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8263 (mmt90) REVERT: F 250 ARG cc_start: 0.7309 (ptp90) cc_final: 0.7051 (mtm-85) REVERT: F 310 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7995 (mm-30) REVERT: F 495 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: H 93 MET cc_start: 0.5816 (mmm) cc_final: 0.5575 (tpt) REVERT: H 95 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8122 (pt0) REVERT: H 120 LYS cc_start: 0.8240 (mttt) cc_final: 0.7806 (pttt) REVERT: H 198 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8787 (mt-10) REVERT: H 245 ASP cc_start: 0.8616 (t0) cc_final: 0.8088 (t0) REVERT: J 37 TRP cc_start: 0.7250 (t60) cc_final: 0.6893 (t60) REVERT: J 98 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7399 (mmtm) REVERT: J 100 ASP cc_start: 0.7897 (m-30) cc_final: 0.7484 (m-30) REVERT: J 216 MET cc_start: 0.7869 (mmt) cc_final: 0.7618 (mmt) REVERT: J 319 TYR cc_start: 0.8487 (t80) cc_final: 0.8072 (t80) REVERT: J 323 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8507 (m110) outliers start: 88 outliers final: 54 residues processed: 302 average time/residue: 0.5823 time to fit residues: 205.4899 Evaluate side-chains 281 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 216 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 28 ARG Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 116 HIS Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 323 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 52 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 299 optimal weight: 10.0000 chunk 304 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 153 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 371 HIS I 323 ASN F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 323 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.110338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079236 restraints weight = 44104.268| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.55 r_work: 0.3105 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25654 Z= 0.114 Angle : 0.526 11.500 34772 Z= 0.270 Chirality : 0.043 0.170 4104 Planarity : 0.004 0.050 4414 Dihedral : 4.980 76.332 3505 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.85 % Allowed : 23.04 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 3174 helix: 1.86 (0.15), residues: 1294 sheet: -0.15 (0.24), residues: 484 loop : -0.24 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 292 TYR 0.021 0.001 TYR J 94 PHE 0.026 0.001 PHE B 57 TRP 0.006 0.001 TRP B 111 HIS 0.010 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00268 (25654) covalent geometry : angle 0.52612 (34772) hydrogen bonds : bond 0.03248 ( 1086) hydrogen bonds : angle 3.89071 ( 3039) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 50 ARG cc_start: 0.8293 (tpm170) cc_final: 0.7946 (tpm170) REVERT: D 171 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7916 (t) REVERT: E 283 GLU cc_start: 0.8670 (tp30) cc_final: 0.8182 (tm-30) REVERT: E 331 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8497 (t0) REVERT: E 415 MET cc_start: 0.9118 (ttp) cc_final: 0.8711 (ttm) REVERT: E 417 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7469 (tpm170) REVERT: G 14 MET cc_start: 0.7163 (tpp) cc_final: 0.6925 (mmm) REVERT: G 120 LYS cc_start: 0.8502 (mttt) cc_final: 0.8290 (mmtp) REVERT: G 121 ASP cc_start: 0.8733 (t0) cc_final: 0.8501 (t70) REVERT: G 245 ASP cc_start: 0.8499 (t0) cc_final: 0.8099 (t0) REVERT: I 50 GLU cc_start: 0.8393 (tp30) cc_final: 0.8120 (tp30) REVERT: I 227 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8080 (mt-10) REVERT: I 325 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8646 (mm-40) REVERT: B 53 ASP cc_start: 0.7656 (OUTLIER) cc_final: 0.7429 (p0) REVERT: B 166 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7504 (tp30) REVERT: B 329 ASP cc_start: 0.8731 (t0) cc_final: 0.8136 (t70) REVERT: B 355 ILE cc_start: 0.8231 (mt) cc_final: 0.7931 (mm) REVERT: B 358 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: B 384 HIS cc_start: 0.7742 (m-70) cc_final: 0.7404 (m-70) REVERT: B 418 GLU cc_start: 0.8710 (tt0) cc_final: 0.7844 (tp30) REVERT: C 44 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: C 48 ASP cc_start: 0.8310 (m-30) cc_final: 0.8099 (m-30) REVERT: C 128 GLN cc_start: 0.7629 (pm20) cc_final: 0.7309 (tp40) REVERT: C 139 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7833 (tm-30) REVERT: C 228 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.8302 (mmt90) REVERT: F 250 ARG cc_start: 0.7312 (ptp90) cc_final: 0.7058 (mtm-85) REVERT: F 310 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8012 (mm-30) REVERT: F 495 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: H 20 MET cc_start: 0.7399 (ttt) cc_final: 0.7187 (ttt) REVERT: H 95 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8142 (pt0) REVERT: H 120 LYS cc_start: 0.8258 (mttt) cc_final: 0.7842 (pttt) REVERT: H 198 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8816 (mt-10) REVERT: H 245 ASP cc_start: 0.8641 (t0) cc_final: 0.8114 (t0) REVERT: J 37 TRP cc_start: 0.7291 (t60) cc_final: 0.6885 (t60) REVERT: J 98 LYS cc_start: 0.7677 (OUTLIER) cc_final: 0.7427 (mmtm) REVERT: J 100 ASP cc_start: 0.7929 (m-30) cc_final: 0.7468 (m-30) REVERT: J 319 TYR cc_start: 0.8502 (t80) cc_final: 0.8075 (t80) REVERT: J 323 ASN cc_start: 0.8999 (OUTLIER) cc_final: 0.8578 (m110) outliers start: 79 outliers final: 51 residues processed: 290 average time/residue: 0.5936 time to fit residues: 200.5150 Evaluate side-chains 276 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 331 ASP Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 444 CYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 51 SER Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 98 LYS Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 323 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 0.7980 chunk 258 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 138 optimal weight: 0.2980 chunk 183 optimal weight: 5.9990 chunk 282 optimal weight: 0.0870 chunk 158 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 202 optimal weight: 0.8980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 371 HIS F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080646 restraints weight = 44022.231| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.57 r_work: 0.3109 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25654 Z= 0.105 Angle : 0.527 14.814 34772 Z= 0.270 Chirality : 0.043 0.179 4104 Planarity : 0.004 0.051 4414 Dihedral : 4.814 74.680 3504 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.49 % Allowed : 23.36 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 3174 helix: 1.94 (0.15), residues: 1294 sheet: -0.09 (0.25), residues: 484 loop : -0.18 (0.17), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 292 TYR 0.027 0.001 TYR J 319 PHE 0.037 0.001 PHE H 75 TRP 0.006 0.001 TRP B 111 HIS 0.020 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00241 (25654) covalent geometry : angle 0.52748 (34772) hydrogen bonds : bond 0.03137 ( 1086) hydrogen bonds : angle 3.84840 ( 3039) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 221 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 50 ARG cc_start: 0.8273 (tpm170) cc_final: 0.7933 (tpm170) REVERT: E 415 MET cc_start: 0.9100 (ttp) cc_final: 0.8701 (ttm) REVERT: E 417 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7362 (tpm170) REVERT: G 10 PHE cc_start: 0.6619 (t80) cc_final: 0.6344 (t80) REVERT: G 14 MET cc_start: 0.7143 (tpp) cc_final: 0.6928 (mmm) REVERT: G 120 LYS cc_start: 0.8475 (mttt) cc_final: 0.8268 (mmtp) REVERT: G 121 ASP cc_start: 0.8741 (t0) cc_final: 0.8516 (t70) REVERT: G 245 ASP cc_start: 0.8448 (t0) cc_final: 0.8012 (t0) REVERT: I 50 GLU cc_start: 0.8382 (tp30) cc_final: 0.8107 (tp30) REVERT: I 227 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8078 (mt-10) REVERT: I 325 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8515 (mm-40) REVERT: B 53 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7397 (p0) REVERT: B 166 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: B 329 ASP cc_start: 0.8715 (t0) cc_final: 0.8182 (t70) REVERT: B 355 ILE cc_start: 0.8184 (mt) cc_final: 0.7880 (mm) REVERT: B 358 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7710 (tp30) REVERT: B 384 HIS cc_start: 0.7744 (m-70) cc_final: 0.7355 (m-70) REVERT: B 418 GLU cc_start: 0.8686 (tt0) cc_final: 0.7842 (tp30) REVERT: C 44 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8572 (tt0) REVERT: C 48 ASP cc_start: 0.8308 (m-30) cc_final: 0.8099 (m-30) REVERT: C 128 GLN cc_start: 0.7592 (pm20) cc_final: 0.7269 (tp40) REVERT: C 139 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7812 (tm-30) REVERT: C 228 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8233 (mmt90) REVERT: F 250 ARG cc_start: 0.7289 (ptp90) cc_final: 0.7033 (mtm-85) REVERT: F 310 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8005 (mm-30) REVERT: F 495 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8418 (pp20) REVERT: H 93 MET cc_start: 0.4849 (tpt) cc_final: 0.4576 (tpt) REVERT: H 95 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8195 (pt0) REVERT: H 120 LYS cc_start: 0.8244 (mttt) cc_final: 0.7819 (pttt) REVERT: H 198 GLU cc_start: 0.9065 (mt-10) cc_final: 0.8822 (mt-10) REVERT: H 245 ASP cc_start: 0.8602 (t0) cc_final: 0.8074 (t0) REVERT: J 37 TRP cc_start: 0.7275 (t60) cc_final: 0.6877 (t60) REVERT: J 100 ASP cc_start: 0.7930 (m-30) cc_final: 0.7509 (m-30) REVERT: J 319 TYR cc_start: 0.8561 (t80) cc_final: 0.8222 (t80) outliers start: 69 outliers final: 48 residues processed: 283 average time/residue: 0.5850 time to fit residues: 193.0903 Evaluate side-chains 267 residues out of total 2834 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 212 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 241 THR Chi-restraints excluded: chain E residue 249 SER Chi-restraints excluded: chain E residue 417 ARG Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 445 GLU Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain G residue 65 VAL Chi-restraints excluded: chain G residue 83 TYR Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 284 LEU Chi-restraints excluded: chain I residue 53 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 166 GLU Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 358 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 44 GLN Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain C residue 228 ARG Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 286 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 HIS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain F residue 495 GLU Chi-restraints excluded: chain F residue 510 SER Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain H residue 48 ASN Chi-restraints excluded: chain H residue 83 TYR Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 273 VAL Chi-restraints excluded: chain H residue 297 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain J residue 188 GLN Chi-restraints excluded: chain J residue 220 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 30 optimal weight: 0.0170 chunk 14 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 258 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 280 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 168 optimal weight: 9.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN E 371 HIS F 455 ASN F 470 HIS ** H 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 172 ASN J 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.111138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.079907 restraints weight = 43849.683| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.58 r_work: 0.3120 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25654 Z= 0.108 Angle : 0.528 14.379 34772 Z= 0.269 Chirality : 0.043 0.178 4104 Planarity : 0.004 0.051 4414 Dihedral : 4.757 73.775 3503 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.34 % Allowed : 23.68 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 3174 helix: 1.95 (0.15), residues: 1296 sheet: -0.06 (0.25), residues: 484 loop : -0.13 (0.17), residues: 1394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 292 TYR 0.019 0.001 TYR J 319 PHE 0.036 0.001 PHE G 75 TRP 0.006 0.001 TRP B 111 HIS 0.012 0.001 HIS F 470 Details of bonding type rmsd covalent geometry : bond 0.00250 (25654) covalent geometry : angle 0.52794 (34772) hydrogen bonds : bond 0.03105 ( 1086) hydrogen bonds : angle 3.83143 ( 3039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10181.72 seconds wall clock time: 173 minutes 20.36 seconds (10400.36 seconds total)