Starting phenix.real_space_refine on Sat Mar 7 10:09:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.map" model { file = "/net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tqc_56131/03_2026/9tqc_56131.cif" } resolution = 2.48 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= 0.000 sd= 0.038 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 196 5.16 5 C 25472 2.51 5 N 6998 2.21 5 O 7469 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 75 residue(s): 0.04s 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: 40135 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4107 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "B" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4107 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "C" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4107 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "D" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4107 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "E" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4102 Classifications: {'peptide': 533} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 507} Chain: "F" Number of atoms: 4107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4107 Classifications: {'peptide': 534} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain: "G" Number of atoms: 5096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 648, 5096 Classifications: {'peptide': 648} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 622} Chain: "J" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 975 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "H" Number of atoms: 4248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4248 Classifications: {'peptide': 534} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 512} Chain breaks: 2 Chain: "I" Number of atoms: 5089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5089 Classifications: {'peptide': 647} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 621} Chain breaks: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.42, per 1000 atoms: 0.23 Number of scatterers: 40135 At special positions: 0 Unit cell: (159.75, 154.5, 192.75, 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 196 16.00 O 7469 8.00 N 6998 7.00 C 25472 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.8 seconds 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9508 Finding SS restraints... Secondary structure from input PDB file: 227 helices and 46 sheets defined 45.9% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 12 through 37 Processing helix chain 'A' and resid 41 through 50 Processing helix chain 'A' and resid 55 through 64 Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 112 through 116 removed outlier: 3.646A pdb=" N THR A 116 " --> pdb=" O LYS A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 136 Processing helix chain 'A' and resid 149 through 156 removed outlier: 5.482A pdb=" N ASP A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 176 removed outlier: 3.771A pdb=" N TYR A 168 " --> pdb=" O GLY A 164 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 176 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 198 removed outlier: 3.814A pdb=" N ALA A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 228 through 234 Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.721A pdb=" N ARG A 240 " --> pdb=" O GLU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.559A pdb=" N SER A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.607A pdb=" N ASP A 288 " --> pdb=" O ASP A 285 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 290 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 292 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.751A pdb=" N ARG A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 315 removed outlier: 6.539A pdb=" N GLY A 313 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 367 Processing helix chain 'A' and resid 382 through 388 removed outlier: 3.702A pdb=" N GLU A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 404 removed outlier: 3.837A pdb=" N HIS A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 4.132A pdb=" N TYR A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 425 No H-bonds generated for 'chain 'A' and resid 424 through 425' Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 446 through 466 removed outlier: 3.796A pdb=" N GLN A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 490 removed outlier: 3.647A pdb=" N ASN A 490 " --> pdb=" O GLU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 497 removed outlier: 3.788A pdb=" N ARG A 497 " --> pdb=" O TYR A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 508 through 521 Processing helix chain 'B' and resid 12 through 37 Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.729A pdb=" N GLN B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 Processing helix chain 'B' and resid 86 through 89 Processing helix chain 'B' and resid 112 through 116 removed outlier: 3.710A pdb=" N THR B 116 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 136 Processing helix chain 'B' and resid 149 through 156 removed outlier: 5.488A pdb=" N ASP B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 176 removed outlier: 3.805A pdb=" N TYR B 168 " --> pdb=" O GLY B 164 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 176 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 198 removed outlier: 3.736A pdb=" N ALA B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 251 through 264 removed outlier: 3.539A pdb=" N SER B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 292 removed outlier: 3.715A pdb=" N ASP B 288 " --> pdb=" O ASP B 285 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 289 " --> pdb=" O SER B 286 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR B 290 " --> pdb=" O GLU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.653A pdb=" N ARG B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 6.377A pdb=" N GLY B 313 " --> pdb=" O VAL B 310 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 314 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 367 Processing helix chain 'B' and resid 382 through 388 Processing helix chain 'B' and resid 389 through 404 removed outlier: 3.554A pdb=" N HIS B 393 " --> pdb=" O GLY B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 423 removed outlier: 4.024A pdb=" N TYR B 422 " --> pdb=" O GLY B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 425 No H-bonds generated for 'chain 'B' and resid 424 through 425' Processing helix chain 'B' and resid 426 through 430 removed outlier: 3.530A pdb=" N ALA B 430 " --> pdb=" O ARG B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 470 through 490 Processing helix chain 'B' and resid 490 through 496 Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 508 through 521 Processing helix chain 'C' and resid 12 through 37 Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.645A pdb=" N GLN C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 Processing helix chain 'C' and resid 86 through 89 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.569A pdb=" N THR C 116 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 136 Processing helix chain 'C' and resid 149 through 156 removed outlier: 5.499A pdb=" N ASP C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 176 removed outlier: 3.826A pdb=" N TYR C 168 " --> pdb=" O GLY C 164 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C 176 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.722A pdb=" N ALA C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 223 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 234 through 241 removed outlier: 3.538A pdb=" N ARG C 240 " --> pdb=" O GLU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.607A pdb=" N SER C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 292 removed outlier: 3.759A pdb=" N THR C 290 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 292 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 309 removed outlier: 3.837A pdb=" N ARG C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 removed outlier: 6.461A pdb=" N GLY C 313 " --> pdb=" O VAL C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 367 Processing helix chain 'C' and resid 382 through 389 Processing helix chain 'C' and resid 389 through 404 Processing helix chain 'C' and resid 418 through 424 removed outlier: 4.180A pdb=" N TYR C 422 " --> pdb=" O GLY C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 430 removed outlier: 6.210A pdb=" N ALA C 428 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA C 430 " --> pdb=" O ARG C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 465 removed outlier: 3.774A pdb=" N GLN C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 490 removed outlier: 3.511A pdb=" N GLU C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN C 490 " --> pdb=" O GLU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 497 removed outlier: 3.802A pdb=" N ARG C 497 " --> pdb=" O TYR C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 507 No H-bonds generated for 'chain 'C' and resid 505 through 507' Processing helix chain 'C' and resid 508 through 521 Processing helix chain 'D' and resid 12 through 37 Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.727A pdb=" N GLN D 51 " --> pdb=" O LYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 64 Processing helix chain 'D' and resid 86 through 89 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 136 Processing helix chain 'D' and resid 149 through 156 removed outlier: 5.422A pdb=" N ASP D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 156 " --> pdb=" O GLN D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 176 removed outlier: 3.694A pdb=" N TYR D 168 " --> pdb=" O GLY D 164 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 175 " --> pdb=" O ALA D 171 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU D 176 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 192 Processing helix chain 'D' and resid 193 through 198 removed outlier: 3.656A pdb=" N ALA D 197 " --> pdb=" O ALA D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 228 through 234 Processing helix chain 'D' and resid 234 through 239 Processing helix chain 'D' and resid 251 through 264 removed outlier: 3.597A pdb=" N SER D 264 " --> pdb=" O ARG D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 291 removed outlier: 3.816A pdb=" N ASP D 288 " --> pdb=" O ASP D 285 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 290 " --> pdb=" O GLU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 309 removed outlier: 3.592A pdb=" N ARG D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 315 removed outlier: 6.282A pdb=" N GLY D 313 " --> pdb=" O VAL D 310 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER D 314 " --> pdb=" O VAL D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 367 Processing helix chain 'D' and resid 383 through 388 Processing helix chain 'D' and resid 389 through 404 removed outlier: 3.779A pdb=" N LYS D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET D 397 " --> pdb=" O HIS D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 424 Processing helix chain 'D' and resid 426 through 430 removed outlier: 3.844A pdb=" N ALA D 430 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 463 Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 470 through 488 Processing helix chain 'D' and resid 490 through 497 removed outlier: 3.845A pdb=" N ARG D 497 " --> pdb=" O TYR D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 508 through 521 Processing helix chain 'E' and resid 12 through 37 removed outlier: 3.723A pdb=" N LEU E 25 " --> pdb=" O ASN E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.841A pdb=" N GLN E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 64 Processing helix chain 'E' and resid 86 through 89 Processing helix chain 'E' and resid 112 through 116 removed outlier: 3.699A pdb=" N THR E 116 " --> pdb=" O LYS E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 136 Processing helix chain 'E' and resid 149 through 156 removed outlier: 5.436A pdb=" N ASP E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 176 removed outlier: 3.947A pdb=" N TYR E 168 " --> pdb=" O GLY E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 192 Processing helix chain 'E' and resid 193 through 198 removed outlier: 3.552A pdb=" N ALA E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 224 Processing helix chain 'E' and resid 228 through 234 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.505A pdb=" N SER E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 removed outlier: 3.720A pdb=" N ASP E 288 " --> pdb=" O ASP E 285 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR E 290 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE E 292 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 309 removed outlier: 3.668A pdb=" N ARG E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 315 removed outlier: 6.458A pdb=" N GLY E 313 " --> pdb=" O VAL E 310 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E 314 " --> pdb=" O VAL E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 367 Processing helix chain 'E' and resid 382 through 388 Processing helix chain 'E' and resid 389 through 404 removed outlier: 3.506A pdb=" N HIS E 393 " --> pdb=" O GLY E 389 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 424 removed outlier: 4.217A pdb=" N TYR E 422 " --> pdb=" O GLY E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'E' and resid 446 through 465 removed outlier: 3.613A pdb=" N GLN E 465 " --> pdb=" O LYS E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 488 Processing helix chain 'E' and resid 490 through 497 removed outlier: 3.770A pdb=" N ARG E 497 " --> pdb=" O TYR E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 505 through 507 No H-bonds generated for 'chain 'E' and resid 505 through 507' Processing helix chain 'E' and resid 508 through 521 Processing helix chain 'F' and resid 12 through 39 removed outlier: 3.888A pdb=" N LYS F 16 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY F 39 " --> pdb=" O GLN F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.758A pdb=" N GLN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 64 Processing helix chain 'F' and resid 86 through 89 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 118 through 136 Processing helix chain 'F' and resid 149 through 156 removed outlier: 5.623A pdb=" N ASP F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 176 removed outlier: 3.831A pdb=" N TYR F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU F 176 " --> pdb=" O GLN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.758A pdb=" N ALA F 197 " --> pdb=" O ALA F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 223 Processing helix chain 'F' and resid 228 through 233 Processing helix chain 'F' and resid 234 through 239 Processing helix chain 'F' and resid 251 through 264 removed outlier: 3.634A pdb=" N SER F 264 " --> pdb=" O ARG F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 292 removed outlier: 3.704A pdb=" N ASP F 288 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR F 290 " --> pdb=" O GLU F 287 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ILE F 292 " --> pdb=" O LEU F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 309 removed outlier: 3.518A pdb=" N ILE F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 315 removed outlier: 6.512A pdb=" N GLY F 313 " --> pdb=" O VAL F 310 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 314 " --> pdb=" O VAL F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 367 Processing helix chain 'F' and resid 382 through 388 Processing helix chain 'F' and resid 389 through 404 Processing helix chain 'F' and resid 418 through 424 removed outlier: 4.251A pdb=" N TYR F 422 " --> pdb=" O GLY F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 430 removed outlier: 6.269A pdb=" N ALA F 428 " --> pdb=" O CYS F 425 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F 430 " --> pdb=" O ARG F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 465 removed outlier: 3.648A pdb=" N GLN F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 489 Processing helix chain 'F' and resid 490 through 497 removed outlier: 3.697A pdb=" N ARG F 497 " --> pdb=" O TYR F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 505 through 507 No H-bonds generated for 'chain 'F' and resid 505 through 507' Processing helix chain 'F' and resid 508 through 521 Processing helix chain 'G' and resid 34 through 47 removed outlier: 3.610A pdb=" N MET G 47 " --> pdb=" O THR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 81 through 84 removed outlier: 3.602A pdb=" N LEU G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 81 through 84' Processing helix chain 'G' and resid 85 through 97 removed outlier: 3.560A pdb=" N ILE G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 110 removed outlier: 4.392A pdb=" N GLU G 110 " --> pdb=" O PHE G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 122 Processing helix chain 'G' and resid 129 through 136 Processing helix chain 'G' and resid 138 through 146 removed outlier: 3.659A pdb=" N ALA G 142 " --> pdb=" O SER G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 149 No H-bonds generated for 'chain 'G' and resid 147 through 149' Processing helix chain 'G' and resid 163 through 175 removed outlier: 3.660A pdb=" N GLY G 175 " --> pdb=" O ALA G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 215 Processing helix chain 'G' and resid 271 through 290 removed outlier: 3.987A pdb=" N ILE G 289 " --> pdb=" O VAL G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 319 through 328 removed outlier: 4.515A pdb=" N THR G 323 " --> pdb=" O GLU G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 340 Processing helix chain 'G' and resid 347 through 351 Processing helix chain 'G' and resid 366 through 370 removed outlier: 3.945A pdb=" N GLY G 370 " --> pdb=" O PRO G 367 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 431 Processing helix chain 'G' and resid 441 through 451 Processing helix chain 'G' and resid 451 through 456 removed outlier: 3.803A pdb=" N GLU G 456 " --> pdb=" O VAL G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 467 Processing helix chain 'G' and resid 475 through 494 removed outlier: 3.525A pdb=" N GLY G 479 " --> pdb=" O ASP G 475 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU G 481 " --> pdb=" O GLU G 477 " (cutoff:3.500A) Processing helix chain 'G' and resid 497 through 503 Processing helix chain 'G' and resid 593 through 602 Processing helix chain 'J' and resid 475 through 495 removed outlier: 3.881A pdb=" N GLY J 479 " --> pdb=" O ASP J 475 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU J 481 " --> pdb=" O GLU J 477 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR J 495 " --> pdb=" O MET J 491 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 503 Processing helix chain 'H' and resid 34 through 48 Processing helix chain 'H' and resid 62 through 68 removed outlier: 3.573A pdb=" N ARG H 66 " --> pdb=" O SER H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.365A pdb=" N GLU H 110 " --> pdb=" O PHE H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 122 removed outlier: 3.545A pdb=" N ALA H 115 " --> pdb=" O ASN H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 138 removed outlier: 3.766A pdb=" N MET H 133 " --> pdb=" O SER H 129 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER H 138 " --> pdb=" O GLU H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 146 Processing helix chain 'H' and resid 271 through 289 removed outlier: 3.816A pdb=" N ILE H 289 " --> pdb=" O VAL H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 328 removed outlier: 3.629A pdb=" N GLU H 324 " --> pdb=" O HIS H 320 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE H 326 " --> pdb=" O VAL H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 340 Processing helix chain 'H' and resid 347 through 351 removed outlier: 3.543A pdb=" N GLN H 350 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 366 through 370 removed outlier: 4.267A pdb=" N GLY H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 418 through 431 removed outlier: 3.789A pdb=" N ALA H 431 " --> pdb=" O GLU H 427 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 450 Processing helix chain 'H' and resid 452 through 457 removed outlier: 3.506A pdb=" N LYS H 455 " --> pdb=" O VAL H 452 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 457 " --> pdb=" O PHE H 454 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 467 removed outlier: 4.197A pdb=" N LYS H 466 " --> pdb=" O ASP H 462 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU H 467 " --> pdb=" O PHE H 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 462 through 467' Processing helix chain 'H' and resid 475 through 494 removed outlier: 3.786A pdb=" N GLY H 479 " --> pdb=" O ASP H 475 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU H 481 " --> pdb=" O GLU H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 503 Processing helix chain 'H' and resid 593 through 602 Processing helix chain 'I' and resid 34 through 47 removed outlier: 3.681A pdb=" N MET I 47 " --> pdb=" O THR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 60 removed outlier: 3.998A pdb=" N ARG I 60 " --> pdb=" O ALA I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 68 removed outlier: 3.639A pdb=" N ARG I 66 " --> pdb=" O SER I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 85 through 97 removed outlier: 3.611A pdb=" N ILE I 89 " --> pdb=" O ASN I 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 121 removed outlier: 3.598A pdb=" N ALA I 115 " --> pdb=" O ASN I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 129 through 136 removed outlier: 3.568A pdb=" N MET I 133 " --> pdb=" O SER I 129 " (cutoff:3.500A) Processing helix chain 'I' and resid 138 through 147 removed outlier: 3.651A pdb=" N LEU I 146 " --> pdb=" O ALA I 142 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU I 147 " --> pdb=" O LYS I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 175 Processing helix chain 'I' and resid 199 through 215 Processing helix chain 'I' and resid 271 through 288 Processing helix chain 'I' and resid 320 through 328 removed outlier: 3.581A pdb=" N ILE I 326 " --> pdb=" O VAL I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 330 through 340 Processing helix chain 'I' and resid 347 through 351 Processing helix chain 'I' and resid 418 through 430 Processing helix chain 'I' and resid 431 through 433 No H-bonds generated for 'chain 'I' and resid 431 through 433' Processing helix chain 'I' and resid 441 through 451 Processing helix chain 'I' and resid 451 through 456 removed outlier: 3.704A pdb=" N GLU I 456 " --> pdb=" O VAL I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 467 removed outlier: 3.779A pdb=" N GLU I 467 " --> pdb=" O PHE I 463 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 494 Processing helix chain 'I' and resid 497 through 503 Processing helix chain 'I' and resid 593 through 602 removed outlier: 3.570A pdb=" N GLN I 599 " --> pdb=" O LYS I 595 " (cutoff:3.500A) Processing helix chain 'I' and resid 602 through 607 removed outlier: 3.625A pdb=" N GLN I 606 " --> pdb=" O ALA I 602 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU I 607 " --> pdb=" O HIS I 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 602 through 607' Processing sheet with id=AA1, first strand: chain 'A' and resid 71 through 72 removed outlier: 8.607A pdb=" N ILE A 140 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 104 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU A 142 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 106 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS A 139 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL A 183 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR A 141 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 201 " --> pdb=" O GLN A 180 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N SER A 202 " --> pdb=" O HIS A 247 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ALA A 249 " --> pdb=" O SER A 202 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET A 204 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 189 removed outlier: 6.453A pdb=" N CYS A 188 " --> pdb=" O PHE A 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 8.342A pdb=" N VAL A 371 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A 340 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU A 373 " --> pdb=" O GLY A 340 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 342 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE A 433 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.802A pdb=" N THR B 93 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N ILE B 140 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N LEU B 142 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 106 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N CYS B 139 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N VAL B 183 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TYR B 141 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU B 201 " --> pdb=" O GLN B 180 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER B 202 " --> pdb=" O HIS B 247 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ALA B 249 " --> pdb=" O SER B 202 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N MET B 204 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 189 removed outlier: 6.297A pdb=" N CYS B 188 " --> pdb=" O PHE B 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 317 through 318 removed outlier: 4.036A pdb=" N PHE B 433 " --> pdb=" O LYS B 408 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 415 through 417 removed outlier: 6.095A pdb=" N SER B 416 " --> pdb=" O SER B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 71 through 73 removed outlier: 4.819A pdb=" N THR C 93 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N ILE C 140 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 104 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU C 142 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 106 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU C 201 " --> pdb=" O GLN C 180 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER C 202 " --> pdb=" O HIS C 247 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA C 249 " --> pdb=" O SER C 202 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N MET C 204 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 187 through 189 removed outlier: 6.654A pdb=" N CYS C 188 " --> pdb=" O PHE C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 317 through 318 removed outlier: 8.278A pdb=" N VAL C 371 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY C 340 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU C 373 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 342 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN C 375 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN C 344 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE C 376 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY C 415 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE C 433 " --> pdb=" O LYS C 408 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 318 removed outlier: 8.278A pdb=" N VAL C 371 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY C 340 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU C 373 " --> pdb=" O GLY C 340 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 342 " --> pdb=" O LEU C 373 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ASN C 375 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASN C 344 " --> pdb=" O ASN C 375 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE C 376 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLY C 415 " --> pdb=" O ILE C 376 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ARG C 441 " --> pdb=" O ILE C 412 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLY C 414 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N SER C 443 " --> pdb=" O GLY C 414 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER C 416 " --> pdb=" O SER C 443 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 71 through 72 removed outlier: 8.602A pdb=" N ILE D 140 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL D 104 " --> pdb=" O ILE D 140 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU D 142 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 106 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS D 139 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 183 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR D 141 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D 201 " --> pdb=" O GLN D 180 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N SER D 202 " --> pdb=" O HIS D 247 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA D 249 " --> pdb=" O SER D 202 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET D 204 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 187 through 188 Processing sheet with id=AB6, first strand: chain 'D' and resid 317 through 318 removed outlier: 8.255A pdb=" N VAL D 371 " --> pdb=" O PRO D 338 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLY D 340 " --> pdb=" O VAL D 371 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 373 " --> pdb=" O GLY D 340 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ILE D 342 " --> pdb=" O LEU D 373 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE D 433 " --> pdb=" O LYS D 408 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 415 through 417 Processing sheet with id=AB8, first strand: chain 'E' and resid 71 through 73 removed outlier: 4.754A pdb=" N THR E 93 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ILE E 140 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 104 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU E 142 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL E 106 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS E 139 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL E 183 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N TYR E 141 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU E 201 " --> pdb=" O GLN E 180 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL E 205 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER E 202 " --> pdb=" O HIS E 247 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA E 249 " --> pdb=" O SER E 202 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N MET E 204 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 317 through 318 removed outlier: 8.301A pdb=" N VAL E 371 " --> pdb=" O PRO E 338 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLY E 340 " --> pdb=" O VAL E 371 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU E 373 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 342 " --> pdb=" O LEU E 373 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N PHE E 433 " --> pdb=" O LYS E 408 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 415 through 417 removed outlier: 6.122A pdb=" N SER E 416 " --> pdb=" O SER E 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 71 through 72 removed outlier: 8.557A pdb=" N ILE F 140 " --> pdb=" O GLU F 102 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL F 104 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LEU F 142 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL F 106 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N CYS F 139 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N VAL F 183 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR F 141 " --> pdb=" O VAL F 183 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU F 201 " --> pdb=" O GLN F 180 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL F 205 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER F 202 " --> pdb=" O HIS F 247 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N ALA F 249 " --> pdb=" O SER F 202 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET F 204 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 187 through 189 Processing sheet with id=AC4, first strand: chain 'F' and resid 317 through 318 removed outlier: 4.035A pdb=" N PHE F 433 " --> pdb=" O LYS F 408 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 415 through 417 removed outlier: 6.225A pdb=" N SER F 416 " --> pdb=" O SER F 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 70 through 73 removed outlier: 4.133A pdb=" N SER G 70 " --> pdb=" O ALA G 51 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL G 54 " --> pdb=" O ILE G 30 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA G 100 " --> pdb=" O LYS G 27 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 306 through 313 removed outlier: 4.913A pdb=" N PHE G 307 " --> pdb=" O ASP G 302 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASP G 302 " --> pdb=" O PHE G 307 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE G 309 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU G 300 " --> pdb=" O PHE G 309 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU G 311 " --> pdb=" O GLU G 298 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG G 230 " --> pdb=" O VAL G 301 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N HIS G 231 " --> pdb=" O CYS G 252 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N PHE G 248 " --> pdb=" O GLN G 235 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N MET G 237 " --> pdb=" O ASN G 246 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N ASN G 246 " --> pdb=" O MET G 237 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N CYS G 252 " --> pdb=" O GLU G 263 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N GLU G 263 " --> pdb=" O CYS G 252 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ILE G 254 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE G 261 " --> pdb=" O ILE G 254 " (cutoff:3.500A) removed outlier: 14.417A pdb=" N GLN G 259 " --> pdb=" O TYR G 363 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N TYR G 363 " --> pdb=" O GLN G 259 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE G 261 " --> pdb=" O ARG G 361 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA G 410 " --> pdb=" O ILE G 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 376 through 377 Processing sheet with id=AC9, first strand: chain 'G' and resid 380 through 382 Processing sheet with id=AD1, first strand: chain 'G' and resid 514 through 520 removed outlier: 6.484A pdb=" N LYS G 536 " --> pdb=" O ILE G 532 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY G 584 " --> pdb=" O THR G 581 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU G 589 " --> pdb=" O GLN G 519 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 631 through 637 removed outlier: 3.885A pdb=" N ILE G 633 " --> pdb=" O ILE G 644 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA G 637 " --> pdb=" O MET G 640 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 514 through 519 removed outlier: 3.669A pdb=" N TYR J 549 " --> pdb=" O GLU J 560 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG J 551 " --> pdb=" O ILE J 558 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE J 558 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP J 553 " --> pdb=" O GLN J 556 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE J 559 " --> pdb=" O VAL J 566 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL J 566 " --> pdb=" O ILE J 559 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE J 561 " --> pdb=" O LYS J 564 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 569 through 572 removed outlier: 3.744A pdb=" N LEU J 577 " --> pdb=" O ILE J 588 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 70 through 73 removed outlier: 3.726A pdb=" N SER H 70 " --> pdb=" O ALA H 51 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N VAL H 54 " --> pdb=" O ILE H 30 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA H 100 " --> pdb=" O LYS H 27 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE H 101 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 244 through 251 removed outlier: 3.793A pdb=" N GLN H 235 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU H 249 " --> pdb=" O GLU H 233 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLU H 233 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASP H 251 " --> pdb=" O HIS H 231 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N HIS H 231 " --> pdb=" O ASP H 251 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 232 " --> pdb=" O PHE H 299 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N THR H 296 " --> pdb=" O MET H 312 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N MET H 312 " --> pdb=" O THR H 296 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N GLU H 298 " --> pdb=" O MET H 310 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 262 through 265 removed outlier: 4.049A pdb=" N ALA H 410 " --> pdb=" O ILE H 362 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 376 through 377 Processing sheet with id=AD9, first strand: chain 'H' and resid 380 through 382 Processing sheet with id=AE1, first strand: chain 'H' and resid 514 through 520 removed outlier: 3.545A pdb=" N ILE H 525 " --> pdb=" O TYR H 518 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 636 through 637 removed outlier: 3.669A pdb=" N ALA H 637 " --> pdb=" O MET H 640 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 70 through 73 removed outlier: 3.986A pdb=" N SER I 70 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL I 54 " --> pdb=" O ILE I 30 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I 100 " --> pdb=" O LYS I 27 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 178 through 179 Processing sheet with id=AE5, first strand: chain 'I' and resid 245 through 251 removed outlier: 5.432A pdb=" N ASN I 246 " --> pdb=" O MET I 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET I 237 " --> pdb=" O ASN I 246 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE I 248 " --> pdb=" O GLN I 235 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN I 235 " --> pdb=" O PHE I 248 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG I 230 " --> pdb=" O VAL I 301 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU I 311 " --> pdb=" O GLU I 298 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU I 300 " --> pdb=" O PHE I 309 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N PHE I 309 " --> pdb=" O LEU I 300 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP I 302 " --> pdb=" O PHE I 307 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N PHE I 307 " --> pdb=" O ASP I 302 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 262 through 264 removed outlier: 4.047A pdb=" N ALA I 410 " --> pdb=" O ILE I 362 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 376 through 377 Processing sheet with id=AE8, first strand: chain 'I' and resid 380 through 382 removed outlier: 3.742A pdb=" N PHE I 380 " --> pdb=" O GLY I 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 514 through 520 removed outlier: 3.728A pdb=" N GLU I 589 " --> pdb=" O GLN I 519 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 614 through 615 removed outlier: 3.728A pdb=" N THR I 614 " --> pdb=" O GLU I 636 " (cutoff:3.500A) 1857 hydrogen bonds defined for protein. 5151 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: 10.06 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8565 1.33 - 1.45: 9088 1.45 - 1.58: 22986 1.58 - 1.70: 0 1.70 - 1.82: 326 Bond restraints: 40965 Sorted by residual: bond pdb=" CA GLN G 348 " pdb=" CB GLN G 348 " ideal model delta sigma weight residual 1.528 1.550 -0.021 1.56e-02 4.11e+03 1.85e+00 bond pdb=" CA ASN I 246 " pdb=" CB ASN I 246 " ideal model delta sigma weight residual 1.536 1.564 -0.028 2.08e-02 2.31e+03 1.85e+00 bond pdb=" C HIS H 320 " pdb=" N PRO H 321 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.28e-02 6.10e+03 1.39e+00 bond pdb=" CB ASN G 349 " pdb=" CG ASN G 349 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.34e+00 bond pdb=" CB ASN I 246 " pdb=" CG ASN I 246 " ideal model delta sigma weight residual 1.516 1.544 -0.028 2.50e-02 1.60e+03 1.23e+00 ... (remaining 40960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 54894 1.85 - 3.71: 482 3.71 - 5.56: 57 5.56 - 7.42: 15 7.42 - 9.27: 1 Bond angle restraints: 55449 Sorted by residual: angle pdb=" C ALA F 190 " pdb=" CA ALA F 190 " pdb=" CB ALA F 190 " ideal model delta sigma weight residual 116.63 110.48 6.15 1.16e+00 7.43e-01 2.81e+01 angle pdb=" C ASN I 441 " pdb=" N ILE I 442 " pdb=" CA ILE I 442 " ideal model delta sigma weight residual 120.33 123.49 -3.16 8.00e-01 1.56e+00 1.56e+01 angle pdb=" C PHE C 149 " pdb=" N LEU C 150 " pdb=" CA LEU C 150 " ideal model delta sigma weight residual 120.09 124.73 -4.64 1.25e+00 6.40e-01 1.38e+01 angle pdb=" C PHE B 149 " pdb=" N LEU B 150 " pdb=" CA LEU B 150 " ideal model delta sigma weight residual 120.09 124.59 -4.50 1.25e+00 6.40e-01 1.30e+01 angle pdb=" CA ALA F 190 " pdb=" C ALA F 190 " pdb=" N GLY F 191 " ideal model delta sigma weight residual 119.63 116.75 2.88 8.10e-01 1.52e+00 1.26e+01 ... (remaining 55444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 21714 17.81 - 35.62: 2172 35.62 - 53.42: 633 53.42 - 71.23: 154 71.23 - 89.04: 80 Dihedral angle restraints: 24753 sinusoidal: 9934 harmonic: 14819 Sorted by residual: dihedral pdb=" CA PHE A 157 " pdb=" C PHE A 157 " pdb=" N ALA A 158 " pdb=" CA ALA A 158 " ideal model delta harmonic sigma weight residual 180.00 -155.29 -24.71 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA PHE C 157 " pdb=" C PHE C 157 " pdb=" N ALA C 158 " pdb=" CA ALA C 158 " ideal model delta harmonic sigma weight residual -180.00 -156.29 -23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA PHE E 157 " pdb=" C PHE E 157 " pdb=" N ALA E 158 " pdb=" CA ALA E 158 " ideal model delta harmonic sigma weight residual -180.00 -156.39 -23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 24750 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3934 0.031 - 0.061: 1409 0.061 - 0.092: 369 0.092 - 0.123: 414 0.123 - 0.153: 26 Chirality restraints: 6152 Sorted by residual: chirality pdb=" CB ILE G 174 " pdb=" CA ILE G 174 " pdb=" CG1 ILE G 174 " pdb=" CG2 ILE G 174 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE H 372 " pdb=" N ILE H 372 " pdb=" C ILE H 372 " pdb=" CB ILE H 372 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ASN I 269 " pdb=" N ASN I 269 " pdb=" C ASN I 269 " pdb=" CB ASN I 269 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 6149 not shown) Planarity restraints: 7237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN G 348 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.60e+00 pdb=" C GLN G 348 " -0.033 2.00e-02 2.50e+03 pdb=" O GLN G 348 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN G 349 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 490 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" CG ASN E 490 " 0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN E 490 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 490 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 247 " -0.008 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C LEU G 247 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU G 247 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE G 248 " -0.010 2.00e-02 2.50e+03 ... (remaining 7234 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 19406 3.00 - 3.48: 37442 3.48 - 3.95: 62178 3.95 - 4.43: 72026 4.43 - 4.90: 117022 Nonbonded interactions: 308074 Sorted by model distance: nonbonded pdb=" O GLN G 348 " pdb=" OE1 GLN G 348 " model vdw 2.527 3.040 nonbonded pdb=" O PRO I 268 " pdb=" OD1 ASN I 269 " model vdw 2.530 3.040 nonbonded pdb=" N ASP G 387 " pdb=" OD1 ASP G 387 " model vdw 2.541 3.120 nonbonded pdb=" O ASN I 269 " pdb=" OD1 ASN I 269 " model vdw 2.568 3.040 nonbonded pdb=" O GLN I 276 " pdb=" OE2 GLU I 280 " model vdw 2.572 3.040 ... (remaining 308069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 535) selection = (chain 'B' and resid 3 through 535) selection = (chain 'C' and resid 3 through 535) selection = (chain 'D' and resid 3 through 535) selection = chain 'E' selection = (chain 'F' and resid 3 through 535) } ncs_group { reference = (chain 'G' and (resid 24 through 392 or resid 394 through 701)) selection = chain 'I' } 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: 17.720 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: 0.030 Extract box with map and model: 0.770 Check model and map are aligned: 0.070 Set scattering table: 0.120 Process input model: 38.180 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.002 0.100 40968 Z= 0.132 Angle : 0.477 9.270 55449 Z= 0.269 Chirality : 0.042 0.153 6152 Planarity : 0.004 0.039 7237 Dihedral : 16.684 89.038 15245 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 0.43 % Allowed : 16.57 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.74 (0.12), residues: 5123 helix: 1.50 (0.12), residues: 1992 sheet: 2.01 (0.17), residues: 822 loop : -1.03 (0.12), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 529 TYR 0.014 0.001 TYR I 105 PHE 0.018 0.001 PHE E 477 TRP 0.014 0.001 TRP B 469 HIS 0.005 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00186 (40965) covalent geometry : angle 0.47662 (55449) hydrogen bonds : bond 0.19363 ( 1842) hydrogen bonds : angle 5.89217 ( 5151) Misc. bond : bond 0.09975 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 325 time to evaluate : 1.453 Fit side-chains REVERT: A 480 GLN cc_start: 0.6743 (tt0) cc_final: 0.6343 (mt0) REVERT: A 529 ARG cc_start: 0.8079 (mtp85) cc_final: 0.7836 (mmt90) REVERT: B 23 GLN cc_start: 0.8132 (mt0) cc_final: 0.7826 (mm-40) REVERT: B 50 GLN cc_start: 0.7284 (tp40) cc_final: 0.6950 (tp40) REVERT: B 220 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6408 (ttmt) REVERT: B 285 ASP cc_start: 0.8109 (t70) cc_final: 0.7640 (t0) REVERT: B 287 GLU cc_start: 0.7950 (mm-30) cc_final: 0.7233 (mm-30) REVERT: B 441 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7032 (mpt180) REVERT: B 490 ASN cc_start: 0.6106 (p0) cc_final: 0.5814 (p0) REVERT: B 526 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8050 (mm-30) REVERT: B 529 ARG cc_start: 0.7993 (ptm160) cc_final: 0.7456 (ttm-80) REVERT: C 42 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7677 (mm-30) REVERT: D 31 GLU cc_start: 0.7372 (tp30) cc_final: 0.7026 (tm-30) REVERT: D 42 GLU cc_start: 0.6171 (tp30) cc_final: 0.5628 (tt0) REVERT: D 185 MET cc_start: 0.8831 (mtt) cc_final: 0.8302 (mtt) REVERT: D 287 GLU cc_start: 0.7360 (mm-30) cc_final: 0.6893 (mp0) REVERT: D 288 ASP cc_start: 0.7222 (m-30) cc_final: 0.5931 (t0) REVERT: D 380 MET cc_start: 0.1741 (ttp) cc_final: 0.1215 (ttp) REVERT: E 30 ARG cc_start: 0.8153 (mtp85) cc_final: 0.7258 (mtt180) REVERT: E 189 THR cc_start: 0.8367 (p) cc_final: 0.7947 (t) REVERT: E 484 GLN cc_start: 0.7758 (tt0) cc_final: 0.7470 (tt0) REVERT: F 3 LYS cc_start: 0.8349 (ttpt) cc_final: 0.7873 (ttmt) REVERT: F 30 ARG cc_start: 0.8068 (mtp85) cc_final: 0.7476 (mtt180) REVERT: F 384 LYS cc_start: 0.6420 (ptmm) cc_final: 0.6079 (mptt) REVERT: F 480 GLN cc_start: 0.6793 (tp40) cc_final: 0.6377 (tt0) REVERT: F 481 MET cc_start: 0.7354 (mmp) cc_final: 0.6946 (mmt) REVERT: G 306 LYS cc_start: 0.4736 (OUTLIER) cc_final: 0.4155 (ptpp) REVERT: G 352 GLN cc_start: 0.5607 (mm-40) cc_final: 0.4227 (tt0) REVERT: G 369 GLN cc_start: 0.5130 (mt0) cc_final: 0.4855 (mm-40) REVERT: G 382 LYS cc_start: 0.5901 (mmtm) cc_final: 0.4996 (tttm) REVERT: G 427 GLU cc_start: 0.5670 (tt0) cc_final: 0.5086 (tm-30) REVERT: G 519 GLN cc_start: 0.7650 (tt0) cc_final: 0.7059 (tp40) REVERT: G 535 LYS cc_start: 0.7593 (pttp) cc_final: 0.7329 (mtpp) REVERT: G 583 LYS cc_start: 0.7232 (mptp) cc_final: 0.6801 (mptm) REVERT: H 73 TYR cc_start: 0.5643 (t80) cc_final: 0.5368 (t80) REVERT: H 76 GLU cc_start: 0.5402 (OUTLIER) cc_final: 0.4977 (tp30) REVERT: H 237 MET cc_start: 0.4477 (mmt) cc_final: 0.3658 (mmm) REVERT: H 250 ARG cc_start: 0.5050 (mtt180) cc_final: 0.3087 (ptm160) REVERT: H 310 MET cc_start: 0.3934 (tmm) cc_final: 0.3724 (tmm) REVERT: H 312 MET cc_start: 0.4238 (ttt) cc_final: 0.3481 (ttp) REVERT: H 313 ASN cc_start: 0.3273 (m-40) cc_final: 0.2856 (m-40) REVERT: H 477 GLU cc_start: 0.6076 (mp0) cc_final: 0.5812 (mp0) REVERT: H 535 LYS cc_start: 0.7874 (mtmm) cc_final: 0.6826 (ptmt) REVERT: H 552 TYR cc_start: 0.7925 (OUTLIER) cc_final: 0.7362 (t80) REVERT: H 583 LYS cc_start: 0.6492 (OUTLIER) cc_final: 0.4732 (ttpp) REVERT: I 42 LYS cc_start: 0.6012 (tptp) cc_final: 0.5225 (ttpp) REVERT: I 136 MET cc_start: 0.0319 (tpp) cc_final: -0.0551 (tmt) REVERT: I 212 MET cc_start: 0.1206 (mmt) cc_final: 0.0989 (mpp) REVERT: I 220 MET cc_start: 0.0199 (mmm) cc_final: -0.0632 (ttp) REVERT: I 249 GLU cc_start: 0.6430 (mm-30) cc_final: 0.5998 (pm20) REVERT: I 400 GLU cc_start: 0.7334 (mm-30) cc_final: 0.7108 (mm-30) REVERT: I 535 LYS cc_start: 0.7938 (mtmm) cc_final: 0.7442 (mttm) REVERT: I 583 LYS cc_start: 0.7462 (mmtp) cc_final: 0.6997 (mptt) outliers start: 18 outliers final: 8 residues processed: 334 average time/residue: 0.9266 time to fit residues: 364.5772 Evaluate side-chains 333 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 319 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain D residue 425 CYS Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 306 LYS Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain H residue 583 LYS Chi-restraints excluded: chain I residue 120 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 7.9990 chunk 494 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN B 208 GLN D 354 GLN E 35 GLN E 452 ASN F 101 ASN I 235 GLN I 350 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.187590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.119815 restraints weight = 43594.850| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.82 r_work: 0.3263 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 40968 Z= 0.150 Angle : 0.539 8.368 55449 Z= 0.295 Chirality : 0.045 0.159 6152 Planarity : 0.004 0.043 7237 Dihedral : 5.057 65.900 5708 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.24 % Favored : 96.68 % Rotamer: Outliers : 2.73 % Allowed : 15.17 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.69 (0.12), residues: 5123 helix: 1.54 (0.12), residues: 2035 sheet: 2.00 (0.18), residues: 758 loop : -1.11 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 390 TYR 0.019 0.002 TYR F 429 PHE 0.016 0.002 PHE H 380 TRP 0.011 0.001 TRP I 514 HIS 0.005 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00344 (40965) covalent geometry : angle 0.53865 (55449) hydrogen bonds : bond 0.06099 ( 1842) hydrogen bonds : angle 4.63343 ( 5151) Misc. bond : bond 0.00046 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 336 time to evaluate : 1.435 Fit side-chains REVERT: A 7 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8169 (mp10) REVERT: A 480 GLN cc_start: 0.6837 (tt0) cc_final: 0.6379 (mt0) REVERT: A 529 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7842 (mmt90) REVERT: B 42 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7053 (tp30) REVERT: B 43 LYS cc_start: 0.7470 (ttmm) cc_final: 0.6721 (tptt) REVERT: B 47 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6627 (tmmt) REVERT: B 50 GLN cc_start: 0.7334 (tp40) cc_final: 0.7036 (tp40) REVERT: B 230 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6553 (tp30) REVERT: B 287 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 309 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8349 (mtt90) REVERT: B 351 GLU cc_start: 0.8095 (mp0) cc_final: 0.7459 (mp0) REVERT: B 526 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 529 ARG cc_start: 0.8192 (ptm160) cc_final: 0.7645 (ttm-80) REVERT: C 42 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7645 (mm-30) REVERT: C 83 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5756 (mp0) REVERT: D 31 GLU cc_start: 0.7476 (tp30) cc_final: 0.7141 (tm-30) REVERT: D 42 GLU cc_start: 0.6137 (tp30) cc_final: 0.5575 (tt0) REVERT: D 86 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8000 (mm) REVERT: D 185 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8535 (mtt) REVERT: D 287 GLU cc_start: 0.7214 (mm-30) cc_final: 0.6776 (mp0) REVERT: D 380 MET cc_start: 0.1844 (ttp) cc_final: 0.1329 (ttp) REVERT: D 526 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: E 30 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7365 (mtt180) REVERT: E 84 ASP cc_start: 0.8669 (m-30) cc_final: 0.8431 (m-30) REVERT: E 189 THR cc_start: 0.8392 (p) cc_final: 0.7987 (t) REVERT: E 220 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6923 (tptm) REVERT: F 3 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7869 (ttmt) REVERT: F 30 ARG cc_start: 0.8231 (mtp85) cc_final: 0.7626 (mtt180) REVERT: F 285 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7933 (t70) REVERT: F 384 LYS cc_start: 0.6147 (ptmm) cc_final: 0.5618 (mmtm) REVERT: F 480 GLN cc_start: 0.6846 (tp40) cc_final: 0.6424 (tt0) REVERT: F 481 MET cc_start: 0.7353 (mmp) cc_final: 0.6934 (mmt) REVERT: F 498 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8845 (mt) REVERT: F 526 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8186 (mm-30) REVERT: G 329 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6052 (mt) REVERT: G 369 GLN cc_start: 0.5073 (mt0) cc_final: 0.4831 (mm-40) REVERT: G 375 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6462 (pp) REVERT: G 382 LYS cc_start: 0.5726 (mmtm) cc_final: 0.4950 (tttm) REVERT: G 403 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.5110 (ppt170) REVERT: G 427 GLU cc_start: 0.5595 (tt0) cc_final: 0.4964 (pp20) REVERT: G 519 GLN cc_start: 0.7729 (tt0) cc_final: 0.7092 (tp40) REVERT: G 535 LYS cc_start: 0.7698 (pttp) cc_final: 0.7282 (mmtt) REVERT: G 560 GLU cc_start: 0.8561 (tt0) cc_final: 0.8328 (tt0) REVERT: G 570 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8424 (p) REVERT: G 583 LYS cc_start: 0.7330 (mptp) cc_final: 0.6910 (mptm) REVERT: G 606 GLN cc_start: 0.5718 (mt0) cc_final: 0.4158 (mm110) REVERT: G 638 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5289 (mtm) REVERT: H 59 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6417 (m-30) REVERT: H 73 TYR cc_start: 0.5536 (t80) cc_final: 0.5062 (t80) REVERT: H 76 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.5275 (tm-30) REVERT: H 312 MET cc_start: 0.4293 (ttt) cc_final: 0.3663 (ttp) REVERT: H 313 ASN cc_start: 0.3358 (m-40) cc_final: 0.2945 (m-40) REVERT: H 375 ILE cc_start: 0.4932 (OUTLIER) cc_final: 0.4586 (mm) REVERT: H 477 GLU cc_start: 0.6046 (mp0) cc_final: 0.5785 (mt-10) REVERT: H 535 LYS cc_start: 0.8026 (mtmm) cc_final: 0.6955 (ptmt) REVERT: H 552 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7468 (t80) REVERT: I 42 LYS cc_start: 0.6040 (tptp) cc_final: 0.5227 (ttpp) REVERT: I 95 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6212 (tt0) REVERT: I 131 LYS cc_start: 0.3652 (OUTLIER) cc_final: 0.3025 (pptt) REVERT: I 136 MET cc_start: -0.0055 (tpp) cc_final: -0.0931 (tmt) REVERT: I 212 MET cc_start: 0.1247 (mmt) cc_final: 0.0989 (mpp) REVERT: I 220 MET cc_start: 0.0158 (mmm) cc_final: -0.0694 (tmm) REVERT: I 249 GLU cc_start: 0.6555 (mm-30) cc_final: 0.5921 (mp0) REVERT: I 312 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.3904 (tmt) REVERT: I 365 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5821 (mt-10) REVERT: I 535 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7542 (mttt) REVERT: I 583 LYS cc_start: 0.7429 (mmtp) cc_final: 0.6952 (mptt) REVERT: I 611 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.6237 (ptt) outliers start: 115 outliers final: 41 residues processed: 419 average time/residue: 0.8576 time to fit residues: 427.1915 Evaluate side-chains 395 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 326 time to evaluate : 1.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 638 MET Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain H residue 576 HIS Chi-restraints excluded: chain H residue 601 SER Chi-restraints excluded: chain I residue 46 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 611 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 381 optimal weight: 6.9990 chunk 363 optimal weight: 8.9990 chunk 80 optimal weight: 7.9990 chunk 349 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 436 optimal weight: 5.9990 chunk 300 optimal weight: 0.9990 chunk 236 optimal weight: 10.0000 chunk 499 optimal weight: 9.9990 chunk 502 optimal weight: 7.9990 chunk 463 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN A 449 GLN E 452 ASN F 101 ASN G 50 GLN G 201 HIS G 642 HIS H 64 HIS I 235 GLN I 450 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.185333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117922 restraints weight = 43607.047| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.72 r_work: 0.3241 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 40968 Z= 0.182 Angle : 0.591 8.324 55449 Z= 0.322 Chirality : 0.047 0.159 6152 Planarity : 0.005 0.073 7237 Dihedral : 5.203 62.330 5686 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.16 % Favored : 96.76 % Rotamer: Outliers : 3.77 % Allowed : 14.84 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.46 (0.11), residues: 5123 helix: 1.41 (0.12), residues: 2027 sheet: 1.79 (0.18), residues: 771 loop : -1.27 (0.11), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 497 TYR 0.022 0.002 TYR F 429 PHE 0.019 0.002 PHE H 380 TRP 0.011 0.002 TRP H 514 HIS 0.006 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00436 (40965) covalent geometry : angle 0.59074 (55449) hydrogen bonds : bond 0.06737 ( 1842) hydrogen bonds : angle 4.50798 ( 5151) Misc. bond : bond 0.00066 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 339 time to evaluate : 1.603 Fit side-chains REVERT: A 7 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: A 480 GLN cc_start: 0.6886 (tt0) cc_final: 0.6469 (mt0) REVERT: A 529 ARG cc_start: 0.8114 (mtp85) cc_final: 0.7866 (mmt90) REVERT: B 14 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6310 (pm20) REVERT: B 42 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7047 (tp30) REVERT: B 43 LYS cc_start: 0.7535 (ttmm) cc_final: 0.7209 (ttpp) REVERT: B 47 LYS cc_start: 0.7517 (OUTLIER) cc_final: 0.6689 (tmmt) REVERT: B 50 GLN cc_start: 0.7369 (tp40) cc_final: 0.7085 (tp40) REVERT: B 220 LYS cc_start: 0.6568 (OUTLIER) cc_final: 0.6318 (ttmt) REVERT: B 230 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6384 (tp30) REVERT: B 287 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 309 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8407 (mtt90) REVERT: B 351 GLU cc_start: 0.8110 (mp0) cc_final: 0.7510 (mp0) REVERT: B 441 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.6744 (mpt180) REVERT: B 472 GLU cc_start: 0.3559 (OUTLIER) cc_final: 0.2716 (pm20) REVERT: B 526 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8079 (mm-30) REVERT: B 529 ARG cc_start: 0.8296 (ptm160) cc_final: 0.7683 (tpp80) REVERT: C 42 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: C 475 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6519 (mm-30) REVERT: D 31 GLU cc_start: 0.7504 (tp30) cc_final: 0.7116 (tm-30) REVERT: D 42 GLU cc_start: 0.6202 (tp30) cc_final: 0.5620 (tt0) REVERT: D 86 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8026 (mm) REVERT: D 113 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (mmtp) REVERT: D 185 MET cc_start: 0.8966 (mtt) cc_final: 0.8442 (mtt) REVERT: D 287 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6779 (mp0) REVERT: D 380 MET cc_start: 0.2041 (ttp) cc_final: 0.1605 (ttp) REVERT: D 526 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: E 30 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7348 (mtt180) REVERT: E 84 ASP cc_start: 0.8730 (m-30) cc_final: 0.8504 (m-30) REVERT: E 189 THR cc_start: 0.8487 (p) cc_final: 0.8054 (t) REVERT: E 220 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.6966 (tptm) REVERT: E 479 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6710 (t) REVERT: F 3 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7903 (ttmt) REVERT: F 30 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7631 (mtt180) REVERT: F 285 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7914 (t70) REVERT: F 480 GLN cc_start: 0.6819 (tp40) cc_final: 0.6357 (tt0) REVERT: F 481 MET cc_start: 0.7345 (mmp) cc_final: 0.6909 (mmt) REVERT: F 498 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8874 (mp) REVERT: F 526 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8171 (mm-30) REVERT: G 76 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5680 (mm-30) REVERT: G 136 MET cc_start: 0.0892 (OUTLIER) cc_final: 0.0143 (mmm) REVERT: G 329 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6010 (mt) REVERT: G 350 GLN cc_start: 0.6072 (mm-40) cc_final: 0.5814 (mp10) REVERT: G 369 GLN cc_start: 0.5029 (mt0) cc_final: 0.4757 (mm-40) REVERT: G 382 LYS cc_start: 0.5745 (mmtm) cc_final: 0.4872 (tttm) REVERT: G 427 GLU cc_start: 0.5642 (tt0) cc_final: 0.5006 (pp20) REVERT: G 466 LYS cc_start: 0.5489 (tptp) cc_final: 0.5168 (tttp) REVERT: G 519 GLN cc_start: 0.7770 (tt0) cc_final: 0.7152 (tp40) REVERT: G 560 GLU cc_start: 0.8585 (tt0) cc_final: 0.8294 (tt0) REVERT: G 583 LYS cc_start: 0.7401 (mptp) cc_final: 0.7000 (mptm) REVERT: G 606 GLN cc_start: 0.5752 (mt0) cc_final: 0.4317 (mm110) REVERT: G 638 MET cc_start: 0.6390 (OUTLIER) cc_final: 0.5710 (mtm) REVERT: H 73 TYR cc_start: 0.5643 (t80) cc_final: 0.5166 (t80) REVERT: H 116 LYS cc_start: 0.3915 (ttmm) cc_final: 0.3526 (ttpt) REVERT: H 237 MET cc_start: 0.4625 (mmt) cc_final: 0.4417 (mmt) REVERT: H 312 MET cc_start: 0.4378 (ttt) cc_final: 0.3951 (ttp) REVERT: H 313 ASN cc_start: 0.3519 (m-40) cc_final: 0.3107 (m-40) REVERT: H 375 ILE cc_start: 0.4794 (OUTLIER) cc_final: 0.4409 (mm) REVERT: H 552 TYR cc_start: 0.7994 (OUTLIER) cc_final: 0.7513 (t80) REVERT: H 644 ILE cc_start: -0.0954 (OUTLIER) cc_final: -0.1424 (pt) REVERT: I 42 LYS cc_start: 0.6047 (tptp) cc_final: 0.5218 (ttpp) REVERT: I 95 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6262 (tt0) REVERT: I 131 LYS cc_start: 0.3738 (OUTLIER) cc_final: 0.3118 (pptt) REVERT: I 136 MET cc_start: -0.0205 (OUTLIER) cc_final: -0.1476 (tmt) REVERT: I 212 MET cc_start: 0.1253 (OUTLIER) cc_final: 0.0954 (mpp) REVERT: I 220 MET cc_start: 0.0301 (mmm) cc_final: -0.0472 (tmm) REVERT: I 249 GLU cc_start: 0.6683 (mm-30) cc_final: 0.5946 (mp0) REVERT: I 292 ARG cc_start: 0.5934 (mmt-90) cc_final: 0.5639 (mmm-85) REVERT: I 312 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4003 (tmt) REVERT: I 365 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.5651 (mt-10) REVERT: I 369 GLN cc_start: 0.6118 (OUTLIER) cc_final: 0.5194 (mp-120) REVERT: I 371 PHE cc_start: 0.5329 (m-80) cc_final: 0.4894 (m-10) REVERT: I 450 GLN cc_start: 0.5534 (OUTLIER) cc_final: 0.5219 (tp-100) REVERT: I 535 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7580 (mttt) REVERT: I 543 ASN cc_start: 0.7098 (m-40) cc_final: 0.6876 (t0) REVERT: I 583 LYS cc_start: 0.7477 (mmtp) cc_final: 0.6999 (mptt) REVERT: I 611 MET cc_start: 0.6453 (OUTLIER) cc_final: 0.6150 (ptt) outliers start: 159 outliers final: 60 residues processed: 455 average time/residue: 0.8179 time to fit residues: 444.5769 Evaluate side-chains 425 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 331 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 344 LEU Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 595 LYS Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 638 MET Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain H residue 576 HIS Chi-restraints excluded: chain H residue 644 ILE Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 212 MET Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 343 THR Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 369 GLN Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 450 GLN Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 611 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 106 optimal weight: 7.9990 chunk 284 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 442 optimal weight: 5.9990 chunk 349 optimal weight: 20.0000 chunk 414 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN B 108 ASN D 207 ASN E 452 ASN G 231 HIS I 235 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.186592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.119440 restraints weight = 43543.287| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.76 r_work: 0.3260 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40968 Z= 0.135 Angle : 0.519 8.071 55449 Z= 0.283 Chirality : 0.045 0.156 6152 Planarity : 0.004 0.041 7237 Dihedral : 4.887 56.228 5683 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Rotamer: Outliers : 3.44 % Allowed : 15.64 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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 (0.11), residues: 5123 helix: 1.57 (0.12), residues: 2027 sheet: 1.83 (0.18), residues: 776 loop : -1.26 (0.11), residues: 2320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 361 TYR 0.018 0.001 TYR C 429 PHE 0.014 0.002 PHE D 319 TRP 0.009 0.001 TRP H 514 HIS 0.005 0.001 HIS I 451 Details of bonding type rmsd covalent geometry : bond 0.00311 (40965) covalent geometry : angle 0.51875 (55449) hydrogen bonds : bond 0.05412 ( 1842) hydrogen bonds : angle 4.30258 ( 5151) Misc. bond : bond 0.00043 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 342 time to evaluate : 1.538 Fit side-chains REVERT: A 3 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7917 (tttp) REVERT: A 7 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8200 (mp10) REVERT: A 480 GLN cc_start: 0.6855 (tt0) cc_final: 0.6436 (mt0) REVERT: A 529 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7861 (mmt90) REVERT: B 14 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6288 (pm20) REVERT: B 42 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7044 (tp30) REVERT: B 43 LYS cc_start: 0.7430 (ttmm) cc_final: 0.6674 (tptt) REVERT: B 47 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6636 (tmmt) REVERT: B 50 GLN cc_start: 0.7348 (tp40) cc_final: 0.7068 (tp40) REVERT: B 220 LYS cc_start: 0.6604 (OUTLIER) cc_final: 0.6364 (ttmt) REVERT: B 287 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 299 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6164 (mtpp) REVERT: B 309 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8365 (mtt90) REVERT: B 351 GLU cc_start: 0.8019 (mp0) cc_final: 0.7458 (mp0) REVERT: B 526 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8085 (mm-30) REVERT: C 42 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7591 (mm-30) REVERT: C 475 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.6482 (mm-30) REVERT: D 31 GLU cc_start: 0.7491 (tp30) cc_final: 0.7104 (tm-30) REVERT: D 42 GLU cc_start: 0.6131 (tp30) cc_final: 0.5559 (tt0) REVERT: D 86 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7983 (mm) REVERT: D 113 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8176 (mmtp) REVERT: D 185 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: D 287 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6730 (mp0) REVERT: D 380 MET cc_start: 0.2025 (ttp) cc_final: 0.1602 (ttp) REVERT: D 498 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (mp) REVERT: D 526 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7781 (mt-10) REVERT: E 30 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7326 (mtt180) REVERT: E 84 ASP cc_start: 0.8687 (m-30) cc_final: 0.8446 (m-30) REVERT: E 189 THR cc_start: 0.8421 (p) cc_final: 0.8027 (t) REVERT: F 3 LYS cc_start: 0.8404 (ttpt) cc_final: 0.7896 (ttmt) REVERT: F 30 ARG cc_start: 0.8253 (mtp85) cc_final: 0.7635 (mtt180) REVERT: F 285 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7918 (t70) REVERT: F 480 GLN cc_start: 0.6852 (tp40) cc_final: 0.6418 (tt0) REVERT: F 481 MET cc_start: 0.7361 (mmp) cc_final: 0.6923 (mmt) REVERT: F 498 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8882 (mp) REVERT: F 526 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8183 (mm-30) REVERT: G 76 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5666 (mm-30) REVERT: G 136 MET cc_start: 0.1011 (mtt) cc_final: 0.0270 (mmm) REVERT: G 329 LEU cc_start: 0.6378 (OUTLIER) cc_final: 0.5975 (mt) REVERT: G 350 GLN cc_start: 0.6112 (mm-40) cc_final: 0.5904 (mp10) REVERT: G 369 GLN cc_start: 0.4982 (mt0) cc_final: 0.4775 (mm-40) REVERT: G 375 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6465 (pp) REVERT: G 382 LYS cc_start: 0.5716 (mmtm) cc_final: 0.4853 (tttm) REVERT: G 427 GLU cc_start: 0.5660 (tt0) cc_final: 0.5015 (pp20) REVERT: G 466 LYS cc_start: 0.5490 (tptp) cc_final: 0.5205 (tttt) REVERT: G 519 GLN cc_start: 0.7724 (tt0) cc_final: 0.7110 (tp40) REVERT: G 560 GLU cc_start: 0.8550 (tt0) cc_final: 0.8284 (tt0) REVERT: G 570 VAL cc_start: 0.8605 (OUTLIER) cc_final: 0.8351 (p) REVERT: G 583 LYS cc_start: 0.7355 (mptp) cc_final: 0.7007 (mptm) REVERT: G 606 GLN cc_start: 0.5739 (mt0) cc_final: 0.4299 (mm110) REVERT: G 638 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.5690 (mtm) REVERT: J 476 ASN cc_start: 0.3848 (OUTLIER) cc_final: 0.2155 (t0) REVERT: J 552 TYR cc_start: 0.0391 (OUTLIER) cc_final: -0.0892 (m-80) REVERT: H 26 ASN cc_start: 0.4576 (OUTLIER) cc_final: 0.4376 (p0) REVERT: H 73 TYR cc_start: 0.5572 (t80) cc_final: 0.5153 (t80) REVERT: H 140 GLN cc_start: 0.2565 (OUTLIER) cc_final: 0.2054 (tt0) REVERT: H 237 MET cc_start: 0.4435 (mmt) cc_final: 0.4226 (mmt) REVERT: H 312 MET cc_start: 0.4388 (ttt) cc_final: 0.3798 (ttp) REVERT: H 313 ASN cc_start: 0.3511 (m-40) cc_final: 0.3109 (m-40) REVERT: H 375 ILE cc_start: 0.4765 (OUTLIER) cc_final: 0.4340 (mm) REVERT: H 477 GLU cc_start: 0.6192 (mp0) cc_final: 0.5693 (pt0) REVERT: H 552 TYR cc_start: 0.7978 (OUTLIER) cc_final: 0.7529 (t80) REVERT: I 42 LYS cc_start: 0.6029 (tptp) cc_final: 0.5216 (ttpp) REVERT: I 80 LYS cc_start: 0.6095 (OUTLIER) cc_final: 0.5421 (tppp) REVERT: I 95 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6274 (tt0) REVERT: I 131 LYS cc_start: 0.3697 (OUTLIER) cc_final: 0.3119 (pptt) REVERT: I 136 MET cc_start: -0.0183 (OUTLIER) cc_final: -0.1531 (tmt) REVERT: I 212 MET cc_start: 0.1334 (OUTLIER) cc_final: 0.1033 (mpp) REVERT: I 220 MET cc_start: 0.0432 (mmm) cc_final: -0.0374 (tmm) REVERT: I 365 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.6056 (mt-10) REVERT: I 535 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7559 (mttt) REVERT: I 543 ASN cc_start: 0.7106 (m-40) cc_final: 0.6869 (t0) REVERT: I 563 GLN cc_start: 0.5050 (mt0) cc_final: 0.4676 (mt0) REVERT: I 583 LYS cc_start: 0.7459 (mmtp) cc_final: 0.6990 (mptt) REVERT: I 611 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.6137 (ptt) REVERT: I 662 GLN cc_start: 0.5516 (mt0) cc_final: 0.5082 (mp10) outliers start: 145 outliers final: 49 residues processed: 442 average time/residue: 0.8315 time to fit residues: 438.7307 Evaluate side-chains 411 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 328 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 3 LYS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 376 ILE Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 638 MET Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 476 ASN Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 541 ILE Chi-restraints excluded: chain J residue 552 TYR Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 522 SER Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 136 MET Chi-restraints excluded: chain I residue 212 MET Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 317 GLN Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 601 SER Chi-restraints excluded: chain I residue 611 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 48 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 83 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 487 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 461 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 351 optimal weight: 7.9990 chunk 440 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN I 235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.187734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.120612 restraints weight = 43542.699| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.81 r_work: 0.3277 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40968 Z= 0.110 Angle : 0.481 7.228 55449 Z= 0.262 Chirality : 0.044 0.155 6152 Planarity : 0.004 0.038 7237 Dihedral : 4.636 57.763 5680 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.95 % Favored : 96.97 % Rotamer: Outliers : 2.87 % Allowed : 16.52 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.78 (0.12), residues: 5123 helix: 1.75 (0.12), residues: 2030 sheet: 2.00 (0.18), residues: 780 loop : -1.21 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 361 TYR 0.015 0.001 TYR I 105 PHE 0.013 0.001 PHE D 319 TRP 0.008 0.001 TRP H 514 HIS 0.003 0.001 HIS B 34 Details of bonding type rmsd covalent geometry : bond 0.00242 (40965) covalent geometry : angle 0.48075 (55449) hydrogen bonds : bond 0.04626 ( 1842) hydrogen bonds : angle 4.13667 ( 5151) Misc. bond : bond 0.00029 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 334 time to evaluate : 1.398 Fit side-chains REVERT: A 3 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7892 (tttp) REVERT: A 7 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8160 (mp10) REVERT: A 480 GLN cc_start: 0.6932 (tt0) cc_final: 0.6476 (mt0) REVERT: A 529 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7870 (mmt90) REVERT: B 42 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: B 43 LYS cc_start: 0.7397 (ttmm) cc_final: 0.6637 (tptt) REVERT: B 47 LYS cc_start: 0.7487 (OUTLIER) cc_final: 0.6612 (tmmt) REVERT: B 50 GLN cc_start: 0.7339 (tp40) cc_final: 0.7054 (tp40) REVERT: B 220 LYS cc_start: 0.6448 (OUTLIER) cc_final: 0.6194 (ttmt) REVERT: B 287 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 309 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8283 (mtt90) REVERT: B 351 GLU cc_start: 0.7951 (mp0) cc_final: 0.7402 (mp0) REVERT: B 396 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8204 (ptpp) REVERT: B 449 GLN cc_start: 0.5786 (OUTLIER) cc_final: 0.5552 (tt0) REVERT: B 526 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 42 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: C 475 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6413 (mm-30) REVERT: D 31 GLU cc_start: 0.7506 (tp30) cc_final: 0.7175 (tm-30) REVERT: D 42 GLU cc_start: 0.6086 (tp30) cc_final: 0.5516 (tt0) REVERT: D 86 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.7935 (mm) REVERT: D 113 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8145 (mmtp) REVERT: D 185 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (mtt) REVERT: D 380 MET cc_start: 0.2002 (ttp) cc_final: 0.1596 (ttp) REVERT: D 526 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: E 30 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7296 (mtt180) REVERT: E 84 ASP cc_start: 0.8665 (m-30) cc_final: 0.8426 (m-30) REVERT: E 185 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8158 (mtt) REVERT: E 189 THR cc_start: 0.8386 (p) cc_final: 0.7980 (t) REVERT: E 220 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6895 (tptm) REVERT: E 480 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6695 (tp40) REVERT: F 3 LYS cc_start: 0.8389 (ttpt) cc_final: 0.7888 (ttmt) REVERT: F 30 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7609 (mtt180) REVERT: F 285 ASP cc_start: 0.8170 (OUTLIER) cc_final: 0.7917 (t70) REVERT: F 480 GLN cc_start: 0.6845 (tp40) cc_final: 0.6396 (tt0) REVERT: F 481 MET cc_start: 0.7352 (mmp) cc_final: 0.6914 (mmt) REVERT: F 498 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8848 (mt) REVERT: F 526 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8201 (mm-30) REVERT: G 76 GLU cc_start: 0.5955 (mm-30) cc_final: 0.5654 (mm-30) REVERT: G 136 MET cc_start: 0.1005 (OUTLIER) cc_final: 0.0327 (mmm) REVERT: G 284 GLU cc_start: 0.6411 (tp30) cc_final: 0.6102 (mt-10) REVERT: G 329 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5966 (mt) REVERT: G 350 GLN cc_start: 0.6158 (mm-40) cc_final: 0.5943 (mp10) REVERT: G 382 LYS cc_start: 0.5700 (mmtm) cc_final: 0.4847 (tttm) REVERT: G 427 GLU cc_start: 0.5631 (tt0) cc_final: 0.4993 (pp20) REVERT: G 466 LYS cc_start: 0.5490 (tptp) cc_final: 0.5184 (tttt) REVERT: G 519 GLN cc_start: 0.7730 (tt0) cc_final: 0.7101 (tp40) REVERT: G 560 GLU cc_start: 0.8512 (tt0) cc_final: 0.8255 (tt0) REVERT: G 570 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8333 (p) REVERT: G 583 LYS cc_start: 0.7333 (mptp) cc_final: 0.6961 (mptm) REVERT: G 606 GLN cc_start: 0.5728 (mt0) cc_final: 0.4288 (mm110) REVERT: J 476 ASN cc_start: 0.3840 (OUTLIER) cc_final: 0.2103 (t0) REVERT: H 26 ASN cc_start: 0.4465 (OUTLIER) cc_final: 0.4262 (p0) REVERT: H 73 TYR cc_start: 0.5382 (t80) cc_final: 0.4856 (t80) REVERT: H 76 GLU cc_start: 0.5561 (OUTLIER) cc_final: 0.4676 (tm-30) REVERT: H 140 GLN cc_start: 0.2585 (OUTLIER) cc_final: 0.2068 (tt0) REVERT: H 312 MET cc_start: 0.4283 (ttt) cc_final: 0.3681 (ttp) REVERT: H 313 ASN cc_start: 0.3451 (m-40) cc_final: 0.3052 (m-40) REVERT: H 375 ILE cc_start: 0.4673 (OUTLIER) cc_final: 0.4216 (mm) REVERT: H 552 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7552 (t80) REVERT: I 42 LYS cc_start: 0.6017 (tptp) cc_final: 0.5204 (ttpp) REVERT: I 131 LYS cc_start: 0.3690 (OUTLIER) cc_final: 0.3143 (pptt) REVERT: I 212 MET cc_start: 0.1335 (OUTLIER) cc_final: 0.1035 (mpp) REVERT: I 220 MET cc_start: 0.0395 (mmm) cc_final: -0.0384 (tmm) REVERT: I 249 GLU cc_start: 0.6658 (mm-30) cc_final: 0.5867 (mp0) REVERT: I 365 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6052 (mt-10) REVERT: I 450 GLN cc_start: 0.5294 (mm-40) cc_final: 0.4969 (tp-100) REVERT: I 535 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7487 (mttt) REVERT: I 583 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6965 (mptt) REVERT: I 611 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.6090 (ptt) REVERT: I 662 GLN cc_start: 0.5607 (mt0) cc_final: 0.5098 (mp10) outliers start: 121 outliers final: 42 residues processed: 421 average time/residue: 0.8308 time to fit residues: 417.8684 Evaluate side-chains 403 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 328 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 396 LYS Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 480 GLN Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 476 ASN Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 541 ILE Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 26 ASN Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 522 SER Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 212 MET Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 418 ASN Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 601 SER Chi-restraints excluded: chain I residue 611 MET Chi-restraints excluded: chain I residue 633 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 283 optimal weight: 5.9990 chunk 192 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 407 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 430 optimal weight: 0.0070 chunk 15 optimal weight: 6.9990 chunk 443 optimal weight: 10.0000 chunk 290 optimal weight: 0.9980 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN A 61 HIS ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN G 349 ASN G 528 GLN I 235 GLN I 424 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.184857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.117577 restraints weight = 43711.687| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.86 r_work: 0.3233 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40968 Z= 0.182 Angle : 0.582 7.192 55449 Z= 0.315 Chirality : 0.047 0.158 6152 Planarity : 0.005 0.073 7237 Dihedral : 4.994 53.797 5680 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.53 % Favored : 96.39 % Rotamer: Outliers : 3.25 % Allowed : 16.54 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.49 (0.11), residues: 5123 helix: 1.47 (0.12), residues: 2036 sheet: 1.77 (0.18), residues: 782 loop : -1.32 (0.11), residues: 2305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 361 TYR 0.021 0.002 TYR F 429 PHE 0.018 0.002 PHE H 380 TRP 0.010 0.002 TRP H 514 HIS 0.005 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00437 (40965) covalent geometry : angle 0.58159 (55449) hydrogen bonds : bond 0.06430 ( 1842) hydrogen bonds : angle 4.35443 ( 5151) Misc. bond : bond 0.00027 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 338 time to evaluate : 1.534 Fit side-chains REVERT: A 3 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7935 (tttp) REVERT: A 7 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: A 480 GLN cc_start: 0.6858 (tt0) cc_final: 0.6422 (mt0) REVERT: A 529 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7877 (mmt90) REVERT: B 14 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6316 (pm20) REVERT: B 42 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7040 (tp30) REVERT: B 43 LYS cc_start: 0.7478 (ttmm) cc_final: 0.6710 (tptt) REVERT: B 47 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.6653 (tmmt) REVERT: B 50 GLN cc_start: 0.7456 (tp40) cc_final: 0.7148 (tp40) REVERT: B 220 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.6250 (ttmt) REVERT: B 230 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6428 (tp30) REVERT: B 287 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7567 (mm-30) REVERT: B 299 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6268 (mtpp) REVERT: B 309 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8401 (mtt90) REVERT: B 351 GLU cc_start: 0.8137 (mp0) cc_final: 0.7534 (mp0) REVERT: B 449 GLN cc_start: 0.5838 (OUTLIER) cc_final: 0.5635 (tt0) REVERT: B 472 GLU cc_start: 0.3510 (OUTLIER) cc_final: 0.2708 (pm20) REVERT: B 526 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8067 (mm-30) REVERT: C 42 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7555 (mm-30) REVERT: C 475 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6548 (mm-30) REVERT: D 31 GLU cc_start: 0.7510 (tp30) cc_final: 0.7107 (tm-30) REVERT: D 42 GLU cc_start: 0.6199 (tp30) cc_final: 0.5610 (tt0) REVERT: D 86 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8009 (mm) REVERT: D 113 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8221 (mmtp) REVERT: D 185 MET cc_start: 0.8928 (OUTLIER) cc_final: 0.8399 (mtt) REVERT: D 380 MET cc_start: 0.2043 (ttp) cc_final: 0.1717 (ttp) REVERT: D 526 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7756 (mt-10) REVERT: E 30 ARG cc_start: 0.8195 (mtp85) cc_final: 0.7333 (mtt180) REVERT: E 84 ASP cc_start: 0.8722 (m-30) cc_final: 0.8499 (m-30) REVERT: E 185 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8245 (mtt) REVERT: E 189 THR cc_start: 0.8477 (p) cc_final: 0.8038 (t) REVERT: E 220 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.6935 (tptm) REVERT: F 3 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7902 (ttmt) REVERT: F 30 ARG cc_start: 0.8281 (mtp85) cc_final: 0.7657 (mtt180) REVERT: F 285 ASP cc_start: 0.8169 (OUTLIER) cc_final: 0.7918 (t70) REVERT: F 480 GLN cc_start: 0.6785 (tp40) cc_final: 0.6336 (tt0) REVERT: F 481 MET cc_start: 0.7325 (mmp) cc_final: 0.6856 (mmt) REVERT: F 498 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8879 (mp) REVERT: F 526 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8214 (mm-30) REVERT: G 76 GLU cc_start: 0.5918 (mm-30) cc_final: 0.5598 (mm-30) REVERT: G 136 MET cc_start: 0.1049 (OUTLIER) cc_final: 0.0374 (mmm) REVERT: G 284 GLU cc_start: 0.6586 (tp30) cc_final: 0.5878 (tt0) REVERT: G 329 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6050 (mt) REVERT: G 350 GLN cc_start: 0.6201 (mm-40) cc_final: 0.5985 (mp10) REVERT: G 382 LYS cc_start: 0.5733 (mmtm) cc_final: 0.4915 (tttm) REVERT: G 427 GLU cc_start: 0.5687 (tt0) cc_final: 0.5061 (pp20) REVERT: G 560 GLU cc_start: 0.8566 (tt0) cc_final: 0.8294 (tt0) REVERT: G 583 LYS cc_start: 0.7383 (mptp) cc_final: 0.7034 (mptm) REVERT: G 606 GLN cc_start: 0.5651 (mt0) cc_final: 0.4267 (mm110) REVERT: J 476 ASN cc_start: 0.3880 (OUTLIER) cc_final: 0.2185 (t0) REVERT: H 73 TYR cc_start: 0.5500 (t80) cc_final: 0.5107 (t80) REVERT: H 76 GLU cc_start: 0.5592 (OUTLIER) cc_final: 0.4581 (tm-30) REVERT: H 136 MET cc_start: 0.1930 (OUTLIER) cc_final: 0.1700 (ttm) REVERT: H 140 GLN cc_start: 0.2517 (OUTLIER) cc_final: 0.1972 (tt0) REVERT: H 237 MET cc_start: 0.4696 (mmt) cc_final: 0.3693 (mmm) REVERT: H 312 MET cc_start: 0.4325 (ttt) cc_final: 0.3709 (ttp) REVERT: H 313 ASN cc_start: 0.3435 (m-40) cc_final: 0.3058 (m-40) REVERT: H 375 ILE cc_start: 0.4655 (OUTLIER) cc_final: 0.4196 (mm) REVERT: H 552 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.7571 (t80) REVERT: I 29 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6100 (tp) REVERT: I 80 LYS cc_start: 0.6115 (OUTLIER) cc_final: 0.5466 (tppp) REVERT: I 95 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6282 (tt0) REVERT: I 131 LYS cc_start: 0.3754 (OUTLIER) cc_final: 0.3161 (pptt) REVERT: I 220 MET cc_start: 0.0433 (mmm) cc_final: -0.0422 (tmm) REVERT: I 259 GLN cc_start: 0.5570 (OUTLIER) cc_final: 0.4497 (mt0) REVERT: I 312 MET cc_start: 0.5273 (OUTLIER) cc_final: 0.3916 (tmt) REVERT: I 365 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5690 (mt-10) REVERT: I 371 PHE cc_start: 0.5157 (m-10) cc_final: 0.4712 (m-10) REVERT: I 450 GLN cc_start: 0.5451 (mm-40) cc_final: 0.5163 (tp-100) REVERT: I 535 LYS cc_start: 0.7996 (mtmm) cc_final: 0.7513 (mttt) REVERT: I 563 GLN cc_start: 0.5122 (mt0) cc_final: 0.4812 (mt0) REVERT: I 583 LYS cc_start: 0.7441 (mmtp) cc_final: 0.6977 (mptt) REVERT: I 611 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.6146 (ptt) REVERT: I 662 GLN cc_start: 0.5567 (mt0) cc_final: 0.5210 (mp10) outliers start: 137 outliers final: 59 residues processed: 436 average time/residue: 0.8713 time to fit residues: 452.3463 Evaluate side-chains 429 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 333 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 384 LYS Chi-restraints excluded: chain C residue 469 TRP Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 377 THR Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 343 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 595 LYS Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 476 ASN Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 541 ILE Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 522 SER Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 601 SER Chi-restraints excluded: chain I residue 611 MET Chi-restraints excluded: chain I residue 633 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 107 optimal weight: 0.7980 chunk 295 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 194 optimal weight: 0.7980 chunk 435 optimal weight: 4.9990 chunk 497 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 186 optimal weight: 7.9990 chunk 328 optimal weight: 0.3980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN E 452 ASN F 170 GLN G 111 ASN G 528 GLN I 235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.188002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121891 restraints weight = 43834.881| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.98 r_work: 0.3284 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40968 Z= 0.101 Angle : 0.472 6.720 55449 Z= 0.256 Chirality : 0.044 0.155 6152 Planarity : 0.004 0.038 7237 Dihedral : 4.581 54.439 5680 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.67 % Favored : 97.25 % Rotamer: Outliers : 2.28 % Allowed : 18.02 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.81 (0.12), residues: 5123 helix: 1.78 (0.12), residues: 2035 sheet: 1.97 (0.18), residues: 788 loop : -1.21 (0.12), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 361 TYR 0.014 0.001 TYR I 105 PHE 0.012 0.001 PHE D 319 TRP 0.009 0.001 TRP B 469 HIS 0.003 0.001 HIS B 393 Details of bonding type rmsd covalent geometry : bond 0.00220 (40965) covalent geometry : angle 0.47171 (55449) hydrogen bonds : bond 0.04236 ( 1842) hydrogen bonds : angle 4.07518 ( 5151) Misc. bond : bond 0.00019 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 339 time to evaluate : 1.570 Fit side-chains REVERT: A 3 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7904 (tttp) REVERT: A 7 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: A 480 GLN cc_start: 0.6922 (tt0) cc_final: 0.6451 (mt0) REVERT: A 529 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7903 (mmt90) REVERT: B 42 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: B 47 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6614 (tmmt) REVERT: B 50 GLN cc_start: 0.7389 (tp40) cc_final: 0.7058 (tp40) REVERT: B 220 LYS cc_start: 0.6477 (OUTLIER) cc_final: 0.6219 (ttmt) REVERT: B 230 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6388 (tp30) REVERT: B 287 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7572 (mm-30) REVERT: B 299 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6189 (mtpp) REVERT: B 309 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8278 (mtt90) REVERT: B 351 GLU cc_start: 0.7959 (mp0) cc_final: 0.7388 (mp0) REVERT: B 449 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.5523 (tt0) REVERT: B 526 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8086 (mm-30) REVERT: C 42 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7537 (mm-30) REVERT: C 475 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6442 (mm-30) REVERT: D 31 GLU cc_start: 0.7500 (tp30) cc_final: 0.7166 (tm-30) REVERT: D 42 GLU cc_start: 0.6095 (tp30) cc_final: 0.5512 (tt0) REVERT: D 86 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7935 (mm) REVERT: D 113 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8172 (mmtp) REVERT: D 185 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8703 (mtt) REVERT: D 380 MET cc_start: 0.1971 (ttp) cc_final: 0.1685 (ttp) REVERT: D 526 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: E 30 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7293 (mtt180) REVERT: E 84 ASP cc_start: 0.8669 (m-30) cc_final: 0.8428 (m-30) REVERT: E 185 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8101 (mtt) REVERT: E 189 THR cc_start: 0.8384 (p) cc_final: 0.7966 (t) REVERT: E 220 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.6858 (tptm) REVERT: F 3 LYS cc_start: 0.8365 (ttpt) cc_final: 0.7863 (ttmt) REVERT: F 30 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7595 (mtt180) REVERT: F 285 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7909 (t70) REVERT: F 480 GLN cc_start: 0.6882 (tp40) cc_final: 0.6400 (tt0) REVERT: F 481 MET cc_start: 0.7352 (mmp) cc_final: 0.6897 (mmt) REVERT: F 498 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8857 (mt) REVERT: F 526 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8252 (mm-30) REVERT: G 76 GLU cc_start: 0.5867 (mm-30) cc_final: 0.5562 (mm-30) REVERT: G 136 MET cc_start: 0.1117 (OUTLIER) cc_final: 0.0425 (mmm) REVERT: G 284 GLU cc_start: 0.6470 (tp30) cc_final: 0.5764 (tt0) REVERT: G 329 LEU cc_start: 0.6359 (OUTLIER) cc_final: 0.6014 (mt) REVERT: G 382 LYS cc_start: 0.5710 (mmtm) cc_final: 0.4882 (tttm) REVERT: G 427 GLU cc_start: 0.5602 (tt0) cc_final: 0.4970 (pp20) REVERT: G 466 LYS cc_start: 0.5477 (tptp) cc_final: 0.5009 (tttt) REVERT: G 519 GLN cc_start: 0.7745 (tt0) cc_final: 0.7149 (tp40) REVERT: G 560 GLU cc_start: 0.8502 (tt0) cc_final: 0.8245 (tt0) REVERT: G 570 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8345 (p) REVERT: G 583 LYS cc_start: 0.7370 (mptp) cc_final: 0.6987 (mptm) REVERT: G 606 GLN cc_start: 0.5698 (mt0) cc_final: 0.4279 (mm110) REVERT: G 638 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.5744 (mpp) REVERT: J 552 TYR cc_start: 0.0422 (OUTLIER) cc_final: -0.1200 (m-80) REVERT: H 73 TYR cc_start: 0.5313 (t80) cc_final: 0.4915 (t80) REVERT: H 76 GLU cc_start: 0.5565 (OUTLIER) cc_final: 0.5135 (tp30) REVERT: H 136 MET cc_start: 0.1872 (OUTLIER) cc_final: 0.1652 (ttm) REVERT: H 140 GLN cc_start: 0.2574 (OUTLIER) cc_final: 0.1997 (tt0) REVERT: H 237 MET cc_start: 0.4632 (mmt) cc_final: 0.3649 (mmm) REVERT: H 312 MET cc_start: 0.4242 (ttt) cc_final: 0.3591 (ttp) REVERT: H 313 ASN cc_start: 0.3490 (m-40) cc_final: 0.3139 (m-40) REVERT: H 375 ILE cc_start: 0.4640 (OUTLIER) cc_final: 0.4168 (mm) REVERT: H 525 ILE cc_start: 0.7040 (OUTLIER) cc_final: 0.6727 (tp) REVERT: H 552 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7505 (t80) REVERT: I 29 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6131 (tp) REVERT: I 42 LYS cc_start: 0.5733 (tptp) cc_final: 0.4937 (ttpp) REVERT: I 95 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6241 (tt0) REVERT: I 131 LYS cc_start: 0.3746 (OUTLIER) cc_final: 0.3229 (pptt) REVERT: I 212 MET cc_start: 0.1469 (mmt) cc_final: 0.1211 (mpp) REVERT: I 220 MET cc_start: 0.0413 (mmm) cc_final: -0.0413 (tmm) REVERT: I 249 GLU cc_start: 0.6644 (mm-30) cc_final: 0.5878 (mp0) REVERT: I 259 GLN cc_start: 0.5439 (OUTLIER) cc_final: 0.4414 (mt0) REVERT: I 312 MET cc_start: 0.5118 (OUTLIER) cc_final: 0.3760 (tmt) REVERT: I 365 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5874 (mt-10) REVERT: I 369 GLN cc_start: 0.5997 (OUTLIER) cc_final: 0.5088 (mp-120) REVERT: I 371 PHE cc_start: 0.5154 (m-10) cc_final: 0.4878 (m-10) REVERT: I 450 GLN cc_start: 0.5521 (mm-40) cc_final: 0.5218 (tp-100) REVERT: I 535 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7466 (mttt) REVERT: I 563 GLN cc_start: 0.5094 (mt0) cc_final: 0.4736 (mt0) REVERT: I 583 LYS cc_start: 0.7435 (mmtp) cc_final: 0.6947 (mptt) REVERT: I 611 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.5959 (ptt) REVERT: I 662 GLN cc_start: 0.5522 (mt0) cc_final: 0.5135 (mp10) outliers start: 96 outliers final: 32 residues processed: 409 average time/residue: 0.8589 time to fit residues: 417.7540 Evaluate side-chains 396 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 326 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LYS Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 449 GLN Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 469 TRP Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 638 MET Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 552 TYR Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 369 GLN Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 611 MET Chi-restraints excluded: chain I residue 633 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 146 optimal weight: 5.9990 chunk 244 optimal weight: 6.9990 chunk 68 optimal weight: 0.0070 chunk 193 optimal weight: 0.9990 chunk 503 optimal weight: 6.9990 chunk 208 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 498 optimal weight: 5.9990 chunk 243 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 chunk 306 optimal weight: 2.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 50 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 452 ASN F 101 ASN ** G 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 235 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.188411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.122032 restraints weight = 43666.036| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.97 r_work: 0.3290 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 40968 Z= 0.097 Angle : 0.466 8.076 55449 Z= 0.252 Chirality : 0.043 0.154 6152 Planarity : 0.004 0.038 7237 Dihedral : 4.429 54.534 5678 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 96.99 % Rotamer: Outliers : 2.23 % Allowed : 18.16 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.93 (0.12), residues: 5123 helix: 1.90 (0.12), residues: 2037 sheet: 2.01 (0.18), residues: 793 loop : -1.16 (0.12), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 361 TYR 0.014 0.001 TYR I 105 PHE 0.012 0.001 PHE D 319 TRP 0.008 0.001 TRP H 514 HIS 0.003 0.001 HIS I 64 Details of bonding type rmsd covalent geometry : bond 0.00207 (40965) covalent geometry : angle 0.46566 (55449) hydrogen bonds : bond 0.04117 ( 1842) hydrogen bonds : angle 3.99203 ( 5151) Misc. bond : bond 0.00009 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 330 time to evaluate : 1.450 Fit side-chains REVERT: A 7 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: A 480 GLN cc_start: 0.6880 (tt0) cc_final: 0.6424 (mt0) REVERT: A 529 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7887 (mmt90) REVERT: B 42 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7008 (tp30) REVERT: B 43 LYS cc_start: 0.7334 (ttmm) cc_final: 0.6561 (tptt) REVERT: B 47 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.6606 (tmmt) REVERT: B 50 GLN cc_start: 0.7359 (tp40) cc_final: 0.7030 (tp40) REVERT: B 220 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6305 (ttmt) REVERT: B 287 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7545 (mm-30) REVERT: B 299 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6187 (mtpp) REVERT: B 309 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8309 (mtt90) REVERT: B 351 GLU cc_start: 0.7950 (mp0) cc_final: 0.7399 (mp0) REVERT: B 526 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8076 (mm-30) REVERT: C 42 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7526 (mm-30) REVERT: C 475 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6434 (mm-30) REVERT: D 31 GLU cc_start: 0.7477 (tp30) cc_final: 0.7126 (tm-30) REVERT: D 42 GLU cc_start: 0.6100 (tp30) cc_final: 0.5522 (tt0) REVERT: D 86 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.7904 (mm) REVERT: D 113 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8193 (mmtp) REVERT: D 185 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8626 (mtt) REVERT: D 380 MET cc_start: 0.1910 (ttp) cc_final: 0.1662 (ttp) REVERT: D 526 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: E 30 ARG cc_start: 0.8182 (mtp85) cc_final: 0.7279 (mtt180) REVERT: E 84 ASP cc_start: 0.8642 (m-30) cc_final: 0.8393 (m-30) REVERT: E 185 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8113 (mtt) REVERT: E 189 THR cc_start: 0.8328 (p) cc_final: 0.7912 (t) REVERT: E 220 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.6897 (tptm) REVERT: F 3 LYS cc_start: 0.8370 (ttpt) cc_final: 0.7866 (ttmt) REVERT: F 30 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7593 (mtt180) REVERT: F 285 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7900 (t70) REVERT: F 480 GLN cc_start: 0.6840 (tp40) cc_final: 0.6390 (tt0) REVERT: F 481 MET cc_start: 0.7348 (mmp) cc_final: 0.6866 (mmt) REVERT: F 498 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8854 (mt) REVERT: F 526 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8231 (mm-30) REVERT: G 76 GLU cc_start: 0.5903 (mm-30) cc_final: 0.5605 (mm-30) REVERT: G 136 MET cc_start: 0.1093 (OUTLIER) cc_final: 0.0452 (mmm) REVERT: G 284 GLU cc_start: 0.6474 (tp30) cc_final: 0.5766 (tt0) REVERT: G 329 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5988 (mt) REVERT: G 382 LYS cc_start: 0.5681 (mmtm) cc_final: 0.4867 (tttm) REVERT: G 427 GLU cc_start: 0.5579 (tt0) cc_final: 0.4950 (pp20) REVERT: G 466 LYS cc_start: 0.5407 (tptp) cc_final: 0.4958 (tttt) REVERT: G 519 GLN cc_start: 0.7703 (tt0) cc_final: 0.7117 (tp40) REVERT: G 560 GLU cc_start: 0.8468 (tt0) cc_final: 0.8202 (tt0) REVERT: G 570 VAL cc_start: 0.8560 (OUTLIER) cc_final: 0.8327 (p) REVERT: G 583 LYS cc_start: 0.7334 (mptp) cc_final: 0.6947 (mptm) REVERT: G 606 GLN cc_start: 0.5666 (mt0) cc_final: 0.4260 (mm110) REVERT: G 638 MET cc_start: 0.5997 (OUTLIER) cc_final: 0.5788 (mpp) REVERT: J 476 ASN cc_start: 0.3961 (OUTLIER) cc_final: 0.2170 (t0) REVERT: J 528 GLN cc_start: 0.6261 (tt0) cc_final: 0.5676 (tm-30) REVERT: J 552 TYR cc_start: 0.0506 (OUTLIER) cc_final: -0.1196 (m-80) REVERT: H 73 TYR cc_start: 0.5303 (t80) cc_final: 0.4778 (t80) REVERT: H 76 GLU cc_start: 0.5543 (OUTLIER) cc_final: 0.5067 (tp30) REVERT: H 136 MET cc_start: 0.1917 (OUTLIER) cc_final: 0.1706 (ttm) REVERT: H 140 GLN cc_start: 0.2541 (OUTLIER) cc_final: 0.1985 (tt0) REVERT: H 237 MET cc_start: 0.4662 (mmt) cc_final: 0.3689 (mmm) REVERT: H 296 THR cc_start: 0.6004 (p) cc_final: 0.5383 (t) REVERT: H 312 MET cc_start: 0.4211 (ttt) cc_final: 0.3549 (ttp) REVERT: H 313 ASN cc_start: 0.3404 (m-40) cc_final: 0.3080 (m-40) REVERT: H 375 ILE cc_start: 0.4374 (OUTLIER) cc_final: 0.3852 (mm) REVERT: H 525 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6721 (tp) REVERT: H 552 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.7509 (t80) REVERT: I 42 LYS cc_start: 0.5792 (tptp) cc_final: 0.4968 (ttpp) REVERT: I 80 LYS cc_start: 0.6057 (OUTLIER) cc_final: 0.5369 (tppp) REVERT: I 95 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6232 (tt0) REVERT: I 131 LYS cc_start: 0.3728 (OUTLIER) cc_final: 0.3230 (pptt) REVERT: I 220 MET cc_start: 0.0355 (mmm) cc_final: -0.0394 (tmm) REVERT: I 249 GLU cc_start: 0.6651 (mm-30) cc_final: 0.5855 (mp0) REVERT: I 259 GLN cc_start: 0.5431 (OUTLIER) cc_final: 0.4445 (mt0) REVERT: I 312 MET cc_start: 0.5115 (OUTLIER) cc_final: 0.3750 (tmt) REVERT: I 365 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6021 (mt-10) REVERT: I 369 GLN cc_start: 0.6013 (OUTLIER) cc_final: 0.5103 (mp-120) REVERT: I 450 GLN cc_start: 0.5463 (mm-40) cc_final: 0.5166 (tp-100) REVERT: I 535 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7445 (mttm) REVERT: I 583 LYS cc_start: 0.7442 (mmtp) cc_final: 0.6976 (mptt) REVERT: I 611 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6105 (ptt) REVERT: I 662 GLN cc_start: 0.5465 (mt0) cc_final: 0.4782 (mp10) outliers start: 94 outliers final: 37 residues processed: 393 average time/residue: 0.8435 time to fit residues: 393.0565 Evaluate side-chains 402 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 329 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 469 TRP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 638 MET Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 476 ASN Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 552 TYR Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 369 GLN Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 611 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 61 optimal weight: 0.0370 chunk 181 optimal weight: 10.0000 chunk 463 optimal weight: 6.9990 chunk 490 optimal weight: 3.9990 chunk 349 optimal weight: 3.9990 chunk 493 optimal weight: 3.9990 chunk 391 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 222 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 overall best weight: 2.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** B 490 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 GLN E 452 ASN F 101 ASN G 111 ASN G 528 GLN J 576 HIS H 99 GLN I 235 GLN I 424 HIS ** I 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.185117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.119023 restraints weight = 43605.890| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.02 r_work: 0.3234 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 40968 Z= 0.164 Angle : 0.561 10.412 55449 Z= 0.303 Chirality : 0.046 0.158 6152 Planarity : 0.005 0.064 7237 Dihedral : 4.797 54.505 5678 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 2.44 % Allowed : 18.02 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % 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: 0.64 (0.12), residues: 5123 helix: 1.64 (0.12), residues: 2035 sheet: 1.81 (0.18), residues: 785 loop : -1.26 (0.12), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 361 TYR 0.020 0.002 TYR F 429 PHE 0.016 0.002 PHE H 380 TRP 0.009 0.001 TRP H 514 HIS 0.005 0.001 HIS C 358 Details of bonding type rmsd covalent geometry : bond 0.00389 (40965) covalent geometry : angle 0.56097 (55449) hydrogen bonds : bond 0.05972 ( 1842) hydrogen bonds : angle 4.23421 ( 5151) Misc. bond : bond 0.00025 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 333 time to evaluate : 1.453 Fit side-chains REVERT: A 7 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8137 (mp10) REVERT: A 480 GLN cc_start: 0.6895 (tt0) cc_final: 0.6449 (mt0) REVERT: A 529 ARG cc_start: 0.8190 (mtp85) cc_final: 0.7911 (mmt90) REVERT: B 14 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6385 (pm20) REVERT: B 42 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: B 43 LYS cc_start: 0.7449 (ttmm) cc_final: 0.6675 (tptt) REVERT: B 47 LYS cc_start: 0.7501 (OUTLIER) cc_final: 0.6649 (tmmt) REVERT: B 50 GLN cc_start: 0.7439 (tp40) cc_final: 0.7110 (tp40) REVERT: B 220 LYS cc_start: 0.6523 (OUTLIER) cc_final: 0.6283 (ttmt) REVERT: B 230 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6456 (tp30) REVERT: B 287 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7559 (mm-30) REVERT: B 299 LYS cc_start: 0.7081 (OUTLIER) cc_final: 0.6209 (mtpp) REVERT: B 309 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8374 (mtt90) REVERT: B 351 GLU cc_start: 0.8127 (mp0) cc_final: 0.7529 (mp0) REVERT: B 441 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.6851 (mpt180) REVERT: B 526 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8091 (mm-30) REVERT: B 529 ARG cc_start: 0.8298 (ptm160) cc_final: 0.7639 (tpp80) REVERT: C 42 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7570 (mm-30) REVERT: C 475 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6542 (mm-30) REVERT: D 31 GLU cc_start: 0.7538 (tp30) cc_final: 0.7202 (tm-30) REVERT: D 42 GLU cc_start: 0.6200 (tp30) cc_final: 0.5599 (tt0) REVERT: D 86 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8010 (mm) REVERT: D 113 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8208 (mmtp) REVERT: D 185 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8647 (mtt) REVERT: D 526 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7822 (mt-10) REVERT: E 30 ARG cc_start: 0.8214 (mtp85) cc_final: 0.7316 (mtt180) REVERT: E 35 GLN cc_start: 0.8217 (tp40) cc_final: 0.8014 (tp-100) REVERT: E 84 ASP cc_start: 0.8703 (m-30) cc_final: 0.8469 (m-30) REVERT: E 185 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8293 (mtt) REVERT: E 189 THR cc_start: 0.8408 (p) cc_final: 0.7989 (t) REVERT: E 220 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.6867 (tptm) REVERT: F 3 LYS cc_start: 0.8398 (ttpt) cc_final: 0.7895 (ttmt) REVERT: F 30 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7662 (mtt180) REVERT: F 285 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7916 (t70) REVERT: F 480 GLN cc_start: 0.6854 (tp40) cc_final: 0.5866 (mt0) REVERT: F 481 MET cc_start: 0.7404 (mmp) cc_final: 0.6912 (mmt) REVERT: F 498 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8900 (mp) REVERT: F 526 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8238 (mm-30) REVERT: G 76 GLU cc_start: 0.5851 (mm-30) cc_final: 0.5558 (mm-30) REVERT: G 136 MET cc_start: 0.1153 (OUTLIER) cc_final: 0.0436 (mmm) REVERT: G 284 GLU cc_start: 0.6619 (tp30) cc_final: 0.5873 (tt0) REVERT: G 329 LEU cc_start: 0.6372 (OUTLIER) cc_final: 0.6023 (mt) REVERT: G 382 LYS cc_start: 0.5729 (mmtm) cc_final: 0.4888 (tttm) REVERT: G 427 GLU cc_start: 0.5659 (tt0) cc_final: 0.5038 (pp20) REVERT: G 466 LYS cc_start: 0.5432 (tptp) cc_final: 0.4962 (tttt) REVERT: G 552 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: G 560 GLU cc_start: 0.8530 (tt0) cc_final: 0.8281 (tt0) REVERT: G 583 LYS cc_start: 0.7360 (mptp) cc_final: 0.6995 (mptm) REVERT: G 606 GLN cc_start: 0.5627 (mt0) cc_final: 0.4270 (mm110) REVERT: J 476 ASN cc_start: 0.4063 (OUTLIER) cc_final: 0.2335 (t0) REVERT: J 528 GLN cc_start: 0.6325 (tt0) cc_final: 0.5752 (tm-30) REVERT: J 552 TYR cc_start: 0.0491 (OUTLIER) cc_final: -0.1259 (m-80) REVERT: H 73 TYR cc_start: 0.5454 (t80) cc_final: 0.5062 (t80) REVERT: H 76 GLU cc_start: 0.5558 (OUTLIER) cc_final: 0.4600 (tm-30) REVERT: H 99 GLN cc_start: 0.4719 (mt0) cc_final: 0.3814 (mp10) REVERT: H 136 MET cc_start: 0.1911 (OUTLIER) cc_final: 0.1681 (ttm) REVERT: H 140 GLN cc_start: 0.2583 (OUTLIER) cc_final: 0.2028 (tt0) REVERT: H 237 MET cc_start: 0.4812 (mmt) cc_final: 0.4557 (mmt) REVERT: H 312 MET cc_start: 0.4256 (ttt) cc_final: 0.3592 (ttp) REVERT: H 313 ASN cc_start: 0.3424 (m-40) cc_final: 0.3064 (m-40) REVERT: H 375 ILE cc_start: 0.4436 (OUTLIER) cc_final: 0.3961 (mm) REVERT: H 525 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6780 (tp) REVERT: H 552 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7599 (t80) REVERT: H 632 LEU cc_start: 0.1935 (OUTLIER) cc_final: 0.1678 (mp) REVERT: I 42 LYS cc_start: 0.5837 (tptp) cc_final: 0.5010 (ttpp) REVERT: I 80 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5393 (tppp) REVERT: I 95 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6265 (tt0) REVERT: I 131 LYS cc_start: 0.3727 (OUTLIER) cc_final: 0.3207 (pptt) REVERT: I 220 MET cc_start: 0.0391 (mmm) cc_final: -0.0426 (tmm) REVERT: I 259 GLN cc_start: 0.5562 (OUTLIER) cc_final: 0.4511 (mt0) REVERT: I 312 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.3914 (tmt) REVERT: I 365 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5719 (mt-10) REVERT: I 369 GLN cc_start: 0.6047 (OUTLIER) cc_final: 0.5103 (mp-120) REVERT: I 450 GLN cc_start: 0.5524 (mm-40) cc_final: 0.5228 (tp-100) REVERT: I 535 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7506 (mttm) REVERT: I 563 GLN cc_start: 0.5142 (mt0) cc_final: 0.4759 (mt0) REVERT: I 583 LYS cc_start: 0.7439 (mmtp) cc_final: 0.6969 (mptt) REVERT: I 608 THR cc_start: 0.5544 (m) cc_final: 0.5333 (p) REVERT: I 662 GLN cc_start: 0.5560 (mt0) cc_final: 0.5127 (mp10) outliers start: 103 outliers final: 48 residues processed: 408 average time/residue: 0.8129 time to fit residues: 394.8513 Evaluate side-chains 416 residues out of total 4213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 331 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 185 MET Chi-restraints excluded: chain A residue 443 SER Chi-restraints excluded: chain A residue 487 THR Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 299 LYS Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 441 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 156 VAL Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain C residue 475 GLU Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 261 VAL Chi-restraints excluded: chain D residue 526 GLU Chi-restraints excluded: chain E residue 10 THR Chi-restraints excluded: chain E residue 14 GLU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 185 MET Chi-restraints excluded: chain E residue 220 LYS Chi-restraints excluded: chain E residue 469 TRP Chi-restraints excluded: chain E residue 479 THR Chi-restraints excluded: chain E residue 495 SER Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 526 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 130 ILE Chi-restraints excluded: chain G residue 136 MET Chi-restraints excluded: chain G residue 228 ASN Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 329 LEU Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 421 GLU Chi-restraints excluded: chain G residue 523 THR Chi-restraints excluded: chain G residue 552 TYR Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain G residue 616 VAL Chi-restraints excluded: chain G residue 634 VAL Chi-restraints excluded: chain G residue 645 HIS Chi-restraints excluded: chain J residue 476 ASN Chi-restraints excluded: chain J residue 512 SER Chi-restraints excluded: chain J residue 552 TYR Chi-restraints excluded: chain J residue 559 ILE Chi-restraints excluded: chain H residue 35 GLU Chi-restraints excluded: chain H residue 59 ASP Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 76 GLU Chi-restraints excluded: chain H residue 136 MET Chi-restraints excluded: chain H residue 140 GLN Chi-restraints excluded: chain H residue 153 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 375 ILE Chi-restraints excluded: chain H residue 413 ILE Chi-restraints excluded: chain H residue 525 ILE Chi-restraints excluded: chain H residue 552 TYR Chi-restraints excluded: chain H residue 632 LEU Chi-restraints excluded: chain I residue 80 LYS Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain I residue 120 GLN Chi-restraints excluded: chain I residue 131 LYS Chi-restraints excluded: chain I residue 226 VAL Chi-restraints excluded: chain I residue 234 VAL Chi-restraints excluded: chain I residue 252 CYS Chi-restraints excluded: chain I residue 259 GLN Chi-restraints excluded: chain I residue 280 GLU Chi-restraints excluded: chain I residue 312 MET Chi-restraints excluded: chain I residue 365 GLU Chi-restraints excluded: chain I residue 369 GLN Chi-restraints excluded: chain I residue 438 VAL Chi-restraints excluded: chain I residue 546 MET Chi-restraints excluded: chain I residue 599 GLN Chi-restraints excluded: chain I residue 633 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.6415 > 50: distance: 55 - 80: 3.117 distance: 59 - 85: 13.963 distance: 70 - 94: 15.617 distance: 75 - 102: 9.564 distance: 80 - 81: 3.392 distance: 81 - 82: 23.142 distance: 81 - 84: 24.845 distance: 82 - 83: 15.623 distance: 82 - 85: 20.454 distance: 85 - 86: 9.593 distance: 86 - 87: 7.721 distance: 86 - 89: 13.334 distance: 87 - 88: 19.983 distance: 87 - 94: 11.915 distance: 89 - 90: 13.964 distance: 90 - 91: 8.835 distance: 91 - 92: 17.498 distance: 91 - 93: 7.308 distance: 94 - 95: 10.351 distance: 95 - 96: 9.036 distance: 95 - 98: 3.699 distance: 96 - 97: 3.479 distance: 96 - 102: 4.656 distance: 98 - 99: 9.323 distance: 99 - 100: 5.300 distance: 100 - 101: 9.669 distance: 102 - 103: 3.941 distance: 103 - 104: 3.795 distance: 104 - 105: 3.094 distance: 104 - 108: 8.503 distance: 106 - 107: 9.136 distance: 108 - 109: 3.851 distance: 109 - 110: 10.033 distance: 109 - 112: 3.529 distance: 110 - 111: 8.112 distance: 110 - 113: 5.059 distance: 114 - 117: 3.761 distance: 115 - 116: 17.391 distance: 115 - 121: 8.869 distance: 117 - 118: 3.218 distance: 118 - 120: 3.411 distance: 121 - 122: 7.070 distance: 122 - 123: 6.872 distance: 122 - 125: 4.415 distance: 123 - 124: 6.442 distance: 123 - 129: 4.828 distance: 125 - 126: 7.266 distance: 126 - 127: 5.926 distance: 126 - 128: 7.581 distance: 129 - 130: 7.305 distance: 130 - 131: 14.461 distance: 130 - 133: 4.460 distance: 131 - 132: 10.139 distance: 131 - 137: 6.882 distance: 133 - 134: 8.887 distance: 133 - 135: 13.980 distance: 134 - 136: 6.965 distance: 137 - 138: 7.143 distance: 137 - 143: 9.047 distance: 138 - 141: 3.073 distance: 139 - 140: 20.168 distance: 139 - 144: 3.889 distance: 141 - 142: 8.019 distance: 142 - 143: 6.518 distance: 144 - 145: 4.109 distance: 145 - 146: 6.474 distance: 145 - 148: 5.058 distance: 146 - 147: 5.383 distance: 146 - 153: 4.358 distance: 149 - 150: 5.651 distance: 150 - 151: 12.587 distance: 150 - 152: 16.701