Starting phenix.real_space_refine on Fri Mar 6 05:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6d_31478/03_2026/7f6d_31478.map" } resolution = 3.85 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= 0.003 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 74 5.16 5 C 18292 2.51 5 N 5240 2.21 5 O 5324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s 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: 28930 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2528 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2528 Classifications: {'peptide': 332} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 21, 'TRANS': 310} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 3979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 3979 Classifications: {'peptide': 521} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 32, 'TRANS': 488} Chain breaks: 3 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.62, per 1000 atoms: 0.23 Number of scatterers: 28930 At special positions: 0 Unit cell: (129.792, 126.75, 154.128, 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 74 16.00 O 5324 8.00 N 5240 7.00 C 18292 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... Secondary structure from input PDB file: 133 helices and 22 sheets defined 36.1% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 209 through 219 removed outlier: 3.582A pdb=" N GLY H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 286 through 301 removed outlier: 3.794A pdb=" N GLY H 294 " --> pdb=" O ALA H 290 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA H 295 " --> pdb=" O ASP H 291 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER H 298 " --> pdb=" O GLY H 294 " (cutoff:3.500A) Processing helix chain 'H' and resid 314 through 328 removed outlier: 3.546A pdb=" N GLN H 322 " --> pdb=" O ALA H 318 " (cutoff:3.500A) Processing helix chain 'H' and resid 330 through 344 removed outlier: 3.616A pdb=" N VAL H 334 " --> pdb=" O ASN H 330 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL H 343 " --> pdb=" O ARG H 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 163 removed outlier: 4.088A pdb=" N MET G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 219 removed outlier: 3.651A pdb=" N GLY G 214 " --> pdb=" O ALA G 210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'G' and resid 286 through 301 removed outlier: 3.781A pdb=" N GLY G 294 " --> pdb=" O ALA G 290 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 295 " --> pdb=" O ASP G 291 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER G 298 " --> pdb=" O GLY G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 314 through 328 removed outlier: 3.715A pdb=" N ALA G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA G 319 " --> pdb=" O ILE G 315 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 344 removed outlier: 3.580A pdb=" N VAL G 334 " --> pdb=" O ASN G 330 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL G 343 " --> pdb=" O ARG G 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 86 removed outlier: 3.815A pdb=" N ALA B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.792A pdb=" N ALA B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 Processing helix chain 'B' and resid 175 through 189 removed outlier: 3.913A pdb=" N ALA B 179 " --> pdb=" O LYS B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 197 removed outlier: 3.534A pdb=" N GLN B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 243 removed outlier: 4.237A pdb=" N GLU B 233 " --> pdb=" O ALA B 229 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 253 Processing helix chain 'B' and resid 267 through 275 removed outlier: 4.079A pdb=" N THR B 275 " --> pdb=" O GLY B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.590A pdb=" N PHE B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 335 removed outlier: 3.667A pdb=" N VAL B 320 " --> pdb=" O ASN B 316 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 387 removed outlier: 3.555A pdb=" N GLU B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 423 Proline residue: B 420 - end of helix Processing helix chain 'B' and resid 424 through 426 No H-bonds generated for 'chain 'B' and resid 424 through 426' Processing helix chain 'B' and resid 454 through 476 removed outlier: 3.603A pdb=" N VAL B 476 " --> pdb=" O TYR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 removed outlier: 3.763A pdb=" N TYR B 492 " --> pdb=" O GLU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 512 Processing helix chain 'B' and resid 530 through 537 removed outlier: 3.648A pdb=" N VAL B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 556 removed outlier: 3.529A pdb=" N ARG B 556 " --> pdb=" O PRO B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 567 removed outlier: 4.069A pdb=" N GLY B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B 565 " --> pdb=" O SER B 561 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLY B 567 " --> pdb=" O ARG B 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 86 Processing helix chain 'A' and resid 121 through 128 removed outlier: 3.952A pdb=" N ALA A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 157 removed outlier: 3.898A pdb=" N ILE A 156 " --> pdb=" O ASN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 189 removed outlier: 3.568A pdb=" N TYR A 178 " --> pdb=" O THR A 174 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 187 " --> pdb=" O LEU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 218 through 222 removed outlier: 4.264A pdb=" N LEU A 221 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 229 through 243 removed outlier: 4.276A pdb=" N GLU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 267 through 275 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 316 through 335 Processing helix chain 'A' and resid 377 through 387 Processing helix chain 'A' and resid 408 through 423 Proline residue: A 420 - end of helix Processing helix chain 'A' and resid 454 through 476 removed outlier: 3.836A pdb=" N VAL A 462 " --> pdb=" O GLN A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 512 Processing helix chain 'A' and resid 530 through 536 removed outlier: 3.990A pdb=" N VAL A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 556 Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.666A pdb=" N GLY A 567 " --> pdb=" O ARG A 563 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.594A pdb=" N ALA C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 128 removed outlier: 3.601A pdb=" N ALA C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 removed outlier: 3.908A pdb=" N ILE C 156 " --> pdb=" O ASN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 189 removed outlier: 3.543A pdb=" N TYR C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 197 removed outlier: 3.594A pdb=" N ALA C 196 " --> pdb=" O MET C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 4.280A pdb=" N LEU C 221 " --> pdb=" O GLY C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.565A pdb=" N GLU C 233 " --> pdb=" O ALA C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 267 through 275 Processing helix chain 'C' and resid 294 through 301 Processing helix chain 'C' and resid 304 through 308 Processing helix chain 'C' and resid 316 through 335 Processing helix chain 'C' and resid 377 through 387 Processing helix chain 'C' and resid 408 through 419 Processing helix chain 'C' and resid 420 through 422 No H-bonds generated for 'chain 'C' and resid 420 through 422' Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'C' and resid 459 through 476 Processing helix chain 'C' and resid 499 through 512 Processing helix chain 'C' and resid 530 through 536 removed outlier: 3.789A pdb=" N VAL C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 536 " --> pdb=" O ARG C 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 556 removed outlier: 4.253A pdb=" N GLU C 551 " --> pdb=" O ALA C 548 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 552 " --> pdb=" O GLU C 549 " (cutoff:3.500A) Proline residue: C 553 - end of helix Processing helix chain 'C' and resid 562 through 567 removed outlier: 4.645A pdb=" N GLY C 567 " --> pdb=" O ARG C 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 86 Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 129 through 133 Processing helix chain 'E' and resid 175 through 190 removed outlier: 4.200A pdb=" N GLY E 190 " --> pdb=" O ILE E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.975A pdb=" N LEU E 221 " --> pdb=" O GLY E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 229 through 243 removed outlier: 3.893A pdb=" N GLU E 233 " --> pdb=" O ALA E 229 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 234 " --> pdb=" O ARG E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 253 Processing helix chain 'E' and resid 267 through 275 Processing helix chain 'E' and resid 294 through 301 Processing helix chain 'E' and resid 304 through 308 Processing helix chain 'E' and resid 316 through 335 removed outlier: 3.612A pdb=" N GLN E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 387 removed outlier: 3.938A pdb=" N ARG E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 423 removed outlier: 3.806A pdb=" N VAL E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Proline residue: E 420 - end of helix Processing helix chain 'E' and resid 454 through 476 Processing helix chain 'E' and resid 488 through 493 removed outlier: 4.207A pdb=" N TYR E 492 " --> pdb=" O GLU E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 499 through 511 removed outlier: 3.584A pdb=" N VAL E 504 " --> pdb=" O PRO E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 537 removed outlier: 3.598A pdb=" N VAL E 534 " --> pdb=" O GLU E 530 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 537 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 552 through 556 Processing helix chain 'E' and resid 559 through 561 No H-bonds generated for 'chain 'E' and resid 559 through 561' Processing helix chain 'E' and resid 562 through 567 removed outlier: 4.500A pdb=" N GLY E 567 " --> pdb=" O ARG E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 86 Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 129 through 133 Processing helix chain 'F' and resid 175 through 190 removed outlier: 4.075A pdb=" N GLY F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 197 Processing helix chain 'F' and resid 218 through 222 removed outlier: 4.096A pdb=" N LEU F 221 " --> pdb=" O GLY F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 229 through 243 removed outlier: 3.552A pdb=" N GLU F 233 " --> pdb=" O ALA F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 294 through 302 removed outlier: 3.856A pdb=" N ARG F 302 " --> pdb=" O PHE F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 316 through 335 removed outlier: 3.560A pdb=" N ARG F 330 " --> pdb=" O GLU F 326 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 335 " --> pdb=" O LEU F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 386 Processing helix chain 'F' and resid 408 through 423 removed outlier: 3.680A pdb=" N ARG F 412 " --> pdb=" O THR F 408 " (cutoff:3.500A) Proline residue: F 420 - end of helix Processing helix chain 'F' and resid 454 through 476 removed outlier: 3.651A pdb=" N GLY F 463 " --> pdb=" O MET F 459 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL F 476 " --> pdb=" O TYR F 472 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 493 removed outlier: 4.220A pdb=" N TYR F 492 " --> pdb=" O GLU F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 511 removed outlier: 3.710A pdb=" N VAL F 504 " --> pdb=" O PRO F 500 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 536 removed outlier: 3.889A pdb=" N VAL F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 556 removed outlier: 3.855A pdb=" N GLU F 551 " --> pdb=" O ALA F 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG F 552 " --> pdb=" O GLU F 549 " (cutoff:3.500A) Proline residue: F 553 - end of helix Processing helix chain 'F' and resid 559 through 561 No H-bonds generated for 'chain 'F' and resid 559 through 561' Processing helix chain 'F' and resid 562 through 567 removed outlier: 4.561A pdb=" N GLY F 567 " --> pdb=" O ARG F 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.805A pdb=" N ALA D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 128 removed outlier: 3.814A pdb=" N ALA D 125 " --> pdb=" O GLY D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'D' and resid 175 through 189 removed outlier: 3.905A pdb=" N ALA D 179 " --> pdb=" O LYS D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 197 removed outlier: 3.526A pdb=" N GLN D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 removed outlier: 4.229A pdb=" N GLU D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG D 240 " --> pdb=" O ASP D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 253 Processing helix chain 'D' and resid 267 through 275 removed outlier: 4.088A pdb=" N THR D 275 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.623A pdb=" N PHE D 308 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 335 removed outlier: 3.615A pdb=" N VAL D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.560A pdb=" N GLU D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 423 Proline residue: D 420 - end of helix Processing helix chain 'D' and resid 424 through 426 No H-bonds generated for 'chain 'D' and resid 424 through 426' Processing helix chain 'D' and resid 454 through 476 removed outlier: 3.590A pdb=" N VAL D 476 " --> pdb=" O TYR D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 493 removed outlier: 3.672A pdb=" N TYR D 492 " --> pdb=" O GLU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 512 Processing helix chain 'D' and resid 530 through 537 removed outlier: 3.639A pdb=" N VAL D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 556 removed outlier: 3.526A pdb=" N ARG D 556 " --> pdb=" O PRO D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 567 removed outlier: 4.065A pdb=" N GLY D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG D 565 " --> pdb=" O SER D 561 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY D 567 " --> pdb=" O ARG D 563 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.581A pdb=" N THR H 12 " --> pdb=" O LEU G 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 95 through 103 removed outlier: 7.002A pdb=" N ALA H 83 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL H 99 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL H 81 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ALA H 101 " --> pdb=" O TYR H 79 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR H 79 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP H 184 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N GLY H 54 " --> pdb=" O ASP H 184 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY H 198 " --> pdb=" O GLU H 272 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG H 270 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TRP H 251 " --> pdb=" O LEU H 271 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLN H 247 " --> pdb=" O ALA H 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA4, first strand: chain 'G' and resid 95 through 103 removed outlier: 6.980A pdb=" N ALA G 83 " --> pdb=" O LEU G 97 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL G 99 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL G 81 " --> pdb=" O VAL G 99 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA G 101 " --> pdb=" O TYR G 79 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N TYR G 79 " --> pdb=" O ALA G 101 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU G 48 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU G 182 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU G 50 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP G 184 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N VAL G 52 " --> pdb=" O ASP G 184 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TRP G 251 " --> pdb=" O LEU G 271 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLN G 247 " --> pdb=" O ALA G 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 18 removed outlier: 5.329A pdb=" N TYR B 93 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N SER B 92 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 68 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ALA B 94 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N VAL B 66 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 96 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP B 64 " --> pdb=" O ARG B 96 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N TYR B 60 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N VAL B 102 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG B 58 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 48 " --> pdb=" O HIS B 115 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N HIS B 115 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL B 116 " --> pdb=" O GLY B 16 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY B 16 " --> pdb=" O VAL B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 137 through 142 removed outlier: 6.150A pdb=" N LEU B 151 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY B 141 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 289 through 290 removed outlier: 8.046A pdb=" N THR B 289 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU B 264 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N GLN B 263 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ASP B 449 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU B 265 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 211 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N VAL B 448 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ILE B 213 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE B 214 " --> pdb=" O VAL B 485 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 482 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE B 520 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 484 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N ALA B 522 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU B 486 " --> pdb=" O ALA B 522 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N MET B 574 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 16 through 17 removed outlier: 4.742A pdb=" N TYR A 93 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER A 92 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS A 68 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ALA A 94 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL A 66 " --> pdb=" O ALA A 94 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG A 96 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 64 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N TYR A 60 " --> pdb=" O THR A 100 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N VAL A 102 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG A 58 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 48 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS A 115 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 116 " --> pdb=" O GLY A 16 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A 16 " --> pdb=" O VAL A 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 138 through 142 removed outlier: 6.942A pdb=" N LEU A 149 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 264 through 265 removed outlier: 6.564A pdb=" N LEU A 265 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N VAL A 448 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE A 213 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG A 210 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N VAL A 485 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 212 " --> pdb=" O VAL A 485 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 16 through 17 removed outlier: 4.758A pdb=" N TYR C 93 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN C 65 " --> pdb=" O ARG C 96 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU C 98 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL C 63 " --> pdb=" O LEU C 98 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N THR C 100 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N GLY C 61 " --> pdb=" O THR C 100 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL C 102 " --> pdb=" O PHE C 59 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE C 59 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 48 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N HIS C 115 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL C 116 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY C 16 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 142 removed outlier: 6.978A pdb=" N LEU C 149 " --> pdb=" O GLY C 140 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 264 through 265 removed outlier: 8.715A pdb=" N VAL C 448 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N ILE C 213 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ARG C 210 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL C 485 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU C 212 " --> pdb=" O VAL C 485 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 28 through 32 removed outlier: 6.228A pdb=" N SER E 90 " --> pdb=" O HIS E 70 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS E 70 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N SER E 92 " --> pdb=" O LYS E 68 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS E 68 " --> pdb=" O SER E 92 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ALA E 94 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL E 66 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG E 96 " --> pdb=" O ASP E 64 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASP E 64 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR E 60 " --> pdb=" O THR E 100 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL E 102 " --> pdb=" O ARG E 58 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ARG E 58 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP E 43 " --> pdb=" O VAL E 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 137 through 142 removed outlier: 6.535A pdb=" N LEU E 149 " --> pdb=" O GLY E 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 289 through 290 removed outlier: 6.387A pdb=" N LEU E 264 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP E 449 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA E 211 " --> pdb=" O THR E 446 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL E 448 " --> pdb=" O ALA E 211 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE E 213 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ARG E 210 " --> pdb=" O PHE E 483 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL E 485 " --> pdb=" O ARG E 210 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU E 212 " --> pdb=" O VAL E 485 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE E 164 " --> pdb=" O GLY E 521 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N GLN E 523 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE E 166 " --> pdb=" O GLN E 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 31 through 32 removed outlier: 5.917A pdb=" N SER F 90 " --> pdb=" O HIS F 70 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS F 70 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N SER F 92 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS F 68 " --> pdb=" O SER F 92 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ALA F 94 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N VAL F 66 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ARG F 96 " --> pdb=" O ASP F 64 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP F 64 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR F 60 " --> pdb=" O THR F 100 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL F 102 " --> pdb=" O ARG F 58 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG F 58 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP F 43 " --> pdb=" O VAL F 63 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 137 through 142 removed outlier: 6.575A pdb=" N LEU F 149 " --> pdb=" O GLY F 140 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 289 through 290 removed outlier: 8.265A pdb=" N THR F 289 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU F 264 " --> pdb=" O THR F 289 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA F 211 " --> pdb=" O THR F 446 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL F 448 " --> pdb=" O ALA F 211 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE F 213 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N ARG F 210 " --> pdb=" O PHE F 483 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL F 485 " --> pdb=" O ARG F 210 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU F 212 " --> pdb=" O VAL F 485 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE F 164 " --> pdb=" O GLY F 521 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N HIS F 163 " --> pdb=" O ILE F 539 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL F 541 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN F 165 " --> pdb=" O VAL F 541 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLY F 543 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N SER F 167 " --> pdb=" O GLY F 543 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLN F 578 " --> pdb=" O ASN F 583 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASN F 583 " --> pdb=" O GLN F 578 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 16 through 18 removed outlier: 5.287A pdb=" N TYR D 93 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N SER D 92 " --> pdb=" O LYS D 68 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LYS D 68 " --> pdb=" O SER D 92 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA D 94 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL D 66 " --> pdb=" O ALA D 94 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG D 96 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP D 64 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TYR D 60 " --> pdb=" O THR D 100 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL D 102 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG D 58 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU D 48 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N HIS D 115 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL D 116 " --> pdb=" O GLY D 16 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLY D 16 " --> pdb=" O VAL D 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 137 through 142 removed outlier: 6.171A pdb=" N LEU D 151 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY D 141 " --> pdb=" O LEU D 149 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 289 through 290 removed outlier: 8.042A pdb=" N THR D 289 " --> pdb=" O VAL D 262 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU D 264 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLN D 263 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP D 449 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 265 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 211 " --> pdb=" O THR D 446 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 448 " --> pdb=" O ALA D 211 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ILE D 213 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 214 " --> pdb=" O VAL D 485 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL D 482 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ILE D 520 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 484 " --> pdb=" O ILE D 520 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ALA D 522 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU D 486 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 574 " --> pdb=" O VAL D 587 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL D 585 " --> pdb=" O VAL D 576 " (cutoff:3.500A) 1018 hydrogen bonds defined for protein. 2916 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: 5.61 Time building geometry restraints manager: 2.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9904 1.34 - 1.46: 3314 1.46 - 1.57: 16132 1.57 - 1.69: 0 1.69 - 1.81: 136 Bond restraints: 29486 Sorted by residual: bond pdb=" C ASP G 257 " pdb=" N ALA G 258 " ideal model delta sigma weight residual 1.331 1.258 0.073 2.07e-02 2.33e+03 1.24e+01 bond pdb=" C PRO G 259 " pdb=" N PHE G 260 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.31e-02 5.83e+03 4.08e+00 bond pdb=" C LEU E 304 " pdb=" N PRO E 305 " ideal model delta sigma weight residual 1.334 1.370 -0.036 2.34e-02 1.83e+03 2.39e+00 bond pdb=" C LEU B 304 " pdb=" N PRO B 305 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.52e+00 bond pdb=" CB PRO G 123 " pdb=" CG PRO G 123 " ideal model delta sigma weight residual 1.492 1.552 -0.060 5.00e-02 4.00e+02 1.42e+00 ... (remaining 29481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 39064 1.69 - 3.37: 714 3.37 - 5.06: 159 5.06 - 6.75: 33 6.75 - 8.43: 10 Bond angle restraints: 39980 Sorted by residual: angle pdb=" N PRO G 9 " pdb=" CA PRO G 9 " pdb=" CB PRO G 9 " ideal model delta sigma weight residual 103.00 110.42 -7.42 1.10e+00 8.26e-01 4.55e+01 angle pdb=" N PRO H 9 " pdb=" CA PRO H 9 " pdb=" CB PRO H 9 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.52e+01 angle pdb=" N LEU G 128 " pdb=" CA LEU G 128 " pdb=" C LEU G 128 " ideal model delta sigma weight residual 108.34 113.33 -4.99 1.31e+00 5.83e-01 1.45e+01 angle pdb=" C PRO A 579 " pdb=" N ASP A 580 " pdb=" CA ASP A 580 " ideal model delta sigma weight residual 125.66 132.58 -6.92 1.85e+00 2.92e-01 1.40e+01 angle pdb=" N ASN G 122 " pdb=" CA ASN G 122 " pdb=" C ASN G 122 " ideal model delta sigma weight residual 109.81 117.60 -7.79 2.21e+00 2.05e-01 1.24e+01 ... (remaining 39975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16158 17.95 - 35.91: 1452 35.91 - 53.86: 202 53.86 - 71.81: 28 71.81 - 89.77: 16 Dihedral angle restraints: 17856 sinusoidal: 7108 harmonic: 10748 Sorted by residual: dihedral pdb=" CA LYS H 303 " pdb=" C LYS H 303 " pdb=" N LEU H 304 " pdb=" CA LEU H 304 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA LEU F 304 " pdb=" C LEU F 304 " pdb=" N PRO F 305 " pdb=" CA PRO F 305 " ideal model delta harmonic sigma weight residual -180.00 -156.73 -23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA ASN G 122 " pdb=" C ASN G 122 " pdb=" N PRO G 123 " pdb=" CA PRO G 123 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 17853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3651 0.051 - 0.102: 678 0.102 - 0.153: 171 0.153 - 0.203: 3 0.203 - 0.254: 3 Chirality restraints: 4506 Sorted by residual: chirality pdb=" CA ASN G 122 " pdb=" N ASN G 122 " pdb=" C ASN G 122 " pdb=" CB ASN G 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA PRO G 9 " pdb=" N PRO G 9 " pdb=" C PRO G 9 " pdb=" CB PRO G 9 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA PRO H 9 " pdb=" N PRO H 9 " pdb=" C PRO H 9 " pdb=" CB PRO H 9 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 4503 not shown) Planarity restraints: 5318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP F 103 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO F 104 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO F 104 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 104 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN G 122 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO G 123 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO G 123 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 123 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 103 " -0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO E 104 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO E 104 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 104 " -0.020 5.00e-02 4.00e+02 ... (remaining 5315 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3344 2.75 - 3.29: 29137 3.29 - 3.83: 44715 3.83 - 4.36: 50515 4.36 - 4.90: 87821 Nonbonded interactions: 215532 Sorted by model distance: nonbonded pdb=" O VAL B 39 " pdb=" OH TYR B 93 " model vdw 2.214 3.040 nonbonded pdb=" O GLN C 415 " pdb=" OG SER C 419 " model vdw 2.214 3.040 nonbonded pdb=" O SER A 185 " pdb=" OG SER A 189 " model vdw 2.216 3.040 nonbonded pdb=" O LEU H 118 " pdb=" NH2 ARG H 337 " model vdw 2.227 3.120 nonbonded pdb=" OD2 ASP H 53 " pdb=" OG1 THR H 317 " model vdw 2.229 3.040 ... (remaining 215527 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.860 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 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 0.073 29486 Z= 0.108 Angle : 0.588 8.433 39980 Z= 0.291 Chirality : 0.042 0.254 4506 Planarity : 0.003 0.044 5318 Dihedral : 13.431 89.768 10952 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.03 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.98 (0.14), residues: 3734 helix: 0.33 (0.16), residues: 1078 sheet: 0.37 (0.21), residues: 680 loop : -1.64 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 441 TYR 0.018 0.001 TYR D 306 PHE 0.016 0.001 PHE E 291 TRP 0.020 0.001 TRP G 34 HIS 0.004 0.000 HIS H 305 Details of bonding type rmsd covalent geometry : bond 0.00230 (29486) covalent geometry : angle 0.58778 (39980) hydrogen bonds : bond 0.27270 ( 1018) hydrogen bonds : angle 8.07075 ( 2916) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ARG cc_start: 0.7775 (ptt90) cc_final: 0.7564 (ptt90) REVERT: B 503 ASP cc_start: 0.7375 (p0) cc_final: 0.7136 (p0) REVERT: C 409 ARG cc_start: 0.7678 (mtt90) cc_final: 0.7416 (mtm-85) REVERT: E 17 MET cc_start: 0.8033 (mpp) cc_final: 0.7769 (mpp) REVERT: D 101 ARG cc_start: 0.7774 (ptt90) cc_final: 0.7560 (ptt90) REVERT: D 286 GLU cc_start: 0.7687 (tt0) cc_final: 0.7476 (tt0) REVERT: D 303 MET cc_start: 0.6725 (mmp) cc_final: 0.5443 (mmt) REVERT: D 306 TYR cc_start: 0.8652 (m-80) cc_final: 0.7718 (m-10) REVERT: D 503 ASP cc_start: 0.7427 (p0) cc_final: 0.7187 (p0) outliers start: 1 outliers final: 1 residues processed: 437 average time/residue: 0.1939 time to fit residues: 132.2856 Evaluate side-chains 343 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 342 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 106 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.0030 chunk 298 optimal weight: 8.9990 overall best weight: 3.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS F 118 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.162654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133782 restraints weight = 51446.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.133621 restraints weight = 44977.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.135167 restraints weight = 44714.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135561 restraints weight = 33809.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.135997 restraints weight = 31300.139| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29486 Z= 0.235 Angle : 0.704 11.769 39980 Z= 0.355 Chirality : 0.046 0.227 4506 Planarity : 0.005 0.042 5318 Dihedral : 4.470 56.574 4176 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.62 % Favored : 91.32 % Rotamer: Outliers : 1.57 % Allowed : 10.61 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.13), residues: 3734 helix: 0.57 (0.16), residues: 1062 sheet: -0.26 (0.19), residues: 734 loop : -1.80 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 260 TYR 0.018 0.002 TYR G 107 PHE 0.018 0.002 PHE E 29 TRP 0.010 0.001 TRP G 34 HIS 0.012 0.002 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00550 (29486) covalent geometry : angle 0.70368 (39980) hydrogen bonds : bond 0.05745 ( 1018) hydrogen bonds : angle 5.82628 ( 2916) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 364 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ASP cc_start: 0.8537 (t0) cc_final: 0.8287 (m-30) REVERT: B 323 ASN cc_start: 0.7960 (m110) cc_final: 0.7755 (m110) REVERT: A 123 GLU cc_start: 0.7977 (tp30) cc_final: 0.7760 (mm-30) REVERT: A 231 MET cc_start: 0.8629 (ppp) cc_final: 0.8315 (ppp) REVERT: C 409 ARG cc_start: 0.7590 (mtt90) cc_final: 0.7168 (mtm-85) REVERT: C 411 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5835 (tp) REVERT: C 536 ASN cc_start: 0.8170 (p0) cc_final: 0.7951 (p0) REVERT: E 17 MET cc_start: 0.8230 (mpp) cc_final: 0.7912 (mpp) REVERT: D 236 ASP cc_start: 0.8659 (t0) cc_final: 0.8350 (m-30) REVERT: D 303 MET cc_start: 0.6980 (mmp) cc_final: 0.5842 (mmt) REVERT: D 306 TYR cc_start: 0.8855 (m-10) cc_final: 0.7642 (m-10) outliers start: 47 outliers final: 32 residues processed: 395 average time/residue: 0.1947 time to fit residues: 118.9547 Evaluate side-chains 368 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 335 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 181 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 508 ILE Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 67 optimal weight: 0.9990 chunk 301 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 233 optimal weight: 6.9990 chunk 367 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 231 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS E 456 HIS F 70 HIS ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.162782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133929 restraints weight = 51422.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.134259 restraints weight = 44468.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.135650 restraints weight = 42798.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136000 restraints weight = 32769.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.136444 restraints weight = 30215.692| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29486 Z= 0.192 Angle : 0.660 11.999 39980 Z= 0.327 Chirality : 0.045 0.231 4506 Planarity : 0.004 0.041 5318 Dihedral : 4.423 24.408 4174 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.01 % Favored : 91.94 % Rotamer: Outliers : 2.21 % Allowed : 13.76 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3734 helix: 0.33 (0.15), residues: 1178 sheet: -0.46 (0.19), residues: 740 loop : -1.98 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 552 TYR 0.021 0.002 TYR F 472 PHE 0.018 0.002 PHE E 29 TRP 0.012 0.001 TRP G 34 HIS 0.015 0.001 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00453 (29486) covalent geometry : angle 0.65970 (39980) hydrogen bonds : bond 0.04686 ( 1018) hydrogen bonds : angle 5.43198 ( 2916) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 356 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 236 ASP cc_start: 0.8452 (t0) cc_final: 0.8245 (m-30) REVERT: B 323 ASN cc_start: 0.8088 (m110) cc_final: 0.7844 (m110) REVERT: B 563 ARG cc_start: 0.8126 (mtt90) cc_final: 0.7632 (ttm110) REVERT: A 123 GLU cc_start: 0.7944 (tp30) cc_final: 0.7708 (mm-30) REVERT: A 536 ASN cc_start: 0.8198 (p0) cc_final: 0.7951 (p0) REVERT: C 70 HIS cc_start: 0.8277 (OUTLIER) cc_final: 0.7798 (t-90) REVERT: C 132 LYS cc_start: 0.7917 (mptt) cc_final: 0.7685 (mptt) REVERT: C 488 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7375 (tt0) REVERT: E 17 MET cc_start: 0.8278 (mpp) cc_final: 0.7965 (mpp) REVERT: E 231 MET cc_start: 0.5159 (pmm) cc_final: 0.4678 (pmm) REVERT: D 236 ASP cc_start: 0.8554 (t0) cc_final: 0.8286 (m-30) REVERT: D 563 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7638 (ttm110) outliers start: 66 outliers final: 53 residues processed: 406 average time/residue: 0.1936 time to fit residues: 122.0314 Evaluate side-chains 383 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 328 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 12 optimal weight: 8.9990 chunk 9 optimal weight: 0.3980 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 181 optimal weight: 9.9990 chunk 82 optimal weight: 0.6980 chunk 363 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 334 optimal weight: 0.9990 chunk 339 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.166177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.139223 restraints weight = 50914.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.138796 restraints weight = 47645.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.140165 restraints weight = 46614.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140550 restraints weight = 36467.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.140875 restraints weight = 34461.412| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29486 Z= 0.124 Angle : 0.612 11.434 39980 Z= 0.300 Chirality : 0.043 0.243 4506 Planarity : 0.004 0.039 5318 Dihedral : 4.229 24.117 4174 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.87 % Favored : 92.07 % Rotamer: Outliers : 2.18 % Allowed : 16.16 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.13), residues: 3734 helix: 0.55 (0.15), residues: 1178 sheet: -0.29 (0.19), residues: 702 loop : -1.92 (0.13), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 552 TYR 0.018 0.001 TYR B 472 PHE 0.013 0.001 PHE E 29 TRP 0.015 0.001 TRP G 34 HIS 0.015 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00284 (29486) covalent geometry : angle 0.61178 (39980) hydrogen bonds : bond 0.03782 ( 1018) hydrogen bonds : angle 5.05888 ( 2916) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 304 LEU cc_start: 0.8808 (pp) cc_final: 0.8585 (pp) REVERT: B 133 MET cc_start: 0.7564 (ptt) cc_final: 0.7361 (ptt) REVERT: B 323 ASN cc_start: 0.7946 (m110) cc_final: 0.7727 (m110) REVERT: B 563 ARG cc_start: 0.8003 (mtt90) cc_final: 0.7723 (ttm110) REVERT: C 247 ASP cc_start: 0.6749 (t70) cc_final: 0.6274 (t0) REVERT: C 249 TYR cc_start: 0.8372 (m-80) cc_final: 0.7909 (m-80) REVERT: C 409 ARG cc_start: 0.7458 (mtt90) cc_final: 0.7070 (mtm-85) REVERT: C 488 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7214 (tt0) REVERT: E 17 MET cc_start: 0.8201 (mpp) cc_final: 0.7894 (mpp) REVERT: F 152 ASN cc_start: 0.8312 (t0) cc_final: 0.8034 (t0) REVERT: F 222 LEU cc_start: 0.8201 (tp) cc_final: 0.7760 (mt) REVERT: D 563 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7697 (ttm110) outliers start: 65 outliers final: 43 residues processed: 410 average time/residue: 0.1965 time to fit residues: 125.4462 Evaluate side-chains 380 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 336 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 523 GLN Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 28 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 303 optimal weight: 10.0000 chunk 348 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 313 optimal weight: 2.9990 chunk 19 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 287 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.163301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136039 restraints weight = 51343.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.135639 restraints weight = 48094.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.136926 restraints weight = 48069.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.137338 restraints weight = 36799.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.137660 restraints weight = 34742.556| |-----------------------------------------------------------------------------| r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29486 Z= 0.179 Angle : 0.646 11.515 39980 Z= 0.317 Chirality : 0.044 0.249 4506 Planarity : 0.004 0.038 5318 Dihedral : 4.324 24.668 4174 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.70 % Favored : 91.24 % Rotamer: Outliers : 2.51 % Allowed : 17.30 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3734 helix: 0.52 (0.15), residues: 1190 sheet: -0.41 (0.19), residues: 702 loop : -1.99 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 441 TYR 0.020 0.002 TYR F 472 PHE 0.019 0.001 PHE E 29 TRP 0.014 0.001 TRP G 34 HIS 0.013 0.001 HIS F 451 Details of bonding type rmsd covalent geometry : bond 0.00425 (29486) covalent geometry : angle 0.64570 (39980) hydrogen bonds : bond 0.03907 ( 1018) hydrogen bonds : angle 5.06531 ( 2916) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 357 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 304 LEU cc_start: 0.8870 (pp) cc_final: 0.8606 (pp) REVERT: B 563 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7648 (ttm110) REVERT: C 247 ASP cc_start: 0.6955 (t70) cc_final: 0.6569 (t0) REVERT: C 249 TYR cc_start: 0.8426 (m-80) cc_final: 0.7973 (m-80) REVERT: C 488 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: E 17 MET cc_start: 0.8322 (mpp) cc_final: 0.8016 (mpp) REVERT: D 563 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7623 (ttm110) outliers start: 75 outliers final: 60 residues processed: 419 average time/residue: 0.1950 time to fit residues: 127.2632 Evaluate side-chains 383 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 322 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 263 optimal weight: 4.9990 chunk 367 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 228 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 276 optimal weight: 0.5980 chunk 69 optimal weight: 8.9990 chunk 305 optimal weight: 9.9990 chunk 248 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.162661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.135290 restraints weight = 51618.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134889 restraints weight = 50566.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.136279 restraints weight = 48616.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.136756 restraints weight = 37599.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.137014 restraints weight = 35089.088| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29486 Z= 0.189 Angle : 0.657 11.743 39980 Z= 0.323 Chirality : 0.045 0.260 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.390 27.413 4174 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.52 % Favored : 91.40 % Rotamer: Outliers : 3.08 % Allowed : 17.77 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.13), residues: 3734 helix: 0.50 (0.15), residues: 1190 sheet: -0.45 (0.19), residues: 714 loop : -2.02 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 337 TYR 0.019 0.002 TYR B 472 PHE 0.019 0.001 PHE E 29 TRP 0.015 0.001 TRP G 34 HIS 0.024 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00445 (29486) covalent geometry : angle 0.65701 (39980) hydrogen bonds : bond 0.03846 ( 1018) hydrogen bonds : angle 5.04718 ( 2916) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 352 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 304 LEU cc_start: 0.8878 (pp) cc_final: 0.8595 (pp) REVERT: B 459 MET cc_start: 0.7557 (tpp) cc_final: 0.7082 (tpt) REVERT: B 563 ARG cc_start: 0.8125 (mtt90) cc_final: 0.7651 (ttm110) REVERT: C 70 HIS cc_start: 0.8140 (OUTLIER) cc_final: 0.7792 (t-90) REVERT: C 123 GLU cc_start: 0.8152 (tp30) cc_final: 0.7637 (mm-30) REVERT: C 247 ASP cc_start: 0.6944 (t70) cc_final: 0.6586 (t0) REVERT: C 249 TYR cc_start: 0.8437 (m-80) cc_final: 0.8003 (m-80) REVERT: C 488 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: E 17 MET cc_start: 0.8346 (mpp) cc_final: 0.8041 (mpp) REVERT: E 240 ARG cc_start: 0.8431 (ptp-110) cc_final: 0.8082 (mtm110) REVERT: F 222 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7648 (mt) REVERT: D 459 MET cc_start: 0.7628 (tpp) cc_final: 0.7170 (tpt) REVERT: D 563 ARG cc_start: 0.8149 (mtt90) cc_final: 0.7594 (ttm110) outliers start: 92 outliers final: 72 residues processed: 428 average time/residue: 0.1879 time to fit residues: 125.4859 Evaluate side-chains 399 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 324 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 214 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 295 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 306 optimal weight: 30.0000 chunk 247 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 288 GLN G 288 GLN B 106 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN D 536 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.159260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.130307 restraints weight = 51598.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.130276 restraints weight = 43883.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131652 restraints weight = 47260.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.132227 restraints weight = 33352.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.132757 restraints weight = 31070.500| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 29486 Z= 0.233 Angle : 0.700 15.825 39980 Z= 0.345 Chirality : 0.046 0.304 4506 Planarity : 0.004 0.041 5318 Dihedral : 4.596 29.660 4174 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 3.38 % Allowed : 18.51 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.13), residues: 3734 helix: 0.39 (0.15), residues: 1190 sheet: -0.62 (0.19), residues: 714 loop : -2.11 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 552 TYR 0.020 0.002 TYR B 472 PHE 0.021 0.002 PHE E 29 TRP 0.013 0.002 TRP G 34 HIS 0.026 0.002 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00557 (29486) covalent geometry : angle 0.70039 (39980) hydrogen bonds : bond 0.04054 ( 1018) hydrogen bonds : angle 5.17371 ( 2916) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 338 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 274 HIS cc_start: 0.6276 (t-90) cc_final: 0.5961 (t-90) REVERT: G 304 LEU cc_start: 0.8903 (pp) cc_final: 0.8606 (pp) REVERT: B 459 MET cc_start: 0.7657 (tpp) cc_final: 0.7148 (tpt) REVERT: B 563 ARG cc_start: 0.8174 (mtt90) cc_final: 0.7934 (ttm110) REVERT: A 409 ARG cc_start: 0.7729 (mtt90) cc_final: 0.6954 (mtm-85) REVERT: C 70 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7963 (t-170) REVERT: C 123 GLU cc_start: 0.8178 (tp30) cc_final: 0.7700 (mm-30) REVERT: C 247 ASP cc_start: 0.7149 (t70) cc_final: 0.6819 (t0) REVERT: C 249 TYR cc_start: 0.8433 (m-80) cc_final: 0.8086 (m-80) REVERT: C 409 ARG cc_start: 0.7662 (mtt90) cc_final: 0.7286 (mtm-85) REVERT: C 488 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7504 (tt0) REVERT: E 17 MET cc_start: 0.8463 (mpp) cc_final: 0.8142 (mpp) REVERT: E 240 ARG cc_start: 0.8476 (ptp-110) cc_final: 0.8115 (mtm110) REVERT: E 459 MET cc_start: 0.7586 (ttm) cc_final: 0.7382 (ttm) REVERT: F 222 LEU cc_start: 0.8392 (tp) cc_final: 0.7740 (mt) REVERT: D 459 MET cc_start: 0.7692 (tpp) cc_final: 0.7208 (tpt) REVERT: D 563 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7564 (ttm110) outliers start: 101 outliers final: 86 residues processed: 420 average time/residue: 0.1927 time to fit residues: 125.8658 Evaluate side-chains 406 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 318 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 149 LYS Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain H residue 343 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 70 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 265 LEU Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 169 ILE Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 459 MET Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 237 LYS Chi-restraints excluded: chain D residue 411 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 596 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 247 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 218 optimal weight: 0.0030 chunk 259 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 292 optimal weight: 0.9990 chunk 298 optimal weight: 0.0270 overall best weight: 0.6052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.167050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140315 restraints weight = 50834.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.140363 restraints weight = 46440.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.141685 restraints weight = 49314.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.142397 restraints weight = 34959.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.143003 restraints weight = 32393.976| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29486 Z= 0.112 Angle : 0.629 12.371 39980 Z= 0.304 Chirality : 0.043 0.209 4506 Planarity : 0.004 0.037 5318 Dihedral : 4.269 29.013 4174 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.31 % Rotamer: Outliers : 2.34 % Allowed : 19.61 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.13), residues: 3734 helix: 0.70 (0.15), residues: 1190 sheet: -0.51 (0.19), residues: 714 loop : -1.96 (0.13), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.026 0.001 TYR B 472 PHE 0.021 0.001 PHE F 298 TRP 0.018 0.001 TRP H 34 HIS 0.028 0.001 HIS C 70 Details of bonding type rmsd covalent geometry : bond 0.00250 (29486) covalent geometry : angle 0.62911 (39980) hydrogen bonds : bond 0.03254 ( 1018) hydrogen bonds : angle 4.78815 ( 2916) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 369 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 274 HIS cc_start: 0.5981 (t-90) cc_final: 0.5690 (t-90) REVERT: G 304 LEU cc_start: 0.8835 (pp) cc_final: 0.8540 (pp) REVERT: G 322 GLN cc_start: 0.8154 (tm-30) cc_final: 0.7882 (tm-30) REVERT: B 459 MET cc_start: 0.7383 (tpp) cc_final: 0.6952 (tpt) REVERT: A 409 ARG cc_start: 0.7544 (mtt90) cc_final: 0.6860 (mtm-85) REVERT: C 247 ASP cc_start: 0.6594 (t70) cc_final: 0.6310 (t0) REVERT: C 249 TYR cc_start: 0.8390 (m-80) cc_final: 0.8030 (m-80) REVERT: C 488 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: C 530 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7814 (tm-30) REVERT: E 17 MET cc_start: 0.8342 (mpp) cc_final: 0.8017 (mpp) REVERT: E 240 ARG cc_start: 0.8426 (ptp-110) cc_final: 0.8065 (mtm110) REVERT: F 152 ASN cc_start: 0.8363 (t0) cc_final: 0.8123 (t0) REVERT: F 222 LEU cc_start: 0.8222 (tp) cc_final: 0.7765 (mt) REVERT: F 416 LYS cc_start: 0.8136 (mttp) cc_final: 0.7482 (mttp) REVERT: D 303 MET cc_start: 0.6741 (mmp) cc_final: 0.6183 (mmp) REVERT: D 459 MET cc_start: 0.7466 (tpp) cc_final: 0.7032 (tpt) outliers start: 70 outliers final: 58 residues processed: 421 average time/residue: 0.1953 time to fit residues: 127.7172 Evaluate side-chains 402 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 343 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 596 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 354 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 242 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 183 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 352 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 chunk 312 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 578 GLN D 118 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.165286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.138306 restraints weight = 51040.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.138731 restraints weight = 46513.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139660 restraints weight = 50613.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140516 restraints weight = 36264.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.140860 restraints weight = 32729.738| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29486 Z= 0.111 Angle : 0.630 12.542 39980 Z= 0.304 Chirality : 0.043 0.197 4506 Planarity : 0.004 0.034 5318 Dihedral : 4.102 28.258 4174 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 2.18 % Allowed : 19.81 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.14), residues: 3734 helix: 0.76 (0.16), residues: 1186 sheet: -0.39 (0.19), residues: 714 loop : -1.93 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 552 TYR 0.028 0.001 TYR B 472 PHE 0.025 0.001 PHE F 298 TRP 0.020 0.001 TRP H 34 HIS 0.019 0.001 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00252 (29486) covalent geometry : angle 0.62983 (39980) hydrogen bonds : bond 0.03112 ( 1018) hydrogen bonds : angle 4.65952 ( 2916) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 354 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 274 HIS cc_start: 0.5967 (t-90) cc_final: 0.5491 (t-90) REVERT: G 304 LEU cc_start: 0.8832 (pp) cc_final: 0.8543 (pp) REVERT: B 459 MET cc_start: 0.7297 (tpp) cc_final: 0.6919 (tpt) REVERT: B 549 GLU cc_start: 0.8299 (tp30) cc_final: 0.8052 (tp30) REVERT: A 308 PHE cc_start: 0.5287 (m-80) cc_final: 0.5052 (m-80) REVERT: A 409 ARG cc_start: 0.7489 (mtt90) cc_final: 0.6847 (mtm-85) REVERT: C 247 ASP cc_start: 0.6480 (t70) cc_final: 0.6198 (t0) REVERT: C 249 TYR cc_start: 0.8388 (m-80) cc_final: 0.8022 (m-80) REVERT: C 409 ARG cc_start: 0.7614 (mtt90) cc_final: 0.7110 (mtm-85) REVERT: C 480 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6677 (m-30) REVERT: C 488 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7480 (tt0) REVERT: E 17 MET cc_start: 0.8249 (mpp) cc_final: 0.7937 (mpp) REVERT: F 152 ASN cc_start: 0.8340 (t0) cc_final: 0.8094 (t0) REVERT: F 222 LEU cc_start: 0.8176 (tp) cc_final: 0.7736 (mt) REVERT: F 303 MET cc_start: 0.6628 (ppp) cc_final: 0.6291 (ppp) REVERT: F 416 LYS cc_start: 0.8045 (mttp) cc_final: 0.7433 (mttp) REVERT: D 303 MET cc_start: 0.6716 (mmp) cc_final: 0.6163 (mmp) REVERT: D 459 MET cc_start: 0.7393 (tpp) cc_final: 0.6967 (tpt) REVERT: D 549 GLU cc_start: 0.8250 (tp30) cc_final: 0.8039 (tp30) outliers start: 65 outliers final: 54 residues processed: 400 average time/residue: 0.1928 time to fit residues: 120.1587 Evaluate side-chains 400 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 70 HIS Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 65 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 332 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 ASN C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.161736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.134509 restraints weight = 51288.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.133880 restraints weight = 48800.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.135264 restraints weight = 48157.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.135553 restraints weight = 37916.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135847 restraints weight = 35935.793| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29486 Z= 0.227 Angle : 0.713 15.101 39980 Z= 0.348 Chirality : 0.046 0.222 4506 Planarity : 0.004 0.040 5318 Dihedral : 4.422 28.030 4174 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.03 % Favored : 90.89 % Rotamer: Outliers : 2.48 % Allowed : 19.81 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.13), residues: 3734 helix: 0.57 (0.15), residues: 1188 sheet: -0.59 (0.19), residues: 704 loop : -2.04 (0.13), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG E 69 TYR 0.021 0.002 TYR B 472 PHE 0.022 0.002 PHE E 29 TRP 0.013 0.001 TRP G 34 HIS 0.020 0.002 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00539 (29486) covalent geometry : angle 0.71347 (39980) hydrogen bonds : bond 0.03822 ( 1018) hydrogen bonds : angle 4.97925 ( 2916) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 335 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 274 HIS cc_start: 0.6103 (t-90) cc_final: 0.5788 (t-90) REVERT: G 304 LEU cc_start: 0.8884 (pp) cc_final: 0.8571 (pp) REVERT: B 459 MET cc_start: 0.7564 (tpp) cc_final: 0.7098 (tpt) REVERT: A 409 ARG cc_start: 0.7709 (mtt90) cc_final: 0.6965 (mtm-85) REVERT: A 530 GLU cc_start: 0.8350 (tm-30) cc_final: 0.8143 (tm-30) REVERT: C 123 GLU cc_start: 0.8147 (tp30) cc_final: 0.7892 (tp30) REVERT: C 247 ASP cc_start: 0.6775 (t70) cc_final: 0.6494 (t0) REVERT: C 249 TYR cc_start: 0.8450 (m-80) cc_final: 0.8151 (m-80) REVERT: C 409 ARG cc_start: 0.7753 (mtt90) cc_final: 0.7307 (mtm-85) REVERT: C 410 ARG cc_start: 0.6646 (mpp-170) cc_final: 0.6420 (mtm180) REVERT: C 480 ASP cc_start: 0.7062 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: C 488 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: E 17 MET cc_start: 0.8432 (mpp) cc_final: 0.8113 (mpp) REVERT: E 240 ARG cc_start: 0.8448 (ptp-110) cc_final: 0.8063 (mtt90) REVERT: F 222 LEU cc_start: 0.8286 (tp) cc_final: 0.7692 (mt) REVERT: F 303 MET cc_start: 0.6997 (ppp) cc_final: 0.6637 (ppp) REVERT: D 303 MET cc_start: 0.6865 (mmp) cc_final: 0.6378 (mmp) REVERT: D 459 MET cc_start: 0.7595 (tpp) cc_final: 0.7127 (tpt) outliers start: 74 outliers final: 63 residues processed: 393 average time/residue: 0.1851 time to fit residues: 114.2995 Evaluate side-chains 383 residues out of total 3080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 318 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 256 CYS Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 149 LYS Chi-restraints excluded: chain G residue 150 LEU Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 158 LEU Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 208 LEU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 256 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 138 PHE Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 303 MET Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 298 PHE Chi-restraints excluded: chain C residue 303 MET Chi-restraints excluded: chain C residue 407 PHE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 ILE Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain C residue 547 LEU Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 439 LEU Chi-restraints excluded: chain E residue 443 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 70 HIS Chi-restraints excluded: chain F residue 116 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 443 ILE Chi-restraints excluded: chain F residue 486 LEU Chi-restraints excluded: chain F residue 501 ILE Chi-restraints excluded: chain D residue 55 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 77 SER Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 482 VAL Chi-restraints excluded: chain D residue 547 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 89 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 200 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 189 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 HIS E 70 HIS ** E 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 70 HIS ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.159965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.131873 restraints weight = 51964.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.132586 restraints weight = 45079.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133421 restraints weight = 48628.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.134169 restraints weight = 33273.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.134484 restraints weight = 30511.167| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 29486 Z= 0.233 Angle : 0.727 12.306 39980 Z= 0.356 Chirality : 0.046 0.220 4506 Planarity : 0.004 0.041 5318 Dihedral : 4.610 28.753 4174 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.13 % Favored : 90.79 % Rotamer: Outliers : 2.51 % Allowed : 19.88 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.13), residues: 3734 helix: 0.44 (0.15), residues: 1186 sheet: -0.74 (0.19), residues: 704 loop : -2.12 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 441 TYR 0.024 0.002 TYR B 472 PHE 0.021 0.002 PHE E 29 TRP 0.013 0.001 TRP G 34 HIS 0.025 0.002 HIS F 70 Details of bonding type rmsd covalent geometry : bond 0.00556 (29486) covalent geometry : angle 0.72684 (39980) hydrogen bonds : bond 0.03946 ( 1018) hydrogen bonds : angle 5.12657 ( 2916) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3715.43 seconds wall clock time: 65 minutes 6.33 seconds (3906.33 seconds total)