Starting phenix.real_space_refine on Tue Aug 26 12:27:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279.map" model { file = "/net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rkl_19279/08_2025/8rkl_19279_trim.cif" } resolution = 4.0 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= 1.000 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: 5 Type Number sf(0) Gaussians S 106 5.16 5 C 11528 2.51 5 N 3440 2.21 5 O 3538 1.98 5 H 17938 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36550 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6071 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "B" Number of atoms: 6081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6081 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6093 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 6071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6071 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "E" Number of atoms: 6081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6081 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "F" Number of atoms: 6093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6093 Classifications: {'peptide': 423} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 405} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'ASP%NH1NOTPRO:plan': 1, 'TYR:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'EPE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.80, per 1000 atoms: 0.16 Number of scatterers: 36550 At special positions: 0 Unit cell: (143.65, 136.85, 98.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 O 3538 8.00 N 3440 7.00 C 11528 6.00 H 17938 1.00 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: 2.90 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 238.4 nanoseconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4656 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 28 sheets defined 44.3% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 106 through 125 removed outlier: 3.974A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 146 Processing helix chain 'A' and resid 150 through 157 removed outlier: 4.708A pdb=" N LEU A 154 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 201 removed outlier: 3.834A pdb=" N GLN A 197 " --> pdb=" O MET A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.660A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.570A pdb=" N LEU A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.678A pdb=" N LEU A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 4.182A pdb=" N ASP A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 400 Processing helix chain 'A' and resid 405 through 417 removed outlier: 3.552A pdb=" N ILE A 409 " --> pdb=" O PRO A 405 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 487 Processing helix chain 'A' and resid 489 through 500 removed outlier: 4.141A pdb=" N LEU A 493 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 106 through 125 removed outlier: 3.590A pdb=" N ARG B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 146 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 188 through 202 removed outlier: 4.055A pdb=" N GLN B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.611A pdb=" N ALA B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 296 removed outlier: 3.953A pdb=" N LEU B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 362 through 372 Processing helix chain 'B' and resid 385 through 400 removed outlier: 3.612A pdb=" N GLY B 400 " --> pdb=" O MET B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.013A pdb=" N ILE B 409 " --> pdb=" O PRO B 405 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.724A pdb=" N TYR B 486 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR B 487 " --> pdb=" O ARG B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 502 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 106 through 125 removed outlier: 4.143A pdb=" N ARG C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 147 Processing helix chain 'C' and resid 150 through 156 removed outlier: 4.343A pdb=" N LEU C 154 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 202 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.772A pdb=" N VAL C 254 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.817A pdb=" N LEU C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 361 through 372 removed outlier: 4.032A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 400 removed outlier: 4.332A pdb=" N SER C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 417 Processing helix chain 'C' and resid 480 through 487 Processing helix chain 'C' and resid 489 through 502 removed outlier: 3.578A pdb=" N ALA C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.987A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 146 Processing helix chain 'D' and resid 150 through 157 removed outlier: 4.690A pdb=" N LEU D 154 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 201 removed outlier: 3.844A pdb=" N GLN D 197 " --> pdb=" O MET D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.664A pdb=" N LEU D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.558A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 345 removed outlier: 3.687A pdb=" N LEU D 341 " --> pdb=" O THR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.176A pdb=" N ASP D 365 " --> pdb=" O PRO D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 400 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.556A pdb=" N ILE D 409 " --> pdb=" O PRO D 405 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS D 410 " --> pdb=" O SER D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 480 through 487 Processing helix chain 'D' and resid 489 through 500 removed outlier: 4.124A pdb=" N LEU D 493 " --> pdb=" O LEU D 489 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA D 494 " --> pdb=" O GLU D 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 97 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.544A pdb=" N ARG E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA E 123 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 146 Processing helix chain 'E' and resid 148 through 150 No H-bonds generated for 'chain 'E' and resid 148 through 150' Processing helix chain 'E' and resid 151 through 156 Processing helix chain 'E' and resid 188 through 202 removed outlier: 4.053A pdb=" N GLN E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 260 through 273 removed outlier: 3.605A pdb=" N ALA E 272 " --> pdb=" O GLY E 268 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.916A pdb=" N LEU E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 362 through 372 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.595A pdb=" N GLY E 400 " --> pdb=" O MET E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 removed outlier: 3.987A pdb=" N ILE E 409 " --> pdb=" O PRO E 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS E 410 " --> pdb=" O SER E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 487 removed outlier: 3.726A pdb=" N TYR E 486 " --> pdb=" O ASP E 482 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E 487 " --> pdb=" O ARG E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 502 Processing helix chain 'F' and resid 81 through 97 Processing helix chain 'F' and resid 98 through 102 Processing helix chain 'F' and resid 106 through 125 removed outlier: 4.145A pdb=" N ARG F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 147 Processing helix chain 'F' and resid 151 through 156 Processing helix chain 'F' and resid 188 through 202 Processing helix chain 'F' and resid 249 through 256 removed outlier: 3.774A pdb=" N VAL F 254 " --> pdb=" O MET F 250 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLU F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.824A pdb=" N LEU F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 372 removed outlier: 4.053A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 400 removed outlier: 4.321A pdb=" N SER F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 417 Processing helix chain 'F' and resid 480 through 487 Processing helix chain 'F' and resid 489 through 502 removed outlier: 3.584A pdb=" N ALA F 502 " --> pdb=" O ASP F 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.729A pdb=" N ARG A 170 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.304A pdb=" N ILE A 279 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 380 through 381 removed outlier: 6.304A pdb=" N ILE A 279 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 437 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N HIS A 435 " --> pdb=" O GLN A 422 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 436 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 305 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 181 removed outlier: 4.168A pdb=" N ASP B 162 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 380 through 382 removed outlier: 6.361A pdb=" N ILE B 279 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N SER B 280 " --> pdb=" O ALA B 423 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N ARG B 425 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 424 " --> pdb=" O ILE B 433 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE B 433 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 320 through 321 removed outlier: 6.539A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE B 354 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.622A pdb=" N VAL B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 453 through 460 removed outlier: 3.512A pdb=" N LYS B 469 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL B 467 " --> pdb=" O THR B 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 178 through 181 removed outlier: 6.804A pdb=" N PHE C 172 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE C 163 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU C 174 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG C 223 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 380 through 381 removed outlier: 8.554A pdb=" N LEU C 381 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE C 279 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA C 423 " --> pdb=" O SER C 280 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 14.196A pdb=" N ARG C 432 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 12.283A pdb=" N ILE C 457 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR C 434 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 436 " --> pdb=" O PHE C 453 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE C 453 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR C 455 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ARG C 471 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE C 457 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS C 469 " --> pdb=" O ILE C 457 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 320 through 321 removed outlier: 6.268A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 439 through 443 removed outlier: 6.787A pdb=" N VAL C 448 " --> pdb=" O VAL C 440 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N LEU C 442 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 179 through 181 removed outlier: 3.890A pdb=" N ARG D 170 " --> pdb=" O ASN D 166 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 380 through 381 removed outlier: 6.306A pdb=" N ILE D 279 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER D 280 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ARG D 425 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 380 through 381 removed outlier: 6.306A pdb=" N ILE D 279 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N SER D 280 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N ARG D 425 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 437 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N HIS D 435 " --> pdb=" O GLN D 422 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE D 436 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 305 through 307 Processing sheet with id=AC1, first strand: chain 'D' and resid 441 through 443 Processing sheet with id=AC2, first strand: chain 'E' and resid 179 through 181 removed outlier: 4.180A pdb=" N ASP E 162 " --> pdb=" O GLU E 174 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 380 through 382 removed outlier: 6.366A pdb=" N ILE E 279 " --> pdb=" O LEU E 381 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N SER E 280 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N ARG E 425 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA E 424 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N ILE E 433 " --> pdb=" O ALA E 424 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 320 through 321 removed outlier: 6.516A pdb=" N VAL E 304 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 442 through 443 removed outlier: 3.527A pdb=" N VAL E 446 " --> pdb=" O GLU E 443 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 453 through 460 removed outlier: 3.511A pdb=" N LYS E 469 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL E 467 " --> pdb=" O THR E 458 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 178 through 181 removed outlier: 6.810A pdb=" N PHE F 172 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE F 163 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU F 174 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG F 223 " --> pdb=" O ARG F 241 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 380 through 381 removed outlier: 8.558A pdb=" N LEU F 381 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE F 279 " --> pdb=" O LEU F 381 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA F 423 " --> pdb=" O SER F 280 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 14.192A pdb=" N ARG F 432 " --> pdb=" O ILE F 457 " (cutoff:3.500A) removed outlier: 12.283A pdb=" N ILE F 457 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR F 434 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 436 " --> pdb=" O PHE F 453 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE F 453 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR F 455 " --> pdb=" O ARG F 471 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARG F 471 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE F 457 " --> pdb=" O LYS F 469 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS F 469 " --> pdb=" O ILE F 457 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 320 through 321 removed outlier: 6.243A pdb=" N VAL F 304 " --> pdb=" O VAL F 321 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 439 through 443 removed outlier: 6.782A pdb=" N VAL F 448 " --> pdb=" O VAL F 440 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU F 442 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N VAL F 446 " --> pdb=" O LEU F 442 " (cutoff:3.500A) 891 hydrogen bonds defined for protein. 2577 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: 6.46 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17902 1.03 - 1.22: 36 1.22 - 1.42: 7408 1.42 - 1.61: 11266 1.61 - 1.81: 172 Bond restraints: 36784 Sorted by residual: bond pdb=" N ASP B 80 " pdb=" H1 ASP B 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N ASP A 80 " pdb=" H1 ASP A 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP E 80 " pdb=" H1 ASP E 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N ASP C 80 " pdb=" H1 ASP C 80 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.48e+01 bond pdb=" N ASP F 80 " pdb=" H1 ASP F 80 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+01 ... (remaining 36779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 66410 5.75 - 11.50: 8 11.50 - 17.25: 0 17.25 - 23.00: 2 23.00 - 28.75: 10 Bond angle restraints: 66430 Sorted by residual: angle pdb=" SD MET B 164 " pdb=" CG MET B 164 " pdb=" HG2 MET B 164 " ideal model delta sigma weight residual 108.00 79.25 28.75 3.00e+00 1.11e-01 9.19e+01 angle pdb=" SD MET E 164 " pdb=" CG MET E 164 " pdb=" HG2 MET E 164 " ideal model delta sigma weight residual 108.00 79.28 28.72 3.00e+00 1.11e-01 9.17e+01 angle pdb=" CB MET B 164 " pdb=" CG MET B 164 " pdb=" HG2 MET B 164 " ideal model delta sigma weight residual 109.00 81.40 27.60 3.00e+00 1.11e-01 8.46e+01 angle pdb=" CB MET E 164 " pdb=" CG MET E 164 " pdb=" HG2 MET E 164 " ideal model delta sigma weight residual 109.00 81.41 27.59 3.00e+00 1.11e-01 8.46e+01 angle pdb=" SD MET E 164 " pdb=" CG MET E 164 " pdb=" HG3 MET E 164 " ideal model delta sigma weight residual 108.00 80.45 27.55 3.00e+00 1.11e-01 8.44e+01 ... (remaining 66425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.30: 16282 22.30 - 44.60: 635 44.60 - 66.90: 280 66.90 - 89.20: 77 89.20 - 111.50: 4 Dihedral angle restraints: 17278 sinusoidal: 9538 harmonic: 7740 Sorted by residual: dihedral pdb=" N1 EPE E 701 " pdb=" C2 EPE E 701 " pdb=" C3 EPE E 701 " pdb=" N4 EPE E 701 " ideal model delta sinusoidal sigma weight residual -57.34 54.16 -111.50 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" N1 EPE B 701 " pdb=" C2 EPE B 701 " pdb=" C3 EPE B 701 " pdb=" N4 EPE B 701 " ideal model delta sinusoidal sigma weight residual -57.34 54.13 -111.47 1 3.00e+01 1.11e-03 1.46e+01 dihedral pdb=" CA ASP E 106 " pdb=" C ASP E 106 " pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta harmonic sigma weight residual 180.00 -160.96 -19.04 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 17275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1785 0.029 - 0.058: 733 0.058 - 0.087: 254 0.087 - 0.117: 205 0.117 - 0.146: 59 Chirality restraints: 3036 Sorted by residual: chirality pdb=" CA ILE D 213 " pdb=" N ILE D 213 " pdb=" C ILE D 213 " pdb=" CB ILE D 213 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CA ILE C 436 " pdb=" N ILE C 436 " pdb=" C ILE C 436 " pdb=" CB ILE C 436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE F 436 " pdb=" N ILE F 436 " pdb=" C ILE F 436 " pdb=" CB ILE F 436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 ... (remaining 3033 not shown) Planarity restraints: 5812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 228 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO A 229 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 228 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.96e+00 pdb=" N PRO D 229 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 229 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 229 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E 229 " 0.043 5.00e-02 4.00e+02 6.44e-02 6.64e+00 pdb=" N PRO E 230 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 230 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 230 " 0.036 5.00e-02 4.00e+02 ... (remaining 5809 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1290 2.15 - 2.76: 70447 2.76 - 3.38: 96228 3.38 - 3.99: 119827 3.99 - 4.60: 192490 Nonbonded interactions: 480282 Sorted by model distance: nonbonded pdb=" OE1 GLU E 262 " pdb=" H GLU E 262 " model vdw 1.538 2.450 nonbonded pdb=" HE ARG D 274 " pdb=" O ASP D 375 " model vdw 1.548 2.450 nonbonded pdb=" OE1 GLU B 262 " pdb=" H GLU B 262 " model vdw 1.558 2.450 nonbonded pdb=" HE ARG A 274 " pdb=" O ASP A 375 " model vdw 1.563 2.450 nonbonded pdb=" H ARG F 359 " pdb=" OE2 GLU F 362 " model vdw 1.566 2.450 ... (remaining 480277 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 27.560 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 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 : 0.005 0.051 18846 Z= 0.229 Angle : 0.622 23.211 25568 Z= 0.337 Chirality : 0.045 0.146 3036 Planarity : 0.005 0.067 3390 Dihedral : 11.797 111.499 6924 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 2.61 % Allowed : 4.67 % Favored : 92.73 % 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 aren not related in a simple way. whole: -1.61 (0.17), residues: 2526 helix: 0.66 (0.17), residues: 980 sheet: -2.66 (0.23), residues: 436 loop : -1.95 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 223 TYR 0.015 0.001 TYR C 148 PHE 0.007 0.001 PHE F 297 TRP 0.009 0.001 TRP E 481 HIS 0.003 0.001 HIS A 319 Details of bonding type rmsd covalent geometry : bond 0.00499 (18846) covalent geometry : angle 0.62194 (25568) hydrogen bonds : bond 0.14288 ( 887) hydrogen bonds : angle 6.63342 ( 2577) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 465 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 417 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 ILE cc_start: 0.6876 (mt) cc_final: 0.6674 (mt) REVERT: A 209 GLU cc_start: 0.8107 (tt0) cc_final: 0.7894 (tm-30) REVERT: A 256 PHE cc_start: 0.6950 (m-10) cc_final: 0.5508 (t80) REVERT: A 265 ARG cc_start: 0.7520 (mtm180) cc_final: 0.6554 (mtt90) REVERT: A 276 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (m-40) REVERT: A 448 VAL cc_start: 0.8067 (t) cc_final: 0.7854 (m) REVERT: B 210 SER cc_start: 0.8263 (m) cc_final: 0.7977 (p) REVERT: B 240 ILE cc_start: 0.8860 (mt) cc_final: 0.8265 (mt) REVERT: C 184 VAL cc_start: 0.8107 (t) cc_final: 0.7782 (t) REVERT: C 185 ARG cc_start: 0.8658 (mtt90) cc_final: 0.8174 (mtp-110) REVERT: C 210 SER cc_start: 0.8436 (m) cc_final: 0.7997 (p) REVERT: C 252 ASN cc_start: 0.8068 (m110) cc_final: 0.7760 (m-40) REVERT: C 314 GLN cc_start: 0.8591 (tt0) cc_final: 0.7962 (tt0) REVERT: C 317 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.6864 (mm-40) REVERT: C 370 MET cc_start: 0.8442 (mtt) cc_final: 0.8111 (mtt) REVERT: C 377 SER cc_start: 0.9529 (m) cc_final: 0.9160 (p) REVERT: D 256 PHE cc_start: 0.6915 (m-10) cc_final: 0.5488 (t80) REVERT: D 265 ARG cc_start: 0.7466 (mtm180) cc_final: 0.6556 (mpt-90) REVERT: D 276 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7740 (m-40) REVERT: D 448 VAL cc_start: 0.8076 (t) cc_final: 0.7874 (m) REVERT: D 461 ASP cc_start: 0.6429 (OUTLIER) cc_final: 0.6193 (m-30) REVERT: E 210 SER cc_start: 0.8279 (m) cc_final: 0.7991 (p) REVERT: E 240 ILE cc_start: 0.8844 (mt) cc_final: 0.8229 (mt) REVERT: E 448 VAL cc_start: 0.8982 (t) cc_final: 0.8697 (m) REVERT: F 170 ARG cc_start: 0.7359 (mtt180) cc_final: 0.6660 (mpp80) REVERT: F 210 SER cc_start: 0.8387 (m) cc_final: 0.7983 (p) REVERT: F 252 ASN cc_start: 0.8077 (m110) cc_final: 0.7782 (m-40) REVERT: F 314 GLN cc_start: 0.8590 (tt0) cc_final: 0.8077 (tm-30) REVERT: F 317 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.6867 (mm-40) REVERT: F 370 MET cc_start: 0.8432 (mtt) cc_final: 0.8112 (mtt) REVERT: F 377 SER cc_start: 0.9514 (m) cc_final: 0.9151 (p) outliers start: 48 outliers final: 27 residues processed: 461 average time/residue: 0.3944 time to fit residues: 245.8746 Evaluate side-chains 230 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 198 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 451 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 244 LYS Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 262 GLU Chi-restraints excluded: chain D residue 276 ASN Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 396 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 461 ASP Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 309 ASP Chi-restraints excluded: chain F residue 317 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 143 ASN A 225 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN B 202 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 344 ASN C 252 ASN C 384 ASN ** D 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 202 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 ASN F 384 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.106478 restraints weight = 109080.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.107839 restraints weight = 90361.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109557 restraints weight = 64036.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110447 restraints weight = 46870.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.110495 restraints weight = 41188.704| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18846 Z= 0.137 Angle : 0.594 23.454 25568 Z= 0.304 Chirality : 0.044 0.162 3036 Planarity : 0.005 0.067 3390 Dihedral : 8.693 88.146 2882 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.01 % Allowed : 10.31 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.25 (0.17), residues: 2526 helix: 0.84 (0.17), residues: 1006 sheet: -2.34 (0.25), residues: 392 loop : -1.80 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 477 TYR 0.008 0.001 TYR C 148 PHE 0.005 0.001 PHE C 297 TRP 0.004 0.001 TRP E 481 HIS 0.004 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00298 (18846) covalent geometry : angle 0.59429 (25568) hydrogen bonds : bond 0.04493 ( 887) hydrogen bonds : angle 5.28480 ( 2577) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 243 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 206 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6230 (m-10) cc_final: 0.5705 (t80) REVERT: A 265 ARG cc_start: 0.7281 (mtm180) cc_final: 0.6580 (mpt180) REVERT: A 319 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6933 (t-90) REVERT: B 388 GLU cc_start: 0.6201 (tt0) cc_final: 0.5883 (tp30) REVERT: C 210 SER cc_start: 0.8762 (m) cc_final: 0.8305 (p) REVERT: C 317 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: D 256 PHE cc_start: 0.6279 (m-10) cc_final: 0.5711 (t80) REVERT: D 265 ARG cc_start: 0.7354 (mtm180) cc_final: 0.6461 (mtt90) REVERT: D 319 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: E 388 GLU cc_start: 0.6204 (tt0) cc_final: 0.5860 (tp30) REVERT: F 210 SER cc_start: 0.8760 (m) cc_final: 0.8334 (p) outliers start: 37 outliers final: 21 residues processed: 237 average time/residue: 0.3078 time to fit residues: 106.2185 Evaluate side-chains 202 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 178 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain E residue 319 HIS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain F residue 213 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 0.0050 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 7 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 143 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN D 225 ASN ** D 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.126381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107746 restraints weight = 109539.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108944 restraints weight = 85967.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.110536 restraints weight = 67721.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.110662 restraints weight = 46247.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112541 restraints weight = 43305.446| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18846 Z= 0.165 Angle : 0.575 23.834 25568 Z= 0.296 Chirality : 0.044 0.156 3036 Planarity : 0.005 0.065 3390 Dihedral : 6.756 64.503 2843 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 2.28 % Allowed : 11.51 % Favored : 86.21 % 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 aren not related in a simple way. whole: -1.26 (0.17), residues: 2526 helix: 0.95 (0.16), residues: 1002 sheet: -2.55 (0.23), residues: 430 loop : -1.78 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 352 TYR 0.012 0.001 TYR C 148 PHE 0.006 0.001 PHE A 297 TRP 0.006 0.001 TRP B 481 HIS 0.003 0.001 HIS F 374 Details of bonding type rmsd covalent geometry : bond 0.00364 (18846) covalent geometry : angle 0.57523 (25568) hydrogen bonds : bond 0.04108 ( 887) hydrogen bonds : angle 5.05867 ( 2577) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6173 (m-10) cc_final: 0.5696 (t80) REVERT: A 265 ARG cc_start: 0.7062 (mtm180) cc_final: 0.6567 (mpt180) REVERT: A 319 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6884 (t-90) REVERT: B 388 GLU cc_start: 0.6289 (tt0) cc_final: 0.5916 (tp30) REVERT: C 210 SER cc_start: 0.8716 (m) cc_final: 0.8310 (p) REVERT: C 359 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6807 (mtm110) REVERT: D 256 PHE cc_start: 0.6178 (m-10) cc_final: 0.5721 (t80) REVERT: D 265 ARG cc_start: 0.7154 (mtm180) cc_final: 0.6535 (mpt180) REVERT: D 319 HIS cc_start: 0.7202 (OUTLIER) cc_final: 0.6845 (t70) REVERT: F 210 SER cc_start: 0.8658 (m) cc_final: 0.8279 (p) REVERT: F 317 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7267 (mm-40) REVERT: F 359 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.6800 (mtm110) outliers start: 42 outliers final: 31 residues processed: 224 average time/residue: 0.3146 time to fit residues: 104.1304 Evaluate side-chains 202 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 359 ARG Chi-restraints excluded: chain C residue 472 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 359 ARG Chi-restraints excluded: chain F residue 472 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 172 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 30 optimal weight: 0.0570 chunk 154 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 168 optimal weight: 40.0000 chunk 218 optimal weight: 9.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.125447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106933 restraints weight = 110808.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108129 restraints weight = 86910.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.109665 restraints weight = 68962.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.109806 restraints weight = 46960.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.110899 restraints weight = 44114.484| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18846 Z= 0.179 Angle : 0.568 23.642 25568 Z= 0.294 Chirality : 0.044 0.154 3036 Planarity : 0.005 0.066 3390 Dihedral : 6.463 64.911 2836 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 2.77 % Allowed : 12.32 % Favored : 84.91 % 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 aren not related in a simple way. whole: -1.25 (0.17), residues: 2526 helix: 0.99 (0.16), residues: 1006 sheet: -2.61 (0.23), residues: 430 loop : -1.79 (0.19), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 352 TYR 0.011 0.001 TYR C 148 PHE 0.010 0.001 PHE D 172 TRP 0.006 0.001 TRP B 481 HIS 0.005 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00400 (18846) covalent geometry : angle 0.56847 (25568) hydrogen bonds : bond 0.03967 ( 887) hydrogen bonds : angle 5.01209 ( 2577) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6186 (m-10) cc_final: 0.5671 (t80) REVERT: A 265 ARG cc_start: 0.7103 (mtm180) cc_final: 0.6568 (mpt180) REVERT: A 319 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6881 (t-90) REVERT: C 210 SER cc_start: 0.8702 (m) cc_final: 0.8270 (p) REVERT: C 317 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7196 (mm-40) REVERT: D 256 PHE cc_start: 0.6196 (m-10) cc_final: 0.5676 (t80) REVERT: D 265 ARG cc_start: 0.7119 (mtm180) cc_final: 0.6563 (mpt180) REVERT: D 319 HIS cc_start: 0.7160 (OUTLIER) cc_final: 0.6830 (t-90) REVERT: F 210 SER cc_start: 0.8683 (m) cc_final: 0.8285 (p) REVERT: F 317 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7278 (mm-40) outliers start: 51 outliers final: 37 residues processed: 210 average time/residue: 0.2923 time to fit residues: 92.8160 Evaluate side-chains 201 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 345 CYS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 105 optimal weight: 4.9990 chunk 186 optimal weight: 3.9990 chunk 235 optimal weight: 7.9990 chunk 36 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 172 optimal weight: 40.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 GLN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN D 422 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 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 = 0.3952 r_free = 0.3952 target = 0.126045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107484 restraints weight = 109762.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108472 restraints weight = 85638.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.110142 restraints weight = 69360.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.110446 restraints weight = 47115.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112430 restraints weight = 42485.313| |-----------------------------------------------------------------------------| r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18846 Z= 0.141 Angle : 0.539 23.763 25568 Z= 0.276 Chirality : 0.044 0.153 3036 Planarity : 0.004 0.064 3390 Dihedral : 6.286 64.615 2836 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.28 % Allowed : 13.25 % Favored : 84.47 % 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 aren not related in a simple way. whole: -1.04 (0.17), residues: 2526 helix: 1.23 (0.16), residues: 1006 sheet: -2.56 (0.24), residues: 418 loop : -1.72 (0.19), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 352 TYR 0.016 0.001 TYR F 148 PHE 0.005 0.001 PHE D 297 TRP 0.004 0.001 TRP B 481 HIS 0.003 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00314 (18846) covalent geometry : angle 0.53852 (25568) hydrogen bonds : bond 0.03666 ( 887) hydrogen bonds : angle 4.79448 ( 2577) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 210 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6054 (m-10) cc_final: 0.5621 (t80) REVERT: A 265 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6523 (mpt180) REVERT: A 319 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6810 (t70) REVERT: C 210 SER cc_start: 0.8644 (m) cc_final: 0.8235 (p) REVERT: D 256 PHE cc_start: 0.6051 (m-10) cc_final: 0.5622 (t80) REVERT: D 265 ARG cc_start: 0.7016 (mtm180) cc_final: 0.6527 (mpt180) REVERT: D 319 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6789 (t70) REVERT: F 210 SER cc_start: 0.8651 (m) cc_final: 0.8242 (p) REVERT: F 317 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7196 (mm-40) outliers start: 42 outliers final: 34 residues processed: 198 average time/residue: 0.2791 time to fit residues: 84.7536 Evaluate side-chains 197 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 345 CYS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 177 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 246 optimal weight: 0.0980 chunk 111 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.125325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106767 restraints weight = 110757.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.107821 restraints weight = 86975.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.109434 restraints weight = 69599.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109621 restraints weight = 46691.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111688 restraints weight = 45117.888| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 18846 Z= 0.161 Angle : 0.547 23.628 25568 Z= 0.281 Chirality : 0.044 0.152 3036 Planarity : 0.004 0.066 3390 Dihedral : 6.288 64.922 2836 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 2.50 % Allowed : 13.41 % Favored : 84.09 % 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 aren not related in a simple way. whole: -1.02 (0.17), residues: 2526 helix: 1.28 (0.16), residues: 1006 sheet: -2.58 (0.24), residues: 422 loop : -1.75 (0.19), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 352 TYR 0.011 0.001 TYR F 148 PHE 0.006 0.001 PHE D 297 TRP 0.005 0.001 TRP B 481 HIS 0.004 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00361 (18846) covalent geometry : angle 0.54654 (25568) hydrogen bonds : bond 0.03697 ( 887) hydrogen bonds : angle 4.79610 ( 2577) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6082 (m-10) cc_final: 0.5599 (t80) REVERT: A 265 ARG cc_start: 0.7016 (mtm180) cc_final: 0.6523 (mpt180) REVERT: A 319 HIS cc_start: 0.7210 (OUTLIER) cc_final: 0.6851 (t70) REVERT: B 262 GLU cc_start: 0.7226 (mp0) cc_final: 0.6423 (mp0) REVERT: B 388 GLU cc_start: 0.6190 (tt0) cc_final: 0.5688 (tp30) REVERT: C 210 SER cc_start: 0.8655 (m) cc_final: 0.8234 (p) REVERT: D 256 PHE cc_start: 0.6108 (m-10) cc_final: 0.5621 (t80) REVERT: D 265 ARG cc_start: 0.7016 (mtm180) cc_final: 0.6485 (mpt180) REVERT: D 319 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.6842 (t70) REVERT: F 210 SER cc_start: 0.8650 (m) cc_final: 0.8246 (p) REVERT: F 317 GLN cc_start: 0.8358 (OUTLIER) cc_final: 0.7236 (mm-40) outliers start: 46 outliers final: 40 residues processed: 198 average time/residue: 0.2617 time to fit residues: 80.6200 Evaluate side-chains 203 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 240 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 180 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 159 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.125123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.106603 restraints weight = 110869.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108053 restraints weight = 86861.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.109426 restraints weight = 65941.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109590 restraints weight = 44494.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.109954 restraints weight = 43518.641| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18846 Z= 0.158 Angle : 0.544 23.548 25568 Z= 0.280 Chirality : 0.044 0.151 3036 Planarity : 0.004 0.065 3390 Dihedral : 6.264 64.660 2836 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 2.82 % Allowed : 12.92 % Favored : 84.26 % 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 aren not related in a simple way. whole: -0.99 (0.17), residues: 2526 helix: 1.30 (0.16), residues: 1008 sheet: -2.47 (0.24), residues: 424 loop : -1.76 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 352 TYR 0.011 0.001 TYR C 148 PHE 0.006 0.001 PHE A 297 TRP 0.005 0.001 TRP B 481 HIS 0.003 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00353 (18846) covalent geometry : angle 0.54365 (25568) hydrogen bonds : bond 0.03661 ( 887) hydrogen bonds : angle 4.76599 ( 2577) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 213 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 161 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6196 (m-10) cc_final: 0.5611 (t80) REVERT: A 265 ARG cc_start: 0.7163 (mtm180) cc_final: 0.6633 (mpt180) REVERT: A 319 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6892 (t70) REVERT: B 139 GLN cc_start: 0.5821 (tp40) cc_final: 0.4983 (pt0) REVERT: B 388 GLU cc_start: 0.6186 (tt0) cc_final: 0.5656 (tp30) REVERT: C 210 SER cc_start: 0.8665 (m) cc_final: 0.8247 (p) REVERT: D 256 PHE cc_start: 0.6174 (m-10) cc_final: 0.5607 (t80) REVERT: D 265 ARG cc_start: 0.7134 (mtm180) cc_final: 0.6618 (mpt180) REVERT: D 319 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6868 (t70) REVERT: F 210 SER cc_start: 0.8650 (m) cc_final: 0.8244 (p) REVERT: F 317 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.7247 (mm-40) outliers start: 52 outliers final: 44 residues processed: 202 average time/residue: 0.2721 time to fit residues: 85.5789 Evaluate side-chains 206 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 159 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 345 CYS Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 345 CYS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 158 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 317 GLN Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 183 optimal weight: 0.0270 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 0.5980 chunk 93 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 212 optimal weight: 40.0000 chunk 218 optimal weight: 8.9990 chunk 178 optimal weight: 3.9990 overall best weight: 0.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 ASN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.127390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.108058 restraints weight = 109469.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.108224 restraints weight = 93633.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110513 restraints weight = 72492.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.111315 restraints weight = 46639.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.111727 restraints weight = 42577.861| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 18846 Z= 0.090 Angle : 0.507 23.647 25568 Z= 0.255 Chirality : 0.044 0.150 3036 Planarity : 0.004 0.064 3390 Dihedral : 5.940 64.261 2836 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.06 % Allowed : 13.95 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.18), residues: 2526 helix: 1.67 (0.17), residues: 1012 sheet: -2.29 (0.25), residues: 406 loop : -1.57 (0.19), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 352 TYR 0.010 0.001 TYR C 148 PHE 0.006 0.001 PHE A 243 TRP 0.003 0.001 TRP D 481 HIS 0.002 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00200 (18846) covalent geometry : angle 0.50711 (25568) hydrogen bonds : bond 0.03214 ( 887) hydrogen bonds : angle 4.40443 ( 2577) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6138 (m-10) cc_final: 0.5532 (t80) REVERT: A 265 ARG cc_start: 0.7131 (mtm180) cc_final: 0.6608 (mpt180) REVERT: B 139 GLN cc_start: 0.5807 (tp40) cc_final: 0.4995 (pt0) REVERT: B 347 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7422 (mtm110) REVERT: B 388 GLU cc_start: 0.5887 (tt0) cc_final: 0.5522 (tp30) REVERT: C 210 SER cc_start: 0.8572 (m) cc_final: 0.8138 (p) REVERT: D 256 PHE cc_start: 0.6099 (m-10) cc_final: 0.5512 (t80) REVERT: D 265 ARG cc_start: 0.7108 (mtm180) cc_final: 0.6586 (mpt180) REVERT: D 319 HIS cc_start: 0.7005 (OUTLIER) cc_final: 0.6668 (t70) REVERT: E 388 GLU cc_start: 0.5806 (tt0) cc_final: 0.5463 (tp30) REVERT: F 210 SER cc_start: 0.8607 (m) cc_final: 0.8186 (p) outliers start: 38 outliers final: 34 residues processed: 197 average time/residue: 0.2672 time to fit residues: 82.1096 Evaluate side-chains 199 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 368 GLN Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 319 HIS Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 368 GLN Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 203 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 37 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.126020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106825 restraints weight = 110658.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.107969 restraints weight = 86373.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.109801 restraints weight = 64534.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.110302 restraints weight = 42751.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.111859 restraints weight = 40424.353| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18846 Z= 0.134 Angle : 0.526 23.681 25568 Z= 0.267 Chirality : 0.044 0.149 3036 Planarity : 0.004 0.062 3390 Dihedral : 5.922 63.645 2834 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 2.12 % Allowed : 13.95 % Favored : 83.93 % 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 aren not related in a simple way. whole: -0.60 (0.17), residues: 2526 helix: 1.68 (0.16), residues: 1012 sheet: -2.31 (0.24), residues: 418 loop : -1.61 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 352 TYR 0.009 0.001 TYR C 148 PHE 0.005 0.001 PHE A 297 TRP 0.005 0.001 TRP B 481 HIS 0.002 0.001 HIS E 319 Details of bonding type rmsd covalent geometry : bond 0.00300 (18846) covalent geometry : angle 0.52646 (25568) hydrogen bonds : bond 0.03354 ( 887) hydrogen bonds : angle 4.48607 ( 2577) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6123 (m-10) cc_final: 0.5563 (t80) REVERT: A 265 ARG cc_start: 0.7064 (mtm180) cc_final: 0.6599 (mpt180) REVERT: B 139 GLN cc_start: 0.5855 (tp40) cc_final: 0.5027 (pt0) REVERT: B 347 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7499 (mtm110) REVERT: B 388 GLU cc_start: 0.6091 (tt0) cc_final: 0.5661 (tp30) REVERT: C 210 SER cc_start: 0.8571 (m) cc_final: 0.8158 (p) REVERT: D 256 PHE cc_start: 0.6084 (m-10) cc_final: 0.5542 (t80) REVERT: D 265 ARG cc_start: 0.7044 (mtm180) cc_final: 0.6566 (mpt180) REVERT: E 388 GLU cc_start: 0.5958 (tt0) cc_final: 0.5568 (tp30) REVERT: F 210 SER cc_start: 0.8613 (m) cc_final: 0.8202 (p) outliers start: 39 outliers final: 36 residues processed: 191 average time/residue: 0.3319 time to fit residues: 98.2910 Evaluate side-chains 197 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 345 CYS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 177 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 237 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 108 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.126082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.107628 restraints weight = 110433.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108831 restraints weight = 86437.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.110201 restraints weight = 69786.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.110574 restraints weight = 47112.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.112784 restraints weight = 43583.437| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18846 Z= 0.129 Angle : 0.526 23.995 25568 Z= 0.267 Chirality : 0.044 0.150 3036 Planarity : 0.004 0.064 3390 Dihedral : 5.534 57.101 2828 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.95 % Allowed : 14.33 % Favored : 83.71 % 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 aren not related in a simple way. whole: -0.58 (0.18), residues: 2526 helix: 1.71 (0.17), residues: 1012 sheet: -2.37 (0.24), residues: 428 loop : -1.57 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 352 TYR 0.008 0.001 TYR C 148 PHE 0.006 0.001 PHE D 297 TRP 0.004 0.001 TRP E 481 HIS 0.003 0.001 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00288 (18846) covalent geometry : angle 0.52638 (25568) hydrogen bonds : bond 0.03322 ( 887) hydrogen bonds : angle 4.45672 ( 2577) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Residue TYR 81 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue THR 85 is missing expected H atoms. Skipping. Residue LYS 86 is missing expected H atoms. Skipping. Residue THR 87 is missing expected H atoms. Skipping. Residue THR 88 is missing expected H atoms. Skipping. Residue ILE 89 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue THR 96 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue LEU 99 is missing expected H atoms. Skipping. Residue SER 100 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LEU 107 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue ILE 114 is missing expected H atoms. Skipping. Residue ILE 117 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 121 is missing expected H atoms. Skipping. Residue VAL 122 is missing expected H atoms. Skipping. Residue ILE 124 is missing expected H atoms. Skipping. Residue LYS 125 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue SER 128 is missing expected H atoms. Skipping. Residue MET 129 is missing expected H atoms. Skipping. Residue SER 130 is missing expected H atoms. Skipping. Residue VAL 131 is missing expected H atoms. Skipping. Residue ALA 132 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 PHE cc_start: 0.6064 (m-10) cc_final: 0.5486 (t80) REVERT: A 265 ARG cc_start: 0.7028 (mtm180) cc_final: 0.6575 (mpt180) REVERT: B 139 GLN cc_start: 0.5734 (tp40) cc_final: 0.4936 (pt0) REVERT: B 347 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7522 (mtm110) REVERT: B 388 GLU cc_start: 0.6132 (tt0) cc_final: 0.5652 (tp30) REVERT: C 210 SER cc_start: 0.8563 (m) cc_final: 0.8129 (p) REVERT: D 256 PHE cc_start: 0.6012 (m-10) cc_final: 0.5507 (t80) REVERT: D 265 ARG cc_start: 0.6965 (mtm180) cc_final: 0.6526 (mpt180) REVERT: E 388 GLU cc_start: 0.6054 (tt0) cc_final: 0.5576 (tp30) REVERT: F 210 SER cc_start: 0.8557 (m) cc_final: 0.8169 (p) outliers start: 36 outliers final: 33 residues processed: 190 average time/residue: 0.2862 time to fit residues: 83.1118 Evaluate side-chains 194 residues out of total 2130 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 241 ARG Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 319 HIS Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 451 ASP Chi-restraints excluded: chain A residue 460 GLU Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 347 ARG Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 385 SER Chi-restraints excluded: chain C residue 498 ASP Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 241 ARG Chi-restraints excluded: chain D residue 260 SER Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 412 MET Chi-restraints excluded: chain D residue 451 ASP Chi-restraints excluded: chain D residue 460 GLU Chi-restraints excluded: chain E residue 227 ILE Chi-restraints excluded: chain E residue 345 CYS Chi-restraints excluded: chain E residue 347 ARG Chi-restraints excluded: chain E residue 377 SER Chi-restraints excluded: chain E residue 381 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 385 SER Chi-restraints excluded: chain F residue 498 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 12 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 174 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN ** B 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN ** E 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 225 ASN ** F 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 317 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.123773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.105394 restraints weight = 111364.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.106800 restraints weight = 87436.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108125 restraints weight = 67167.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108266 restraints weight = 46005.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108372 restraints weight = 44366.717| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18846 Z= 0.215 Angle : 0.587 23.784 25568 Z= 0.305 Chirality : 0.045 0.151 3036 Planarity : 0.005 0.063 3390 Dihedral : 5.852 56.158 2828 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 2.06 % Allowed : 14.17 % Favored : 83.77 % 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 aren not related in a simple way. whole: -0.90 (0.17), residues: 2526 helix: 1.48 (0.16), residues: 1010 sheet: -2.58 (0.23), residues: 422 loop : -1.78 (0.19), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 352 TYR 0.011 0.001 TYR C 148 PHE 0.009 0.001 PHE A 297 TRP 0.006 0.001 TRP B 481 HIS 0.005 0.001 HIS B 319 Details of bonding type rmsd covalent geometry : bond 0.00489 (18846) covalent geometry : angle 0.58683 (25568) hydrogen bonds : bond 0.03774 ( 887) hydrogen bonds : angle 4.78487 ( 2577) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4025.34 seconds wall clock time: 69 minutes 31.83 seconds (4171.83 seconds total)