Starting phenix.real_space_refine on Tue Aug 26 12:36:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rjf_19209/08_2025/8rjf_19209.map" } resolution = 3.1 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 106 5.16 5 C 11624 2.51 5 N 3476 2.21 5 O 3604 1.98 5 H 17962 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 36790 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6089 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6091 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6101 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 6089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6089 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 6091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6091 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 6101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 6101 Classifications: {'peptide': 424} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 406} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {' MG': 1, 'ADP': 1, 'EPE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.03, per 1000 atoms: 0.16 Number of scatterers: 36790 At special positions: 0 Unit cell: (149.22, 135.127, 97.822, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 106 16.00 P 12 15.00 Mg 6 11.99 O 3604 8.00 N 3476 7.00 C 11624 6.00 H 17962 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: 2.77 Conformation dependent library (CDL) restraints added in 970.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 18 sheets defined 45.0% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 80 through 97 removed outlier: 3.871A pdb=" N ALA A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 102 removed outlier: 3.649A pdb=" N LEU A 102 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 125 removed outlier: 3.946A pdb=" N ALA A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 188 through 201 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 286 through 295 removed outlier: 3.672A pdb=" N LEU A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 346 removed outlier: 3.531A pdb=" N LEU A 346 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 4.079A 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 Processing helix chain 'A' and resid 480 through 487 removed outlier: 3.620A pdb=" N TYR A 487 " --> pdb=" O ARG A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 502 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 Processing helix chain 'B' and resid 130 through 147 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 157 removed outlier: 3.601A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 202 removed outlier: 3.857A 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 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 337 through 346 Processing helix chain 'B' and resid 361 through 371 removed outlier: 4.083A pdb=" N ASP B 365 " --> pdb=" O PRO B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 401 removed outlier: 3.846A pdb=" N GLY B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.843A 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: 3.666A 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 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.596A pdb=" N ARG C 157 " --> pdb=" O PRO C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.655A pdb=" N ALA C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 346 Processing helix chain 'C' and resid 361 through 372 removed outlier: 4.089A pdb=" N ASP C 365 " --> pdb=" O PRO C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 401 removed outlier: 3.799A pdb=" N GLY C 401 " --> pdb=" O ILE C 397 " (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 Processing helix chain 'D' and resid 81 through 97 Processing helix chain 'D' and resid 98 through 102 removed outlier: 3.687A pdb=" N LEU D 102 " --> pdb=" O LEU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.937A pdb=" N ALA D 123 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 188 through 201 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 286 through 295 removed outlier: 3.672A pdb=" N LEU D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 346 removed outlier: 3.531A pdb=" N LEU D 346 " --> pdb=" O VAL D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 372 removed outlier: 4.078A 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 Processing helix chain 'D' and resid 480 through 487 removed outlier: 3.620A pdb=" N TYR D 487 " --> pdb=" O ARG D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 502 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 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 157 removed outlier: 3.570A pdb=" N ARG E 157 " --> pdb=" O PRO E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.848A 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 Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 337 through 346 Processing helix chain 'E' and resid 361 through 371 removed outlier: 4.084A pdb=" N ASP E 365 " --> pdb=" O PRO E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 401 removed outlier: 3.846A pdb=" N GLY E 401 " --> pdb=" O ILE E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 417 Processing helix chain 'E' and resid 480 through 487 removed outlier: 3.843A 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: 3.663A 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 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'F' and resid 151 through 157 removed outlier: 3.598A pdb=" N ARG F 157 " --> pdb=" O PRO F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 260 through 273 Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.655A pdb=" N ALA F 296 " --> pdb=" O ASN F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 346 Processing helix chain 'F' and resid 361 through 372 removed outlier: 4.089A pdb=" N ASP F 365 " --> pdb=" O PRO F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 401 removed outlier: 3.799A pdb=" N GLY F 401 " --> pdb=" O ILE F 397 " (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 Processing sheet with id=AA1, first strand: chain 'A' and resid 178 through 181 removed outlier: 3.771A pdb=" N ASP A 162 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 277 through 280 removed outlier: 6.496A pdb=" N VAL A 278 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA A 423 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER A 280 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG A 425 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE A 420 " --> pdb=" O ILE A 436 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE A 436 " --> pdb=" O ILE A 420 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 16.318A pdb=" N ARG A 431 " --> pdb=" O THR A 458 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N THR A 458 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N ILE A 433 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU A 456 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS A 435 " --> pdb=" O VAL A 454 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL A 454 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR A 437 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU A 452 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL A 439 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN A 450 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY A 441 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 467 " --> pdb=" O THR A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 322 removed outlier: 6.708A pdb=" N VAL A 305 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY A 356 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS A 307 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL A 358 " --> pdb=" O CYS A 307 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET A 378 " --> pdb=" O ILE A 354 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY A 356 " --> pdb=" O MET A 378 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A 380 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 178 through 182 removed outlier: 3.527A pdb=" N LYS B 178 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B 175 " --> pdb=" O LYS B 178 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL B 171 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE B 172 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE B 163 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU B 174 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 378 through 380 removed outlier: 6.785A pdb=" N HIS B 435 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL B 454 " --> pdb=" O HIS B 435 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR B 437 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU B 452 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL B 439 " --> pdb=" O GLN B 450 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN B 450 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY B 441 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 446 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR B 455 " --> pdb=" O ARG B 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG B 471 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE B 457 " --> pdb=" O LYS B 469 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS B 469 " --> pdb=" O ILE B 457 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 320 through 322 removed outlier: 6.516A pdb=" N VAL B 304 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL B 305 " --> pdb=" O ILE B 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 178 through 181 removed outlier: 3.880A pdb=" N ASP C 162 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA C 161 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 320 through 324 removed outlier: 6.501A pdb=" N VAL C 304 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU C 323 " --> pdb=" O VAL C 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR C 306 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 305 " --> pdb=" O ILE C 354 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR C 380 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 379 " --> pdb=" O LEU C 277 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS C 435 " --> pdb=" O GLN C 422 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA C 424 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE C 433 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 14.046A pdb=" N ARG C 432 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE C 457 " --> pdb=" O ARG C 432 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR C 434 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 453 " --> pdb=" O ILE C 436 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 467 " --> pdb=" O THR C 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 439 through 443 Processing sheet with id=AB1, first strand: chain 'D' and resid 178 through 181 removed outlier: 3.771A pdb=" N ASP D 162 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 277 through 280 removed outlier: 6.496A pdb=" N VAL D 278 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ALA D 423 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER D 280 " --> pdb=" O ALA D 423 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N ARG D 425 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE D 420 " --> pdb=" O ILE D 436 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE D 436 " --> pdb=" O ILE D 420 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN D 422 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 16.318A pdb=" N ARG D 431 " --> pdb=" O THR D 458 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N THR D 458 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N ILE D 433 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N GLU D 456 " --> pdb=" O ILE D 433 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N HIS D 435 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL D 454 " --> pdb=" O HIS D 435 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR D 437 " --> pdb=" O LEU D 452 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N LEU D 452 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N VAL D 439 " --> pdb=" O GLN D 450 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN D 450 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY D 441 " --> pdb=" O VAL D 448 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL D 467 " --> pdb=" O THR D 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 320 through 322 removed outlier: 6.708A pdb=" N VAL D 305 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N GLY D 356 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS D 307 " --> pdb=" O GLY D 356 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N VAL D 358 " --> pdb=" O CYS D 307 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N MET D 378 " --> pdb=" O ILE D 354 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLY D 356 " --> pdb=" O MET D 378 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR D 380 " --> pdb=" O GLY D 356 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 178 through 182 removed outlier: 3.527A pdb=" N LYS E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL E 175 " --> pdb=" O LYS E 178 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 171 " --> pdb=" O THR E 182 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N PHE E 172 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE E 163 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLU E 174 " --> pdb=" O ALA E 161 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 378 through 380 removed outlier: 6.785A pdb=" N HIS E 435 " --> pdb=" O VAL E 454 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL E 454 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR E 437 " --> pdb=" O LEU E 452 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU E 452 " --> pdb=" O THR E 437 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL E 439 " --> pdb=" O GLN E 450 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN E 450 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY E 441 " --> pdb=" O VAL E 448 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL E 446 " --> pdb=" O GLU E 443 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N TYR E 455 " --> pdb=" O ARG E 471 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ARG E 471 " --> pdb=" O TYR E 455 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ILE E 457 " --> pdb=" O LYS E 469 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS E 469 " --> pdb=" O ILE E 457 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 320 through 322 removed outlier: 6.516A pdb=" N VAL E 304 " --> pdb=" O VAL E 321 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL E 305 " --> pdb=" O ILE E 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'F' and resid 178 through 181 removed outlier: 3.879A pdb=" N ASP F 162 " --> pdb=" O GLU F 174 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA F 161 " --> pdb=" O LYS F 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 320 through 324 removed outlier: 6.501A pdb=" N VAL F 304 " --> pdb=" O VAL F 321 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU F 323 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR F 306 " --> pdb=" O LEU F 323 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL F 305 " --> pdb=" O ILE F 354 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N THR F 380 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 379 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS F 435 " --> pdb=" O GLN F 422 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA F 424 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE F 433 " --> pdb=" O ALA F 424 " (cutoff:3.500A) removed outlier: 14.045A pdb=" N ARG F 432 " --> pdb=" O ILE F 457 " (cutoff:3.500A) removed outlier: 12.044A pdb=" N ILE F 457 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR F 434 " --> pdb=" O TYR F 455 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE F 453 " --> pdb=" O ILE F 436 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL F 467 " --> pdb=" O THR F 458 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 439 through 443 945 hydrogen bonds defined for protein. 2733 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: 8.32 Time building geometry restraints manager: 3.66 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: 17926 1.03 - 1.22: 38 1.22 - 1.42: 7472 1.42 - 1.61: 11422 1.61 - 1.80: 172 Bond restraints: 37030 Sorted by residual: 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 2.52e+01 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 2.49e+01 bond pdb=" N ASP D 80 " pdb=" H1 ASP D 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 E 80 " pdb=" H1 ASP E 80 " ideal model delta sigma weight residual 0.960 0.861 0.099 2.00e-02 2.50e+03 2.47e+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 2.46e+01 ... (remaining 37025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.40: 66818 10.40 - 20.80: 2 20.80 - 31.21: 0 31.21 - 41.61: 0 41.61 - 52.01: 4 Bond angle restraints: 66824 Sorted by residual: angle pdb=" C ASN E 183 " pdb=" N VAL E 184 " pdb=" H VAL E 184 " ideal model delta sigma weight residual 123.66 71.65 52.01 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C ASN B 183 " pdb=" N VAL B 184 " pdb=" H VAL B 184 " ideal model delta sigma weight residual 123.66 71.65 52.01 3.00e+00 1.11e-01 3.01e+02 angle pdb=" CA VAL B 184 " pdb=" N VAL B 184 " pdb=" H VAL B 184 " ideal model delta sigma weight residual 113.36 62.48 50.88 3.00e+00 1.11e-01 2.88e+02 angle pdb=" CA VAL E 184 " pdb=" N VAL E 184 " pdb=" H VAL E 184 " ideal model delta sigma weight residual 113.36 62.48 50.88 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C ASN B 183 " pdb=" N VAL B 184 " pdb=" CA VAL B 184 " ideal model delta sigma weight residual 122.99 134.12 -11.13 1.39e+00 5.18e-01 6.42e+01 ... (remaining 66819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 16938 35.21 - 70.42: 422 70.42 - 105.62: 28 105.62 - 140.83: 2 140.83 - 176.04: 2 Dihedral angle restraints: 17392 sinusoidal: 9620 harmonic: 7772 Sorted by residual: dihedral pdb=" C5' ADP F 702 " pdb=" O5' ADP F 702 " pdb=" PA ADP F 702 " pdb=" O2A ADP F 702 " ideal model delta sinusoidal sigma weight residual 300.00 123.96 176.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 702 " pdb=" O5' ADP C 702 " pdb=" PA ADP C 702 " pdb=" O2A ADP C 702 " ideal model delta sinusoidal sigma weight residual 300.00 123.96 176.04 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual -60.00 -170.21 110.21 1 2.00e+01 2.50e-03 3.23e+01 ... (remaining 17389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1831 0.030 - 0.061: 762 0.061 - 0.091: 202 0.091 - 0.122: 237 0.122 - 0.152: 40 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CA ILE E 436 " pdb=" N ILE E 436 " pdb=" C ILE E 436 " pdb=" CB ILE E 436 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE B 436 " pdb=" N ILE B 436 " pdb=" C ILE B 436 " pdb=" CB ILE B 436 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CA ILE A 436 " pdb=" N ILE A 436 " pdb=" C ILE A 436 " pdb=" CB ILE A 436 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 3069 not shown) Planarity restraints: 5828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 229 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.64e+00 pdb=" N PRO C 230 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 229 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO F 230 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO F 230 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 230 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 149 " 0.021 5.00e-02 4.00e+02 3.16e-02 1.60e+00 pdb=" N PRO D 150 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 150 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 150 " 0.018 5.00e-02 4.00e+02 ... (remaining 5825 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 450 2.05 - 2.69: 58411 2.69 - 3.33: 105329 3.33 - 3.96: 133322 3.96 - 4.60: 213322 Nonbonded interactions: 510834 Sorted by model distance: nonbonded pdb=" H VAL E 184 " pdb=" HA VAL E 184 " model vdw 1.417 1.816 nonbonded pdb=" H VAL B 184 " pdb=" HA VAL B 184 " model vdw 1.418 1.816 nonbonded pdb=" OE1 GLU F 262 " pdb=" H GLU F 262 " model vdw 1.566 2.450 nonbonded pdb=" OE1 GLU C 262 " pdb=" H GLU C 262 " model vdw 1.566 2.450 nonbonded pdb=" HZ2 LYS E 287 " pdb=" O2B ADP E 702 " model vdw 1.601 2.450 ... (remaining 510829 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 80 through 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 242 through 469 or (resid 470 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 471 through 503)) selection = (chain 'B' and (resid 80 through 143 or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2)) or resid 145 throu \ gh 147 or (resid 148 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) o \ r resid 149 through 469 or (resid 470 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or res \ id 471 through 503)) selection = (chain 'C' and (resid 80 through 143 or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2)) or resid 145 throu \ gh 147 or (resid 148 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) o \ r resid 149 through 240 or (resid 241 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA )) or resid 242 through 503)) selection = (chain 'D' and (resid 80 through 240 or (resid 241 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 242 through 469 or (resid 470 and \ (name N or name CA or name C or name O or name CB or name CG or name ND1 or name \ CD2 or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or nam \ e HD1 or name HD2 or name HE1)) or resid 471 through 503)) selection = (chain 'E' and (resid 80 through 143 or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2)) or resid 145 throu \ gh 147 or (resid 148 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) o \ r resid 149 through 469 or (resid 470 and (name N or name CA or name C or name O \ or name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2 or name H \ or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name HE1)) or res \ id 471 through 503)) selection = (chain 'F' and (resid 80 through 143 or (resid 144 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name OD2)) or resid 145 throu \ gh 147 or (resid 148 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) o \ r resid 149 through 240 or (resid 241 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ or name H or name HA )) or resid 242 through 503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.430 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.060 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 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 : 0.004 0.036 19068 Z= 0.190 Angle : 0.567 11.134 25904 Z= 0.285 Chirality : 0.045 0.152 3072 Planarity : 0.003 0.032 3402 Dihedral : 10.827 176.041 7008 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.41 % Allowed : 3.35 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.14 (0.17), residues: 2532 helix: 1.45 (0.16), residues: 1060 sheet: -1.85 (0.21), residues: 512 loop : -0.71 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 322 TYR 0.009 0.001 TYR B 148 PHE 0.009 0.001 PHE D 480 TRP 0.004 0.001 TRP A 481 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00427 (19068) covalent geometry : angle 0.56726 (25904) hydrogen bonds : bond 0.14608 ( 945) hydrogen bonds : angle 5.91114 ( 2733) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 235 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 209 time to evaluate : 1.007 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: B 183 ASN cc_start: 0.7212 (p0) cc_final: 0.6978 (p0) REVERT: B 190 LEU cc_start: 0.8582 (tp) cc_final: 0.8351 (tt) REVERT: B 427 ARG cc_start: 0.7963 (ttp-110) cc_final: 0.7422 (ttp80) REVERT: B 442 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.6621 (tp) REVERT: E 183 ASN cc_start: 0.7211 (p0) cc_final: 0.6978 (p0) REVERT: E 190 LEU cc_start: 0.8586 (tp) cc_final: 0.8366 (tt) REVERT: E 427 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7424 (ttp80) REVERT: E 442 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.6620 (tp) outliers start: 26 outliers final: 12 residues processed: 235 average time/residue: 0.5138 time to fit residues: 156.1042 Evaluate side-chains 126 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 442 LEU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain E residue 166 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN C 319 HIS D 139 GLN E 319 HIS F 314 GLN F 319 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.114083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.083170 restraints weight = 92631.562| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.99 r_work: 0.3114 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19068 Z= 0.164 Angle : 0.582 11.208 25904 Z= 0.293 Chirality : 0.046 0.155 3072 Planarity : 0.004 0.038 3402 Dihedral : 8.970 166.670 2908 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.08 % Allowed : 5.09 % Favored : 93.83 % 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: -0.00 (0.17), residues: 2532 helix: 1.51 (0.16), residues: 1070 sheet: -1.84 (0.21), residues: 512 loop : -0.55 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.008 0.001 TYR B 148 PHE 0.010 0.001 PHE A 172 TRP 0.003 0.001 TRP D 481 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00370 (19068) covalent geometry : angle 0.58217 (25904) hydrogen bonds : bond 0.03925 ( 945) hydrogen bonds : angle 4.82469 ( 2733) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 134 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8189 (p0) cc_final: 0.7921 (p0) REVERT: B 190 LEU cc_start: 0.8327 (tp) cc_final: 0.8101 (tt) REVERT: B 427 ARG cc_start: 0.8198 (ttp-110) cc_final: 0.7112 (ttp80) REVERT: E 183 ASN cc_start: 0.8216 (p0) cc_final: 0.7946 (p0) REVERT: E 190 LEU cc_start: 0.8334 (tp) cc_final: 0.8105 (tt) REVERT: E 427 ARG cc_start: 0.8209 (ttp-110) cc_final: 0.7132 (ttp80) outliers start: 20 outliers final: 12 residues processed: 132 average time/residue: 0.4134 time to fit residues: 74.8366 Evaluate side-chains 119 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain C residue 438 GLU Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 438 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 154 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 141 optimal weight: 0.4980 chunk 209 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.085966 restraints weight = 91348.144| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 3.66 r_work: 0.3142 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19068 Z= 0.158 Angle : 0.553 11.216 25904 Z= 0.275 Chirality : 0.045 0.150 3072 Planarity : 0.004 0.036 3402 Dihedral : 8.681 148.081 2900 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.76 % Allowed : 5.84 % Favored : 93.40 % 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: 0.11 (0.17), residues: 2532 helix: 1.71 (0.16), residues: 1074 sheet: -1.86 (0.21), residues: 512 loop : -0.59 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 206 TYR 0.010 0.001 TYR C 487 PHE 0.008 0.001 PHE D 172 TRP 0.003 0.001 TRP A 481 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00360 (19068) covalent geometry : angle 0.55338 (25904) hydrogen bonds : bond 0.03617 ( 945) hydrogen bonds : angle 4.41995 ( 2733) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 119 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8006 (p0) cc_final: 0.7731 (p0) REVERT: B 187 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7406 (ttp80) REVERT: B 190 LEU cc_start: 0.8359 (tp) cc_final: 0.8126 (tt) REVERT: B 427 ARG cc_start: 0.8155 (ttp-110) cc_final: 0.7094 (ttp80) REVERT: C 339 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7606 (ttt180) REVERT: E 183 ASN cc_start: 0.8035 (p0) cc_final: 0.7759 (p0) REVERT: E 187 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7405 (ttp80) REVERT: E 190 LEU cc_start: 0.8352 (tp) cc_final: 0.8118 (tt) REVERT: E 427 ARG cc_start: 0.8159 (ttp-110) cc_final: 0.7105 (ttp80) REVERT: F 339 ARG cc_start: 0.8171 (ttt-90) cc_final: 0.7618 (ttt180) outliers start: 14 outliers final: 10 residues processed: 117 average time/residue: 0.4135 time to fit residues: 66.4569 Evaluate side-chains 112 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 437 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 18 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 178 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** D 319 HIS ** 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 = 0.3769 r_free = 0.3769 target = 0.115357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.084454 restraints weight = 91099.604| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.95 r_work: 0.3157 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19068 Z= 0.161 Angle : 0.547 11.252 25904 Z= 0.272 Chirality : 0.045 0.149 3072 Planarity : 0.004 0.050 3402 Dihedral : 7.980 117.038 2894 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.76 % Allowed : 6.01 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.32 (0.17), residues: 2532 helix: 1.96 (0.16), residues: 1070 sheet: -1.82 (0.21), residues: 516 loop : -0.52 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 206 TYR 0.010 0.001 TYR F 487 PHE 0.009 0.001 PHE D 172 TRP 0.004 0.001 TRP D 481 HIS 0.003 0.001 HIS C 136 Details of bonding type rmsd covalent geometry : bond 0.00370 (19068) covalent geometry : angle 0.54731 (25904) hydrogen bonds : bond 0.03195 ( 945) hydrogen bonds : angle 4.24405 ( 2733) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 124 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8128 (p0) cc_final: 0.7842 (p0) REVERT: B 427 ARG cc_start: 0.8175 (ttp-110) cc_final: 0.7092 (ttp80) REVERT: C 339 ARG cc_start: 0.8356 (ttt-90) cc_final: 0.7826 (ttt180) REVERT: E 183 ASN cc_start: 0.8169 (p0) cc_final: 0.7882 (p0) REVERT: E 427 ARG cc_start: 0.8179 (ttp-110) cc_final: 0.7101 (ttp80) REVERT: F 339 ARG cc_start: 0.8366 (ttt-90) cc_final: 0.7840 (ttt180) outliers start: 14 outliers final: 8 residues processed: 122 average time/residue: 0.4433 time to fit residues: 75.3096 Evaluate side-chains 113 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 105 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 437 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 160 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 84 optimal weight: 40.0000 chunk 139 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 198 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.116815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086116 restraints weight = 90412.336| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.92 r_work: 0.3188 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 19068 Z= 0.094 Angle : 0.512 11.290 25904 Z= 0.252 Chirality : 0.044 0.149 3072 Planarity : 0.004 0.044 3402 Dihedral : 7.361 96.712 2892 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.54 % Allowed : 6.22 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.18), residues: 2532 helix: 2.17 (0.16), residues: 1078 sheet: -1.64 (0.23), residues: 468 loop : -0.49 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 206 TYR 0.009 0.001 TYR C 487 PHE 0.007 0.001 PHE A 172 TRP 0.003 0.001 TRP A 481 HIS 0.002 0.000 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00208 (19068) covalent geometry : angle 0.51205 (25904) hydrogen bonds : bond 0.02956 ( 945) hydrogen bonds : angle 4.00259 ( 2733) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 108 time to evaluate : 1.041 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: B 183 ASN cc_start: 0.8162 (p0) cc_final: 0.7857 (p0) REVERT: B 427 ARG cc_start: 0.8070 (ttp-110) cc_final: 0.6924 (ttp80) REVERT: C 339 ARG cc_start: 0.8270 (ttt-90) cc_final: 0.7711 (ttt180) REVERT: E 183 ASN cc_start: 0.8200 (p0) cc_final: 0.7893 (p0) REVERT: E 427 ARG cc_start: 0.8081 (ttp-110) cc_final: 0.6935 (ttp80) REVERT: F 339 ARG cc_start: 0.8284 (ttt-90) cc_final: 0.7727 (ttt180) outliers start: 10 outliers final: 10 residues processed: 118 average time/residue: 0.4839 time to fit residues: 77.7402 Evaluate side-chains 117 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain C residue 437 THR Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Chi-restraints excluded: chain F residue 437 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 203 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** 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 = 0.3759 r_free = 0.3759 target = 0.114686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.083904 restraints weight = 91569.993| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.95 r_work: 0.3147 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19068 Z= 0.209 Angle : 0.561 11.192 25904 Z= 0.279 Chirality : 0.046 0.148 3072 Planarity : 0.004 0.043 3402 Dihedral : 7.534 97.940 2892 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.54 % Allowed : 6.49 % Favored : 92.97 % 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: 0.44 (0.17), residues: 2532 helix: 2.11 (0.16), residues: 1072 sheet: -1.78 (0.22), residues: 484 loop : -0.59 (0.21), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.007 0.001 TYR C 487 PHE 0.009 0.001 PHE A 172 TRP 0.003 0.001 TRP A 481 HIS 0.003 0.001 HIS F 382 Details of bonding type rmsd covalent geometry : bond 0.00485 (19068) covalent geometry : angle 0.56082 (25904) hydrogen bonds : bond 0.03224 ( 945) hydrogen bonds : angle 4.14262 ( 2733) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 115 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8157 (p0) cc_final: 0.7844 (p0) REVERT: B 427 ARG cc_start: 0.8149 (ttp-110) cc_final: 0.7035 (ttp80) REVERT: C 339 ARG cc_start: 0.8343 (ttt-90) cc_final: 0.7797 (ttt180) REVERT: E 183 ASN cc_start: 0.8193 (p0) cc_final: 0.7879 (p0) REVERT: E 427 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7046 (ttp80) REVERT: F 339 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7813 (ttt180) outliers start: 10 outliers final: 10 residues processed: 115 average time/residue: 0.4380 time to fit residues: 69.2719 Evaluate side-chains 115 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 207 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 238 optimal weight: 0.9980 chunk 45 optimal weight: 20.0000 chunk 170 optimal weight: 40.0000 chunk 37 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 GLN D 143 ASN ** D 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.114844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084127 restraints weight = 91346.459| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 2.94 r_work: 0.3152 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19068 Z= 0.172 Angle : 0.545 11.243 25904 Z= 0.270 Chirality : 0.045 0.148 3072 Planarity : 0.004 0.037 3402 Dihedral : 7.494 96.927 2890 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.65 % Allowed : 6.76 % Favored : 92.59 % 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: 0.46 (0.17), residues: 2532 helix: 2.13 (0.16), residues: 1068 sheet: -1.79 (0.22), residues: 480 loop : -0.54 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.008 0.001 TYR F 487 PHE 0.008 0.001 PHE A 172 TRP 0.003 0.001 TRP A 481 HIS 0.003 0.001 HIS C 382 Details of bonding type rmsd covalent geometry : bond 0.00398 (19068) covalent geometry : angle 0.54460 (25904) hydrogen bonds : bond 0.03092 ( 945) hydrogen bonds : angle 4.07637 ( 2733) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 120 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8149 (p0) cc_final: 0.7818 (p0) REVERT: B 427 ARG cc_start: 0.8142 (ttp-110) cc_final: 0.7024 (ttp80) REVERT: B 462 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: C 339 ARG cc_start: 0.8338 (ttt-90) cc_final: 0.7781 (ttt180) REVERT: E 183 ASN cc_start: 0.8176 (p0) cc_final: 0.7847 (p0) REVERT: E 427 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7039 (ttp80) REVERT: E 462 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: F 339 ARG cc_start: 0.8346 (ttt-90) cc_final: 0.7791 (ttt180) outliers start: 12 outliers final: 10 residues processed: 120 average time/residue: 0.4865 time to fit residues: 80.1264 Evaluate side-chains 116 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 236 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 171 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 37 optimal weight: 0.7980 chunk 202 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 319 HIS ** 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 = 0.3770 r_free = 0.3770 target = 0.115372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084203 restraints weight = 90754.963| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.01 r_work: 0.3152 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19068 Z= 0.157 Angle : 0.539 11.215 25904 Z= 0.266 Chirality : 0.045 0.147 3072 Planarity : 0.004 0.037 3402 Dihedral : 7.460 97.054 2890 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.65 % Allowed : 6.76 % Favored : 92.59 % 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: 0.61 (0.17), residues: 2532 helix: 2.26 (0.16), residues: 1068 sheet: -1.70 (0.22), residues: 472 loop : -0.51 (0.20), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 206 TYR 0.008 0.001 TYR F 487 PHE 0.007 0.001 PHE A 172 TRP 0.004 0.001 TRP D 481 HIS 0.002 0.001 HIS C 382 Details of bonding type rmsd covalent geometry : bond 0.00363 (19068) covalent geometry : angle 0.53874 (25904) hydrogen bonds : bond 0.02970 ( 945) hydrogen bonds : angle 4.01324 ( 2733) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8108 (p0) cc_final: 0.7782 (p0) REVERT: B 427 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7001 (ttp80) REVERT: B 462 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: C 339 ARG cc_start: 0.8426 (ttt-90) cc_final: 0.7891 (ttt180) REVERT: E 183 ASN cc_start: 0.8141 (p0) cc_final: 0.7816 (p0) REVERT: E 427 ARG cc_start: 0.8125 (ttp-110) cc_final: 0.7024 (ttp80) REVERT: E 462 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7712 (pm20) REVERT: F 339 ARG cc_start: 0.8434 (ttt-90) cc_final: 0.7901 (ttt180) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.4919 time to fit residues: 79.7677 Evaluate side-chains 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 201 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 243 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 chunk 249 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 319 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.116524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.087085 restraints weight = 92613.546| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.30 r_work: 0.3125 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19068 Z= 0.193 Angle : 0.559 11.170 25904 Z= 0.277 Chirality : 0.046 0.148 3072 Planarity : 0.004 0.037 3402 Dihedral : 7.530 96.772 2890 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.65 % Allowed : 6.93 % Favored : 92.42 % 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: 0.45 (0.17), residues: 2532 helix: 2.16 (0.16), residues: 1068 sheet: -1.87 (0.21), residues: 516 loop : -0.49 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.008 0.001 TYR C 487 PHE 0.008 0.001 PHE A 480 TRP 0.004 0.001 TRP D 481 HIS 0.003 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00447 (19068) covalent geometry : angle 0.55888 (25904) hydrogen bonds : bond 0.03152 ( 945) hydrogen bonds : angle 4.08483 ( 2733) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 119 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.8022 (p0) cc_final: 0.7700 (p0) REVERT: B 427 ARG cc_start: 0.8083 (ttp-110) cc_final: 0.7004 (ttp80) REVERT: B 462 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: C 339 ARG cc_start: 0.8174 (ttt-90) cc_final: 0.7595 (ttt180) REVERT: E 183 ASN cc_start: 0.8040 (p0) cc_final: 0.7718 (p0) REVERT: E 427 ARG cc_start: 0.8088 (ttp-110) cc_final: 0.7013 (ttp80) REVERT: E 462 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7696 (pm20) REVERT: F 339 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7601 (ttt180) outliers start: 12 outliers final: 10 residues processed: 119 average time/residue: 0.4996 time to fit residues: 81.8276 Evaluate side-chains 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 73 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.115401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.084230 restraints weight = 91293.889| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.04 r_work: 0.3149 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 19068 Z= 0.147 Angle : 0.535 11.224 25904 Z= 0.264 Chirality : 0.045 0.148 3072 Planarity : 0.004 0.037 3402 Dihedral : 7.442 96.576 2890 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.65 % Allowed : 7.14 % Favored : 92.21 % 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: 0.62 (0.18), residues: 2532 helix: 2.29 (0.16), residues: 1068 sheet: -1.75 (0.21), residues: 504 loop : -0.44 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.009 0.001 TYR F 487 PHE 0.007 0.001 PHE A 480 TRP 0.004 0.001 TRP A 481 HIS 0.002 0.001 HIS B 470 Details of bonding type rmsd covalent geometry : bond 0.00337 (19068) covalent geometry : angle 0.53495 (25904) hydrogen bonds : bond 0.02933 ( 945) hydrogen bonds : angle 3.99464 ( 2733) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5064 Ramachandran restraints generated. 2532 Oldfield, 0 Emsley, 2532 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 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 ASN cc_start: 0.7900 (p0) cc_final: 0.7574 (p0) REVERT: B 427 ARG cc_start: 0.8058 (ttp-110) cc_final: 0.7034 (ttp80) REVERT: B 462 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7663 (pm20) REVERT: C 339 ARG cc_start: 0.8298 (ttt-90) cc_final: 0.7718 (ttt180) REVERT: E 183 ASN cc_start: 0.7920 (p0) cc_final: 0.7594 (p0) REVERT: E 427 ARG cc_start: 0.8066 (ttp-110) cc_final: 0.7046 (ttp80) REVERT: E 462 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: F 339 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.7723 (ttt180) outliers start: 12 outliers final: 10 residues processed: 118 average time/residue: 0.4996 time to fit residues: 81.2188 Evaluate side-chains 118 residues out of total 2136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 462 GLU Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain C residue 223 ARG Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 471 ARG Chi-restraints excluded: chain F residue 223 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 86 optimal weight: 40.0000 chunk 176 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 225 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 128 optimal weight: 30.0000 chunk 130 optimal weight: 0.2980 chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 40.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.116130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.085222 restraints weight = 90523.300| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.99 r_work: 0.3167 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19068 Z= 0.113 Angle : 0.515 11.243 25904 Z= 0.253 Chirality : 0.044 0.149 3072 Planarity : 0.004 0.037 3402 Dihedral : 7.189 94.767 2890 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.49 % Allowed : 7.36 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2532 helix: 2.50 (0.16), residues: 1068 sheet: -1.62 (0.23), residues: 468 loop : -0.46 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 206 TYR 0.009 0.001 TYR C 487 PHE 0.007 0.001 PHE A 172 TRP 0.004 0.001 TRP A 481 HIS 0.003 0.000 HIS D 319 Details of bonding type rmsd covalent geometry : bond 0.00255 (19068) covalent geometry : angle 0.51542 (25904) hydrogen bonds : bond 0.02754 ( 945) hydrogen bonds : angle 3.86082 ( 2733) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8890.58 seconds wall clock time: 151 minutes 23.24 seconds (9083.24 seconds total)