Starting phenix.real_space_refine on Sun Dec 29 00:17:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl3_38436/12_2024/8xl3_38436.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.108 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 312 5.16 5 C 34134 2.51 5 N 9510 2.21 5 O 10248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 54204 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "B" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "C" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "D" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "E" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "F" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "G" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "H" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "I" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "J" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "K" Number of atoms: 5146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5146 Classifications: {'peptide': 668} Link IDs: {'PTRANS': 23, 'TRANS': 644} Chain: "L" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 3873 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 25, 'TRANS': 481} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 23.73, per 1000 atoms: 0.44 Number of scatterers: 54204 At special positions: 0 Unit cell: (233.774, 221.924, 239.161, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 312 16.00 O 10248 8.00 N 9510 7.00 C 34134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.47 Conformation dependent library (CDL) restraints added in 5.9 seconds 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12984 Finding SS restraints... Secondary structure from input PDB file: 282 helices and 72 sheets defined 39.1% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 72 through 86 Processing helix chain 'A' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER A 99 " --> pdb=" O VAL A 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 96 through 99' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 149 through 158 Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 309 through 325 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 368 through 379 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 458 through 472 Processing helix chain 'A' and resid 481 through 489 Processing helix chain 'A' and resid 491 through 497 Processing helix chain 'A' and resid 502 through 508 Processing helix chain 'A' and resid 518 through 540 Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.857A pdb=" N LYS A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 128 through 132 Processing helix chain 'B' and resid 134 through 152 Processing helix chain 'B' and resid 170 through 186 Processing helix chain 'B' and resid 201 through 205 removed outlier: 3.754A pdb=" N ALA B 204 " --> pdb=" O ALA B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 Processing helix chain 'B' and resid 227 through 235 Processing helix chain 'B' and resid 240 through 246 Processing helix chain 'B' and resid 246 through 253 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 299 through 303 Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 325 through 328 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 367 through 384 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 407 through 422 removed outlier: 3.913A pdb=" N LYS B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 415 " --> pdb=" O HIS B 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 442 Processing helix chain 'B' and resid 444 through 448 removed outlier: 3.636A pdb=" N CYS B 448 " --> pdb=" O LYS B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 473 Processing helix chain 'B' and resid 478 through 491 Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'B' and resid 510 through 523 removed outlier: 3.520A pdb=" N ALA B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 86 Processing helix chain 'C' and resid 96 through 99 removed outlier: 4.321A pdb=" N SER C 99 " --> pdb=" O VAL C 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 96 through 99' Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 149 through 158 Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE C 171 " --> pdb=" O ASP C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER C 180 " --> pdb=" O ASP C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 213 removed outlier: 3.896A pdb=" N ALA C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 249 Processing helix chain 'C' and resid 250 through 252 No H-bonds generated for 'chain 'C' and resid 250 through 252' Processing helix chain 'C' and resid 309 through 325 Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 368 through 379 Processing helix chain 'C' and resid 385 through 389 Processing helix chain 'C' and resid 458 through 472 Processing helix chain 'C' and resid 481 through 489 Processing helix chain 'C' and resid 491 through 497 Processing helix chain 'C' and resid 502 through 508 Processing helix chain 'C' and resid 518 through 540 Processing helix chain 'C' and resid 641 through 648 removed outlier: 3.857A pdb=" N LYS C 648 " --> pdb=" O ALA C 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 49 Processing helix chain 'D' and resid 51 through 61 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 134 through 152 Processing helix chain 'D' and resid 170 through 186 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.754A pdb=" N ALA D 204 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 211 Processing helix chain 'D' and resid 227 through 235 Processing helix chain 'D' and resid 240 through 246 Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 263 through 276 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'D' and resid 325 through 328 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 367 through 384 Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 407 through 422 removed outlier: 3.912A pdb=" N LYS D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 415 " --> pdb=" O HIS D 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 442 Processing helix chain 'D' and resid 444 through 448 removed outlier: 3.636A pdb=" N CYS D 448 " --> pdb=" O LYS D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 473 Processing helix chain 'D' and resid 478 through 491 Processing helix chain 'D' and resid 493 through 498 Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'D' and resid 510 through 523 removed outlier: 3.520A pdb=" N ALA D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 86 Processing helix chain 'E' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER E 99 " --> pdb=" O VAL E 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 99' Processing helix chain 'E' and resid 100 through 106 Processing helix chain 'E' and resid 123 through 134 Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 167 through 174 removed outlier: 3.547A pdb=" N ILE E 171 " --> pdb=" O ASP E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.531A pdb=" N SER E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA E 209 " --> pdb=" O ALA E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 249 Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 309 through 325 Processing helix chain 'E' and resid 361 through 366 Processing helix chain 'E' and resid 368 through 379 Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'E' and resid 458 through 472 Processing helix chain 'E' and resid 481 through 489 Processing helix chain 'E' and resid 491 through 497 Processing helix chain 'E' and resid 502 through 508 Processing helix chain 'E' and resid 518 through 540 Processing helix chain 'E' and resid 641 through 648 removed outlier: 3.857A pdb=" N LYS E 648 " --> pdb=" O ALA E 644 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 49 Processing helix chain 'F' and resid 51 through 61 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 128 through 132 Processing helix chain 'F' and resid 134 through 152 Processing helix chain 'F' and resid 170 through 186 Processing helix chain 'F' and resid 201 through 205 removed outlier: 3.754A pdb=" N ALA F 204 " --> pdb=" O ALA F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 211 Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 240 through 246 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 263 through 276 Processing helix chain 'F' and resid 299 through 303 Processing helix chain 'F' and resid 316 through 324 Processing helix chain 'F' and resid 325 through 328 Processing helix chain 'F' and resid 361 through 365 Processing helix chain 'F' and resid 367 through 384 Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 407 through 422 removed outlier: 3.913A pdb=" N LYS F 414 " --> pdb=" O ARG F 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU F 415 " --> pdb=" O HIS F 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA F 422 " --> pdb=" O ALA F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 442 Processing helix chain 'F' and resid 444 through 448 removed outlier: 3.637A pdb=" N CYS F 448 " --> pdb=" O LYS F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 473 Processing helix chain 'F' and resid 478 through 491 Processing helix chain 'F' and resid 493 through 498 Processing helix chain 'F' and resid 507 through 509 No H-bonds generated for 'chain 'F' and resid 507 through 509' Processing helix chain 'F' and resid 510 through 523 removed outlier: 3.520A pdb=" N ALA F 523 " --> pdb=" O LEU F 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 86 Processing helix chain 'G' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER G 99 " --> pdb=" O VAL G 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 96 through 99' Processing helix chain 'G' and resid 100 through 106 Processing helix chain 'G' and resid 123 through 134 Processing helix chain 'G' and resid 149 through 158 Processing helix chain 'G' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE G 171 " --> pdb=" O ASP G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER G 180 " --> pdb=" O ASP G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 213 removed outlier: 3.896A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 249 Processing helix chain 'G' and resid 250 through 252 No H-bonds generated for 'chain 'G' and resid 250 through 252' Processing helix chain 'G' and resid 309 through 325 Processing helix chain 'G' and resid 361 through 366 Processing helix chain 'G' and resid 368 through 379 Processing helix chain 'G' and resid 385 through 389 Processing helix chain 'G' and resid 458 through 472 Processing helix chain 'G' and resid 481 through 489 Processing helix chain 'G' and resid 491 through 497 Processing helix chain 'G' and resid 502 through 508 Processing helix chain 'G' and resid 518 through 540 Processing helix chain 'G' and resid 641 through 648 removed outlier: 3.857A pdb=" N LYS G 648 " --> pdb=" O ALA G 644 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 49 Processing helix chain 'H' and resid 51 through 61 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 128 through 132 Processing helix chain 'H' and resid 134 through 152 Processing helix chain 'H' and resid 170 through 186 Processing helix chain 'H' and resid 201 through 205 removed outlier: 3.754A pdb=" N ALA H 204 " --> pdb=" O ALA H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 211 Processing helix chain 'H' and resid 227 through 235 Processing helix chain 'H' and resid 240 through 246 Processing helix chain 'H' and resid 246 through 253 Processing helix chain 'H' and resid 263 through 276 Processing helix chain 'H' and resid 299 through 303 Processing helix chain 'H' and resid 316 through 324 Processing helix chain 'H' and resid 325 through 328 Processing helix chain 'H' and resid 361 through 365 Processing helix chain 'H' and resid 367 through 384 Processing helix chain 'H' and resid 400 through 405 Processing helix chain 'H' and resid 407 through 422 removed outlier: 3.913A pdb=" N LYS H 414 " --> pdb=" O ARG H 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU H 415 " --> pdb=" O HIS H 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA H 422 " --> pdb=" O ALA H 418 " (cutoff:3.500A) Processing helix chain 'H' and resid 437 through 442 Processing helix chain 'H' and resid 444 through 448 removed outlier: 3.636A pdb=" N CYS H 448 " --> pdb=" O LYS H 445 " (cutoff:3.500A) Processing helix chain 'H' and resid 464 through 473 Processing helix chain 'H' and resid 478 through 491 Processing helix chain 'H' and resid 493 through 498 Processing helix chain 'H' and resid 507 through 509 No H-bonds generated for 'chain 'H' and resid 507 through 509' Processing helix chain 'H' and resid 510 through 523 removed outlier: 3.520A pdb=" N ALA H 523 " --> pdb=" O LEU H 519 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 86 Processing helix chain 'I' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER I 99 " --> pdb=" O VAL I 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 96 through 99' Processing helix chain 'I' and resid 100 through 106 Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 149 through 158 Processing helix chain 'I' and resid 167 through 174 removed outlier: 3.548A pdb=" N ILE I 171 " --> pdb=" O ASP I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER I 180 " --> pdb=" O ASP I 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA I 209 " --> pdb=" O ALA I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 249 Processing helix chain 'I' and resid 250 through 252 No H-bonds generated for 'chain 'I' and resid 250 through 252' Processing helix chain 'I' and resid 309 through 325 Processing helix chain 'I' and resid 361 through 366 Processing helix chain 'I' and resid 368 through 379 Processing helix chain 'I' and resid 385 through 389 Processing helix chain 'I' and resid 458 through 472 Processing helix chain 'I' and resid 481 through 489 Processing helix chain 'I' and resid 491 through 497 Processing helix chain 'I' and resid 502 through 508 Processing helix chain 'I' and resid 518 through 540 Processing helix chain 'I' and resid 641 through 648 removed outlier: 3.857A pdb=" N LYS I 648 " --> pdb=" O ALA I 644 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 49 Processing helix chain 'J' and resid 51 through 61 Processing helix chain 'J' and resid 65 through 74 Processing helix chain 'J' and resid 97 through 101 Processing helix chain 'J' and resid 128 through 132 Processing helix chain 'J' and resid 134 through 152 Processing helix chain 'J' and resid 170 through 186 Processing helix chain 'J' and resid 201 through 205 removed outlier: 3.755A pdb=" N ALA J 204 " --> pdb=" O ALA J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 211 Processing helix chain 'J' and resid 227 through 235 Processing helix chain 'J' and resid 240 through 246 Processing helix chain 'J' and resid 246 through 253 Processing helix chain 'J' and resid 263 through 276 Processing helix chain 'J' and resid 299 through 303 Processing helix chain 'J' and resid 316 through 324 Processing helix chain 'J' and resid 325 through 328 Processing helix chain 'J' and resid 361 through 365 Processing helix chain 'J' and resid 367 through 384 Processing helix chain 'J' and resid 400 through 405 Processing helix chain 'J' and resid 407 through 422 removed outlier: 3.913A pdb=" N LYS J 414 " --> pdb=" O ARG J 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU J 415 " --> pdb=" O HIS J 411 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA J 422 " --> pdb=" O ALA J 418 " (cutoff:3.500A) Processing helix chain 'J' and resid 437 through 442 Processing helix chain 'J' and resid 444 through 448 removed outlier: 3.637A pdb=" N CYS J 448 " --> pdb=" O LYS J 445 " (cutoff:3.500A) Processing helix chain 'J' and resid 464 through 473 Processing helix chain 'J' and resid 478 through 491 Processing helix chain 'J' and resid 493 through 498 Processing helix chain 'J' and resid 507 through 509 No H-bonds generated for 'chain 'J' and resid 507 through 509' Processing helix chain 'J' and resid 510 through 523 removed outlier: 3.520A pdb=" N ALA J 523 " --> pdb=" O LEU J 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 86 Processing helix chain 'K' and resid 96 through 99 removed outlier: 4.322A pdb=" N SER K 99 " --> pdb=" O VAL K 96 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 96 through 99' Processing helix chain 'K' and resid 100 through 106 Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 167 through 174 removed outlier: 3.549A pdb=" N ILE K 171 " --> pdb=" O ASP K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 187 removed outlier: 3.532A pdb=" N SER K 180 " --> pdb=" O ASP K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 213 removed outlier: 3.895A pdb=" N ALA K 209 " --> pdb=" O ALA K 205 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 249 Processing helix chain 'K' and resid 250 through 252 No H-bonds generated for 'chain 'K' and resid 250 through 252' Processing helix chain 'K' and resid 309 through 325 Processing helix chain 'K' and resid 361 through 366 Processing helix chain 'K' and resid 368 through 379 Processing helix chain 'K' and resid 385 through 389 Processing helix chain 'K' and resid 458 through 472 Processing helix chain 'K' and resid 481 through 489 Processing helix chain 'K' and resid 491 through 497 Processing helix chain 'K' and resid 502 through 508 Processing helix chain 'K' and resid 518 through 540 Processing helix chain 'K' and resid 641 through 648 removed outlier: 3.858A pdb=" N LYS K 648 " --> pdb=" O ALA K 644 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 49 Processing helix chain 'L' and resid 51 through 61 Processing helix chain 'L' and resid 65 through 74 Processing helix chain 'L' and resid 97 through 101 Processing helix chain 'L' and resid 128 through 132 Processing helix chain 'L' and resid 134 through 152 Processing helix chain 'L' and resid 170 through 186 Processing helix chain 'L' and resid 201 through 205 removed outlier: 3.754A pdb=" N ALA L 204 " --> pdb=" O ALA L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 211 Processing helix chain 'L' and resid 227 through 235 Processing helix chain 'L' and resid 240 through 246 Processing helix chain 'L' and resid 246 through 253 Processing helix chain 'L' and resid 263 through 276 Processing helix chain 'L' and resid 299 through 303 Processing helix chain 'L' and resid 316 through 324 Processing helix chain 'L' and resid 325 through 328 Processing helix chain 'L' and resid 361 through 365 Processing helix chain 'L' and resid 367 through 384 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 407 through 422 removed outlier: 3.913A pdb=" N LYS L 414 " --> pdb=" O ARG L 410 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU L 415 " --> pdb=" O HIS L 411 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA L 422 " --> pdb=" O ALA L 418 " (cutoff:3.500A) Processing helix chain 'L' and resid 437 through 442 Processing helix chain 'L' and resid 444 through 448 removed outlier: 3.636A pdb=" N CYS L 448 " --> pdb=" O LYS L 445 " (cutoff:3.500A) Processing helix chain 'L' and resid 464 through 473 Processing helix chain 'L' and resid 478 through 491 Processing helix chain 'L' and resid 493 through 498 Processing helix chain 'L' and resid 507 through 509 No H-bonds generated for 'chain 'L' and resid 507 through 509' Processing helix chain 'L' and resid 510 through 523 removed outlier: 3.519A pdb=" N ALA L 523 " --> pdb=" O LEU L 519 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 113 removed outlier: 3.821A pdb=" N ILE A 92 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 138 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 230 through 232 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE A 347 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU A 338 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS A 269 " --> pdb=" O GLU A 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU A 289 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU A 271 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU A 287 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN A 273 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER A 291 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 300 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN A 293 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A 298 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN A 297 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR A 401 " --> pdb=" O GLN A 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL A 299 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA5, first strand: chain 'A' and resid 415 through 416 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 421 Processing sheet with id=AA7, first strand: chain 'A' and resid 559 through 564 removed outlier: 6.478A pdb=" N SER A 626 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG A 619 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN A 624 " --> pdb=" O ARG A 619 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 661 through 663 removed outlier: 7.196A pdb=" N LEU A 662 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU A 724 " --> pdb=" O VAL A 710 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A 710 " --> pdb=" O LEU A 724 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU A 726 " --> pdb=" O LYS A 708 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 696 through 700 removed outlier: 7.821A pdb=" N ILE A 687 " --> pdb=" O VAL A 673 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 673 " --> pdb=" O ILE A 687 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL A 689 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL A 669 " --> pdb=" O GLU A 691 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.490A pdb=" N VAL B 155 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU B 195 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY B 157 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 213 " --> pdb=" O GLN B 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 217 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 214 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE B 261 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET B 216 " --> pdb=" O PHE B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.786A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU B 459 " --> pdb=" O ILE B 430 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG B 432 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA B 461 " --> pdb=" O ARG B 432 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 434 " --> pdb=" O ALA B 461 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332 removed outlier: 4.786A pdb=" N VAL B 342 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP B 393 " --> pdb=" O ASN B 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 388 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL B 429 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR B 390 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR B 431 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL B 392 " --> pdb=" O THR B 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B 433 " --> pdb=" O VAL B 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS B 426 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR B 453 " --> pdb=" O LYS B 426 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR B 428 " --> pdb=" O TYR B 453 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP B 504 " --> pdb=" O ASN B 452 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 108 through 113 removed outlier: 3.822A pdb=" N ILE C 92 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 138 " --> pdb=" O LYS C 65 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 230 through 232 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 351 removed outlier: 5.400A pdb=" N PHE C 347 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU C 338 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS C 269 " --> pdb=" O GLU C 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU C 289 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU C 271 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU C 287 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER C 291 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL C 300 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN C 293 " --> pdb=" O LYS C 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS C 298 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 14.034A pdb=" N GLN C 297 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR C 401 " --> pdb=" O GLN C 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 299 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 403 through 404 Processing sheet with id=AB8, first strand: chain 'C' and resid 415 through 416 Processing sheet with id=AB9, first strand: chain 'C' and resid 419 through 421 Processing sheet with id=AC1, first strand: chain 'C' and resid 559 through 564 removed outlier: 6.478A pdb=" N SER C 626 " --> pdb=" O LEU C 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG C 619 " --> pdb=" O ASN C 624 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN C 624 " --> pdb=" O ARG C 619 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 661 through 663 removed outlier: 7.196A pdb=" N LEU C 662 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU C 724 " --> pdb=" O VAL C 710 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL C 710 " --> pdb=" O LEU C 724 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU C 726 " --> pdb=" O LYS C 708 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 696 through 700 removed outlier: 7.821A pdb=" N ILE C 687 " --> pdb=" O VAL C 673 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL C 673 " --> pdb=" O ILE C 687 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 689 " --> pdb=" O VAL C 671 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL C 669 " --> pdb=" O GLU C 691 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.490A pdb=" N VAL D 155 " --> pdb=" O ILE D 193 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU D 195 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY D 157 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE D 213 " --> pdb=" O GLN D 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 217 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N THR D 214 " --> pdb=" O ARG D 259 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE D 261 " --> pdb=" O THR D 214 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET D 216 " --> pdb=" O PHE D 261 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL D 342 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP D 393 " --> pdb=" O ASN D 357 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 388 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL D 429 " --> pdb=" O LEU D 388 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR D 390 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR D 431 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL D 392 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 433 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLU D 459 " --> pdb=" O ILE D 430 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG D 432 " --> pdb=" O GLU D 459 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ALA D 461 " --> pdb=" O ARG D 432 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA D 434 " --> pdb=" O ALA D 461 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL D 342 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASP D 393 " --> pdb=" O ASN D 357 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU D 388 " --> pdb=" O VAL D 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL D 429 " --> pdb=" O LEU D 388 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR D 390 " --> pdb=" O VAL D 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR D 431 " --> pdb=" O THR D 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL D 392 " --> pdb=" O THR D 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS D 433 " --> pdb=" O VAL D 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS D 426 " --> pdb=" O THR D 451 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR D 453 " --> pdb=" O LYS D 426 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR D 428 " --> pdb=" O TYR D 453 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP D 504 " --> pdb=" O ASN D 452 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 108 through 113 removed outlier: 3.821A pdb=" N ILE E 92 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA E 138 " --> pdb=" O LYS E 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 230 through 232 Processing sheet with id=AC9, first strand: chain 'E' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE E 347 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU E 338 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS E 269 " --> pdb=" O GLU E 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU E 289 " --> pdb=" O HIS E 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU E 271 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU E 287 " --> pdb=" O GLU E 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER E 291 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL E 300 " --> pdb=" O SER E 291 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN E 293 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LYS E 298 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN E 297 " --> pdb=" O TYR E 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR E 401 " --> pdb=" O GLN E 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL E 299 " --> pdb=" O ARG E 399 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 403 through 404 Processing sheet with id=AD2, first strand: chain 'E' and resid 415 through 416 Processing sheet with id=AD3, first strand: chain 'E' and resid 419 through 421 Processing sheet with id=AD4, first strand: chain 'E' and resid 559 through 564 removed outlier: 6.479A pdb=" N SER E 626 " --> pdb=" O LEU E 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG E 619 " --> pdb=" O ASN E 624 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN E 624 " --> pdb=" O ARG E 619 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 661 through 663 removed outlier: 7.196A pdb=" N LEU E 662 " --> pdb=" O LEU E 724 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU E 724 " --> pdb=" O VAL E 710 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL E 710 " --> pdb=" O LEU E 724 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU E 726 " --> pdb=" O LYS E 708 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 696 through 700 removed outlier: 7.821A pdb=" N ILE E 687 " --> pdb=" O VAL E 673 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL E 673 " --> pdb=" O ILE E 687 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL E 689 " --> pdb=" O VAL E 671 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL E 669 " --> pdb=" O GLU E 691 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 80 through 81 removed outlier: 6.491A pdb=" N VAL F 155 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU F 195 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY F 157 " --> pdb=" O LEU F 195 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE F 213 " --> pdb=" O GLN F 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 217 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR F 214 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE F 261 " --> pdb=" O THR F 214 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET F 216 " --> pdb=" O PHE F 261 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL F 342 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP F 393 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 388 " --> pdb=" O VAL F 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL F 429 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR F 390 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR F 431 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 392 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS F 433 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU F 459 " --> pdb=" O ILE F 430 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG F 432 " --> pdb=" O GLU F 459 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA F 461 " --> pdb=" O ARG F 432 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA F 434 " --> pdb=" O ALA F 461 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL F 342 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP F 393 " --> pdb=" O ASN F 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 388 " --> pdb=" O VAL F 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL F 429 " --> pdb=" O LEU F 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR F 390 " --> pdb=" O VAL F 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR F 431 " --> pdb=" O THR F 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL F 392 " --> pdb=" O THR F 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS F 433 " --> pdb=" O VAL F 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS F 426 " --> pdb=" O THR F 451 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR F 453 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR F 428 " --> pdb=" O TYR F 453 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP F 504 " --> pdb=" O ASN F 452 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 108 through 113 removed outlier: 3.822A pdb=" N ILE G 92 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA G 138 " --> pdb=" O LYS G 65 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 230 through 232 Processing sheet with id=AE3, first strand: chain 'G' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE G 347 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LEU G 338 " --> pdb=" O PHE G 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS G 269 " --> pdb=" O GLU G 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU G 289 " --> pdb=" O HIS G 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU G 271 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU G 287 " --> pdb=" O GLU G 271 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N GLN G 273 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER G 291 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL G 300 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN G 293 " --> pdb=" O LYS G 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS G 298 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN G 297 " --> pdb=" O TYR G 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR G 401 " --> pdb=" O GLN G 297 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 299 " --> pdb=" O ARG G 399 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 403 through 404 Processing sheet with id=AE5, first strand: chain 'G' and resid 415 through 416 Processing sheet with id=AE6, first strand: chain 'G' and resid 419 through 421 Processing sheet with id=AE7, first strand: chain 'G' and resid 559 through 564 removed outlier: 6.478A pdb=" N SER G 626 " --> pdb=" O LEU G 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG G 619 " --> pdb=" O ASN G 624 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN G 624 " --> pdb=" O ARG G 619 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 661 through 663 removed outlier: 7.196A pdb=" N LEU G 662 " --> pdb=" O LEU G 724 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU G 724 " --> pdb=" O VAL G 710 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL G 710 " --> pdb=" O LEU G 724 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLU G 726 " --> pdb=" O LYS G 708 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 696 through 700 removed outlier: 7.820A pdb=" N ILE G 687 " --> pdb=" O VAL G 673 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL G 673 " --> pdb=" O ILE G 687 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL G 689 " --> pdb=" O VAL G 671 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL G 669 " --> pdb=" O GLU G 691 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 80 through 81 removed outlier: 6.491A pdb=" N VAL H 155 " --> pdb=" O ILE H 193 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU H 195 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY H 157 " --> pdb=" O LEU H 195 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE H 213 " --> pdb=" O GLN H 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL H 217 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR H 214 " --> pdb=" O ARG H 259 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE H 261 " --> pdb=" O THR H 214 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET H 216 " --> pdb=" O PHE H 261 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL H 342 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP H 393 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU H 388 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL H 429 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR H 390 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR H 431 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL H 392 " --> pdb=" O THR H 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS H 433 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU H 459 " --> pdb=" O ILE H 430 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG H 432 " --> pdb=" O GLU H 459 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA H 461 " --> pdb=" O ARG H 432 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA H 434 " --> pdb=" O ALA H 461 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL H 342 " --> pdb=" O ILE H 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP H 393 " --> pdb=" O ASN H 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU H 388 " --> pdb=" O VAL H 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL H 429 " --> pdb=" O LEU H 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR H 390 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR H 431 " --> pdb=" O THR H 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL H 392 " --> pdb=" O THR H 431 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS H 433 " --> pdb=" O VAL H 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS H 426 " --> pdb=" O THR H 451 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR H 453 " --> pdb=" O LYS H 426 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR H 428 " --> pdb=" O TYR H 453 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP H 504 " --> pdb=" O ASN H 452 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 108 through 113 removed outlier: 3.821A pdb=" N ILE I 92 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA I 138 " --> pdb=" O LYS I 65 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 230 through 232 Processing sheet with id=AF6, first strand: chain 'I' and resid 345 through 351 removed outlier: 5.399A pdb=" N PHE I 347 " --> pdb=" O LEU I 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU I 338 " --> pdb=" O PHE I 347 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N HIS I 269 " --> pdb=" O GLU I 289 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N GLU I 289 " --> pdb=" O HIS I 269 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU I 271 " --> pdb=" O GLU I 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU I 287 " --> pdb=" O GLU I 271 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN I 273 " --> pdb=" O LEU I 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER I 291 " --> pdb=" O VAL I 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL I 300 " --> pdb=" O SER I 291 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N GLN I 293 " --> pdb=" O LYS I 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS I 298 " --> pdb=" O GLN I 293 " (cutoff:3.500A) removed outlier: 14.033A pdb=" N GLN I 297 " --> pdb=" O TYR I 401 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N TYR I 401 " --> pdb=" O GLN I 297 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL I 299 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 403 through 404 Processing sheet with id=AF8, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AF9, first strand: chain 'I' and resid 419 through 421 Processing sheet with id=AG1, first strand: chain 'I' and resid 559 through 564 removed outlier: 6.478A pdb=" N SER I 626 " --> pdb=" O LEU I 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG I 619 " --> pdb=" O ASN I 624 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN I 624 " --> pdb=" O ARG I 619 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 661 through 663 removed outlier: 7.197A pdb=" N LEU I 662 " --> pdb=" O LEU I 724 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N LEU I 724 " --> pdb=" O VAL I 710 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL I 710 " --> pdb=" O LEU I 724 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU I 726 " --> pdb=" O LYS I 708 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 696 through 700 removed outlier: 7.821A pdb=" N ILE I 687 " --> pdb=" O VAL I 673 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL I 673 " --> pdb=" O ILE I 687 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL I 689 " --> pdb=" O VAL I 671 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL I 669 " --> pdb=" O GLU I 691 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 80 through 81 removed outlier: 6.490A pdb=" N VAL J 155 " --> pdb=" O ILE J 193 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU J 195 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY J 157 " --> pdb=" O LEU J 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE J 213 " --> pdb=" O GLN J 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL J 217 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR J 214 " --> pdb=" O ARG J 259 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE J 261 " --> pdb=" O THR J 214 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET J 216 " --> pdb=" O PHE J 261 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 330 through 332 removed outlier: 4.786A pdb=" N VAL J 342 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP J 393 " --> pdb=" O ASN J 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU J 388 " --> pdb=" O VAL J 427 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL J 429 " --> pdb=" O LEU J 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR J 390 " --> pdb=" O VAL J 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR J 431 " --> pdb=" O THR J 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL J 392 " --> pdb=" O THR J 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS J 433 " --> pdb=" O VAL J 392 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLU J 459 " --> pdb=" O ILE J 430 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG J 432 " --> pdb=" O GLU J 459 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA J 461 " --> pdb=" O ARG J 432 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA J 434 " --> pdb=" O ALA J 461 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 330 through 332 removed outlier: 4.786A pdb=" N VAL J 342 " --> pdb=" O ILE J 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP J 393 " --> pdb=" O ASN J 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU J 388 " --> pdb=" O VAL J 427 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL J 429 " --> pdb=" O LEU J 388 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N THR J 390 " --> pdb=" O VAL J 429 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N THR J 431 " --> pdb=" O THR J 390 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N VAL J 392 " --> pdb=" O THR J 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS J 433 " --> pdb=" O VAL J 392 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS J 426 " --> pdb=" O THR J 451 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N TYR J 453 " --> pdb=" O LYS J 426 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR J 428 " --> pdb=" O TYR J 453 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP J 504 " --> pdb=" O ASN J 452 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 108 through 113 removed outlier: 3.822A pdb=" N ILE K 92 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 138 " --> pdb=" O LYS K 65 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 230 through 232 Processing sheet with id=AG9, first strand: chain 'K' and resid 345 through 351 removed outlier: 5.400A pdb=" N PHE K 347 " --> pdb=" O LEU K 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU K 338 " --> pdb=" O PHE K 347 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS K 269 " --> pdb=" O GLU K 289 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLU K 289 " --> pdb=" O HIS K 269 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU K 271 " --> pdb=" O GLU K 287 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLU K 287 " --> pdb=" O GLU K 271 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN K 273 " --> pdb=" O LEU K 285 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER K 291 " --> pdb=" O VAL K 300 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL K 300 " --> pdb=" O SER K 291 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLN K 293 " --> pdb=" O LYS K 298 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS K 298 " --> pdb=" O GLN K 293 " (cutoff:3.500A) removed outlier: 14.032A pdb=" N GLN K 297 " --> pdb=" O TYR K 401 " (cutoff:3.500A) removed outlier: 10.666A pdb=" N TYR K 401 " --> pdb=" O GLN K 297 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL K 299 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 403 through 404 Processing sheet with id=AH2, first strand: chain 'K' and resid 415 through 416 Processing sheet with id=AH3, first strand: chain 'K' and resid 419 through 421 Processing sheet with id=AH4, first strand: chain 'K' and resid 559 through 564 removed outlier: 6.478A pdb=" N SER K 626 " --> pdb=" O LEU K 617 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG K 619 " --> pdb=" O ASN K 624 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN K 624 " --> pdb=" O ARG K 619 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 661 through 663 removed outlier: 7.196A pdb=" N LEU K 662 " --> pdb=" O LEU K 724 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU K 724 " --> pdb=" O VAL K 710 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VAL K 710 " --> pdb=" O LEU K 724 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU K 726 " --> pdb=" O LYS K 708 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 696 through 700 removed outlier: 7.821A pdb=" N ILE K 687 " --> pdb=" O VAL K 673 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL K 673 " --> pdb=" O ILE K 687 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL K 689 " --> pdb=" O VAL K 671 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL K 669 " --> pdb=" O GLU K 691 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 80 through 81 removed outlier: 6.491A pdb=" N VAL L 155 " --> pdb=" O ILE L 193 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N LEU L 195 " --> pdb=" O VAL L 155 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLY L 157 " --> pdb=" O LEU L 195 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE L 213 " --> pdb=" O GLN L 192 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 217 " --> pdb=" O ILE L 196 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR L 214 " --> pdb=" O ARG L 259 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N PHE L 261 " --> pdb=" O THR L 214 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET L 216 " --> pdb=" O PHE L 261 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL L 342 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP L 393 " --> pdb=" O ASN L 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU L 388 " --> pdb=" O VAL L 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL L 429 " --> pdb=" O LEU L 388 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR L 390 " --> pdb=" O VAL L 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 431 " --> pdb=" O THR L 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL L 392 " --> pdb=" O THR L 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS L 433 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N GLU L 459 " --> pdb=" O ILE L 430 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG L 432 " --> pdb=" O GLU L 459 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ALA L 461 " --> pdb=" O ARG L 432 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA L 434 " --> pdb=" O ALA L 461 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 330 through 332 removed outlier: 4.787A pdb=" N VAL L 342 " --> pdb=" O ILE L 332 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP L 393 " --> pdb=" O ASN L 357 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU L 388 " --> pdb=" O VAL L 427 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N VAL L 429 " --> pdb=" O LEU L 388 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR L 390 " --> pdb=" O VAL L 429 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR L 431 " --> pdb=" O THR L 390 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL L 392 " --> pdb=" O THR L 431 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LYS L 433 " --> pdb=" O VAL L 392 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LYS L 426 " --> pdb=" O THR L 451 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N TYR L 453 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N THR L 428 " --> pdb=" O TYR L 453 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP L 504 " --> pdb=" O ASN L 452 " (cutoff:3.500A) 2592 hydrogen bonds defined for protein. 7146 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: 30.12 Time building geometry restraints manager: 12.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 10956 1.32 - 1.44: 12281 1.44 - 1.57: 31447 1.57 - 1.69: 6 1.69 - 1.81: 498 Bond restraints: 55188 Sorted by residual: bond pdb=" C3 BTN E 801 " pdb=" O3 BTN E 801 " ideal model delta sigma weight residual 1.220 1.404 -0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C3 BTN K 801 " pdb=" O3 BTN K 801 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" C3 BTN A 801 " pdb=" O3 BTN A 801 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" C3 BTN C 801 " pdb=" O3 BTN C 801 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C3 BTN I 801 " pdb=" O3 BTN I 801 " ideal model delta sigma weight residual 1.220 1.403 -0.183 2.00e-02 2.50e+03 8.34e+01 ... (remaining 55183 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 72613 2.57 - 5.15: 1673 5.15 - 7.72: 252 7.72 - 10.30: 60 10.30 - 12.87: 42 Bond angle restraints: 74640 Sorted by residual: angle pdb=" N ALA K 187 " pdb=" CA ALA K 187 " pdb=" C ALA K 187 " ideal model delta sigma weight residual 113.18 101.49 11.69 1.21e+00 6.83e-01 9.34e+01 angle pdb=" N ALA G 187 " pdb=" CA ALA G 187 " pdb=" C ALA G 187 " ideal model delta sigma weight residual 113.18 101.49 11.69 1.21e+00 6.83e-01 9.33e+01 angle pdb=" N ALA I 187 " pdb=" CA ALA I 187 " pdb=" C ALA I 187 " ideal model delta sigma weight residual 113.18 101.50 11.68 1.21e+00 6.83e-01 9.32e+01 angle pdb=" N ALA A 187 " pdb=" CA ALA A 187 " pdb=" C ALA A 187 " ideal model delta sigma weight residual 113.18 101.51 11.67 1.21e+00 6.83e-01 9.29e+01 angle pdb=" N ALA C 187 " pdb=" CA ALA C 187 " pdb=" C ALA C 187 " ideal model delta sigma weight residual 113.18 101.52 11.66 1.21e+00 6.83e-01 9.29e+01 ... (remaining 74635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 31897 17.59 - 35.18: 1133 35.18 - 52.78: 354 52.78 - 70.37: 102 70.37 - 87.96: 42 Dihedral angle restraints: 33528 sinusoidal: 13338 harmonic: 20190 Sorted by residual: dihedral pdb=" CA ILE J 505 " pdb=" C ILE J 505 " pdb=" N ILE J 506 " pdb=" CA ILE J 506 " ideal model delta harmonic sigma weight residual -180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE B 505 " pdb=" C ILE B 505 " pdb=" N ILE B 506 " pdb=" CA ILE B 506 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE L 505 " pdb=" C ILE L 505 " pdb=" N ILE L 506 " pdb=" CA ILE L 506 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 33525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 6321 0.069 - 0.138: 1713 0.138 - 0.207: 388 0.207 - 0.276: 38 0.276 - 0.345: 18 Chirality restraints: 8478 Sorted by residual: chirality pdb=" C2 BTN I 801 " pdb=" C4 BTN I 801 " pdb=" C7 BTN I 801 " pdb=" S1 BTN I 801 " both_signs ideal model delta sigma weight residual False 3.08 2.74 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA MET F 253 " pdb=" N MET F 253 " pdb=" C MET F 253 " pdb=" CB MET F 253 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" C2 BTN E 801 " pdb=" C4 BTN E 801 " pdb=" C7 BTN E 801 " pdb=" S1 BTN E 801 " both_signs ideal model delta sigma weight residual False 3.08 2.74 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 8475 not shown) Planarity restraints: 9738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS H 517 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.33e+01 pdb=" C CYS H 517 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS H 517 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP H 518 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 517 " -0.018 2.00e-02 2.50e+03 3.64e-02 1.32e+01 pdb=" C CYS B 517 " 0.063 2.00e-02 2.50e+03 pdb=" O CYS B 517 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP B 518 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 517 " 0.018 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C CYS F 517 " -0.063 2.00e-02 2.50e+03 pdb=" O CYS F 517 " 0.023 2.00e-02 2.50e+03 pdb=" N ASP F 518 " 0.021 2.00e-02 2.50e+03 ... (remaining 9735 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 6396 2.75 - 3.29: 52140 3.29 - 3.82: 87025 3.82 - 4.36: 109144 4.36 - 4.90: 183912 Nonbonded interactions: 438617 Sorted by model distance: nonbonded pdb=" OG1 THR H 423 " pdb=" CE LYS J 533 " model vdw 2.212 3.440 nonbonded pdb=" NH2 ARG H 379 " pdb=" OE1 GLU H 421 " model vdw 2.220 3.120 nonbonded pdb=" NH2 ARG D 379 " pdb=" OE1 GLU D 421 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG B 379 " pdb=" OE1 GLU B 421 " model vdw 2.221 3.120 nonbonded pdb=" NH2 ARG F 379 " pdb=" OE1 GLU F 421 " model vdw 2.221 3.120 ... (remaining 438612 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 6.510 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: 0.070 Extract box with map and model: 1.830 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 107.920 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.390 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 0.010 0.184 55188 Z= 0.667 Angle : 1.021 12.874 74640 Z= 0.669 Chirality : 0.064 0.345 8478 Planarity : 0.005 0.060 9738 Dihedral : 11.379 87.960 20544 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.82 % Favored : 96.58 % Rotamer: Outliers : 1.54 % Allowed : 1.40 % Favored : 97.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.09), residues: 7026 helix: -0.74 (0.09), residues: 2370 sheet: 0.68 (0.13), residues: 1524 loop : -0.48 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 394 HIS 0.005 0.000 HIS H 534 PHE 0.002 0.000 PHE H 215 TYR 0.003 0.000 TYR L 405 ARG 0.003 0.000 ARG B 532 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1656 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 1566 time to evaluate : 4.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.6027 (mmtp) REVERT: A 218 ILE cc_start: 0.5861 (mt) cc_final: 0.5547 (mt) REVERT: A 336 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7207 (mp0) REVERT: A 348 LEU cc_start: 0.7896 (tp) cc_final: 0.7567 (mt) REVERT: A 382 LEU cc_start: 0.8135 (mt) cc_final: 0.7656 (mp) REVERT: A 466 MET cc_start: 0.8360 (tpp) cc_final: 0.7777 (tpp) REVERT: A 501 THR cc_start: 0.8133 (p) cc_final: 0.7523 (p) REVERT: A 650 MET cc_start: 0.8072 (mmp) cc_final: 0.7653 (mmm) REVERT: A 662 LEU cc_start: 0.6705 (mt) cc_final: 0.5855 (tt) REVERT: A 665 PRO cc_start: 0.7158 (Cg_endo) cc_final: 0.6751 (Cg_exo) REVERT: B 38 ARG cc_start: 0.5178 (OUTLIER) cc_final: 0.4754 (mtm-85) REVERT: B 499 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7447 (mtt90) REVERT: C 68 VAL cc_start: 0.8442 (t) cc_final: 0.8165 (p) REVERT: C 85 MET cc_start: 0.5547 (mtp) cc_final: 0.5165 (mtm) REVERT: C 272 ILE cc_start: 0.8263 (mt) cc_final: 0.7983 (tt) REVERT: C 290 CYS cc_start: 0.6821 (m) cc_final: 0.6531 (m) REVERT: C 398 CYS cc_start: 0.5601 (m) cc_final: 0.5371 (m) REVERT: C 503 PHE cc_start: 0.6253 (t80) cc_final: 0.5802 (t80) REVERT: C 549 MET cc_start: 0.8102 (mmm) cc_final: 0.7792 (mmm) REVERT: C 665 PRO cc_start: 0.5369 (Cg_endo) cc_final: 0.4558 (Cg_exo) REVERT: E 77 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6150 (tpt170) REVERT: F 525 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7376 (tttp) REVERT: G 272 ILE cc_start: 0.7881 (mt) cc_final: 0.7644 (tp) REVERT: G 316 MET cc_start: 0.6232 (mmp) cc_final: 0.5984 (mmt) REVERT: G 339 VAL cc_start: 0.6627 (p) cc_final: 0.6419 (t) REVERT: G 452 LEU cc_start: 0.8174 (tp) cc_final: 0.7957 (tp) REVERT: H 525 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7396 (tttt) REVERT: I 290 CYS cc_start: 0.6753 (m) cc_final: 0.6454 (m) REVERT: I 607 VAL cc_start: 0.8253 (t) cc_final: 0.7854 (t) REVERT: I 665 PRO cc_start: 0.6187 (Cg_endo) cc_final: 0.5212 (Cg_exo) REVERT: I 666 MET cc_start: 0.4703 (ttt) cc_final: 0.4396 (ttm) REVERT: I 695 MET cc_start: 0.6082 (tpp) cc_final: 0.5564 (tpp) REVERT: K 107 ASP cc_start: 0.7593 (m-30) cc_final: 0.6624 (t0) REVERT: K 177 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6700 (ttmt) outliers start: 90 outliers final: 10 residues processed: 1632 average time/residue: 0.5969 time to fit residues: 1539.8547 Evaluate side-chains 726 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 710 time to evaluate : 4.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 499 ARG Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain C residue 459 ARG Chi-restraints excluded: chain E residue 71 ARG Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain G residue 185 LYS Chi-restraints excluded: chain H residue 525 LYS Chi-restraints excluded: chain J residue 525 LYS Chi-restraints excluded: chain J residue 534 HIS Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 691 GLU Chi-restraints excluded: chain L residue 492 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 587 optimal weight: 0.9990 chunk 527 optimal weight: 10.0000 chunk 292 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 355 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 545 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 406 optimal weight: 1.9990 chunk 632 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN A 358 HIS A 371 GLN A 611 GLN A 697 ASN B 115 ASN C 102 HIS C 140 HIS C 611 GLN D 115 ASN ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN E 140 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS E 371 GLN F 115 ASN F 446 HIS F 534 HIS G 140 HIS G 169 HIS G 611 GLN G 696 GLN H 88 HIS H 115 ASN H 139 GLN H 241 GLN H 483 GLN H 528 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 358 HIS I 419 GLN I 425 HIS I 611 GLN I 713 GLN J 88 HIS J 147 GLN J 483 GLN ** J 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 ASN K 371 GLN ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 611 GLN L 58 GLN L 115 ASN L 446 HIS L 492 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 55188 Z= 0.212 Angle : 0.634 16.675 74640 Z= 0.337 Chirality : 0.046 0.196 8478 Planarity : 0.005 0.079 9738 Dihedral : 5.438 70.511 7781 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.35 % Favored : 97.48 % Rotamer: Outliers : 1.92 % Allowed : 8.52 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.10), residues: 7026 helix: 0.58 (0.10), residues: 2478 sheet: 0.62 (0.13), residues: 1524 loop : -0.17 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 284 HIS 0.015 0.001 HIS E 358 PHE 0.031 0.002 PHE C 152 TYR 0.023 0.001 TYR J 222 ARG 0.014 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 822 time to evaluate : 5.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6545 (mtm180) cc_final: 0.6306 (mtm180) REVERT: A 334 THR cc_start: 0.8178 (m) cc_final: 0.6979 (t) REVERT: A 349 GLU cc_start: 0.6319 (tm-30) cc_final: 0.6081 (tm-30) REVERT: A 382 LEU cc_start: 0.7977 (mt) cc_final: 0.7521 (mp) REVERT: A 466 MET cc_start: 0.8403 (tpp) cc_final: 0.7621 (tpp) REVERT: A 662 LEU cc_start: 0.6693 (mt) cc_final: 0.6103 (tt) REVERT: A 696 GLN cc_start: 0.7226 (mt0) cc_final: 0.6907 (mp10) REVERT: B 525 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8821 (tttt) REVERT: C 68 VAL cc_start: 0.8473 (t) cc_final: 0.8197 (p) REVERT: C 84 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5453 (tmtt) REVERT: C 179 GLU cc_start: 0.6747 (mp0) cc_final: 0.5623 (tm-30) REVERT: C 272 ILE cc_start: 0.8187 (mt) cc_final: 0.7907 (tt) REVERT: C 549 MET cc_start: 0.8368 (mmm) cc_final: 0.8166 (mmm) REVERT: D 105 ASP cc_start: 0.7684 (t0) cc_final: 0.7397 (t0) REVERT: E 143 TYR cc_start: 0.6285 (p90) cc_final: 0.5750 (p90) REVERT: E 295 ARG cc_start: 0.6416 (mmp80) cc_final: 0.5930 (ptp-170) REVERT: E 502 LYS cc_start: 0.8172 (mmmm) cc_final: 0.7924 (mmmm) REVERT: F 333 MET cc_start: 0.7875 (mtt) cc_final: 0.7584 (mtt) REVERT: F 525 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8300 (tttt) REVERT: G 89 THR cc_start: 0.7692 (m) cc_final: 0.7095 (p) REVERT: G 316 MET cc_start: 0.6190 (mmp) cc_final: 0.5909 (mmt) REVERT: G 451 LYS cc_start: 0.7126 (pttt) cc_final: 0.6800 (pttt) REVERT: G 549 MET cc_start: 0.9075 (mmm) cc_final: 0.8821 (mmm) REVERT: G 652 GLU cc_start: 0.6417 (pp20) cc_final: 0.5615 (pm20) REVERT: H 178 ASP cc_start: 0.7841 (OUTLIER) cc_final: 0.7418 (t0) REVERT: H 525 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7747 (tttt) REVERT: I 85 MET cc_start: 0.6492 (mtm) cc_final: 0.6205 (mtm) REVERT: I 156 LEU cc_start: 0.6763 (tp) cc_final: 0.6364 (pp) REVERT: I 695 MET cc_start: 0.6069 (tpp) cc_final: 0.5726 (tpp) REVERT: J 525 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8565 (tttt) REVERT: K 169 HIS cc_start: 0.8244 (t70) cc_final: 0.7468 (p90) REVERT: K 177 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6714 (ttmt) REVERT: K 243 ARG cc_start: 0.5720 (ptm-80) cc_final: 0.5484 (mmm160) REVERT: K 351 ASN cc_start: 0.6509 (m-40) cc_final: 0.6090 (m-40) REVERT: K 459 ARG cc_start: 0.6986 (OUTLIER) cc_final: 0.6769 (ttt-90) outliers start: 112 outliers final: 56 residues processed: 897 average time/residue: 0.5571 time to fit residues: 829.9039 Evaluate side-chains 680 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 617 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain B residue 525 LYS Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 178 ASP Chi-restraints excluded: chain F residue 193 ILE Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 475 ILE Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 88 HIS Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 525 LYS Chi-restraints excluded: chain I residue 323 LEU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain J residue 492 ASN Chi-restraints excluded: chain J residue 525 LYS Chi-restraints excluded: chain K residue 64 ASP Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 445 LYS Chi-restraints excluded: chain L residue 471 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 351 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 526 optimal weight: 6.9990 chunk 430 optimal weight: 7.9990 chunk 174 optimal weight: 4.9990 chunk 633 optimal weight: 7.9990 chunk 684 optimal weight: 5.9990 chunk 563 optimal weight: 8.9990 chunk 627 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 507 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 88 HIS B 241 GLN B 483 GLN C 169 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN D 88 HIS D 124 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 88 HIS F 124 GLN ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN H 59 HIS H 88 HIS ** H 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN I 421 GLN J 115 ASN J 241 GLN J 492 ASN K 140 HIS L 88 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 55188 Z= 0.413 Angle : 0.720 18.528 74640 Z= 0.379 Chirality : 0.050 0.266 8478 Planarity : 0.006 0.117 9738 Dihedral : 5.445 58.261 7746 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % Rotamer: Outliers : 2.58 % Allowed : 9.99 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.10), residues: 7026 helix: 0.34 (0.10), residues: 2544 sheet: 0.58 (0.13), residues: 1452 loop : -0.55 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP I 394 HIS 0.035 0.002 HIS H 88 PHE 0.033 0.003 PHE L 501 TYR 0.025 0.003 TYR F 435 ARG 0.011 0.001 ARG D 499 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 649 time to evaluate : 4.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 MET cc_start: 0.5134 (tpt) cc_final: 0.4690 (tpt) REVERT: A 191 THR cc_start: 0.5322 (OUTLIER) cc_final: 0.4821 (p) REVERT: A 334 THR cc_start: 0.7818 (m) cc_final: 0.7287 (t) REVERT: A 459 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7512 (tmt90) REVERT: A 466 MET cc_start: 0.8528 (tpp) cc_final: 0.7855 (tpp) REVERT: A 662 LEU cc_start: 0.7170 (mt) cc_final: 0.6478 (tt) REVERT: A 691 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7059 (tp30) REVERT: B 81 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.5490 (tp30) REVERT: C 179 GLU cc_start: 0.6962 (mp0) cc_final: 0.5396 (tp30) REVERT: C 316 MET cc_start: 0.2585 (mmp) cc_final: 0.2329 (mmt) REVERT: C 503 PHE cc_start: 0.6982 (t80) cc_final: 0.6214 (t80) REVERT: D 105 ASP cc_start: 0.8238 (t0) cc_final: 0.7869 (t0) REVERT: E 143 TYR cc_start: 0.6663 (p90) cc_final: 0.5807 (p90) REVERT: E 373 MET cc_start: 0.6987 (ttm) cc_final: 0.6728 (mtp) REVERT: E 466 MET cc_start: 0.7849 (tpp) cc_final: 0.7644 (tpt) REVERT: E 697 ASN cc_start: 0.6488 (m-40) cc_final: 0.5659 (p0) REVERT: F 146 ASP cc_start: 0.7440 (m-30) cc_final: 0.7088 (m-30) REVERT: F 172 SER cc_start: 0.8579 (p) cc_final: 0.8378 (t) REVERT: F 333 MET cc_start: 0.8081 (mtt) cc_final: 0.7792 (mtm) REVERT: G 350 MET cc_start: 0.6855 (tmm) cc_final: 0.6473 (tmm) REVERT: G 693 MET cc_start: 0.6676 (mtm) cc_final: 0.6161 (ttm) REVERT: H 216 MET cc_start: 0.8431 (ttm) cc_final: 0.8103 (mtp) REVERT: H 525 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8460 (tttt) REVERT: I 85 MET cc_start: 0.6459 (mtm) cc_final: 0.6021 (mtm) REVERT: I 156 LEU cc_start: 0.6768 (tp) cc_final: 0.6510 (pp) REVERT: I 350 MET cc_start: 0.8202 (tpt) cc_final: 0.7715 (tpt) REVERT: I 394 TRP cc_start: 0.6482 (OUTLIER) cc_final: 0.6197 (t-100) REVERT: K 177 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6706 (ttmt) REVERT: K 287 GLU cc_start: 0.6205 (pm20) cc_final: 0.5740 (pm20) REVERT: K 448 MET cc_start: 0.8712 (tpp) cc_final: 0.8143 (ttt) REVERT: L 160 ASP cc_start: 0.6669 (t0) cc_final: 0.6290 (p0) outliers start: 151 outliers final: 102 residues processed: 760 average time/residue: 0.5243 time to fit residues: 666.3683 Evaluate side-chains 642 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 534 time to evaluate : 4.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 459 ARG Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 625 MET Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain F residue 200 CYS Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 390 THR Chi-restraints excluded: chain F residue 463 MET Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 487 ILE Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 431 VAL Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 547 SER Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 627 ILE Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 224 PHE Chi-restraints excluded: chain H residue 291 CYS Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain H residue 525 LYS Chi-restraints excluded: chain I residue 65 LYS Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 161 VAL Chi-restraints excluded: chain I residue 287 GLU Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 394 TRP Chi-restraints excluded: chain I residue 454 THR Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 547 SER Chi-restraints excluded: chain I residue 613 THR Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 70 ILE Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 299 VAL Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 131 ILE Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 459 ARG Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 552 ILE Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 107 VAL Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 166 ILE Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 372 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 625 optimal weight: 0.3980 chunk 476 optimal weight: 0.3980 chunk 328 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 302 optimal weight: 0.6980 chunk 425 optimal weight: 1.9990 chunk 635 optimal weight: 1.9990 chunk 672 optimal weight: 1.9990 chunk 331 optimal weight: 2.9990 chunk 602 optimal weight: 0.9990 chunk 181 optimal weight: 7.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 GLN E 190 ASN E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN I 351 ASN K 355 GLN ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 55188 Z= 0.167 Angle : 0.573 16.744 74640 Z= 0.299 Chirality : 0.044 0.201 8478 Planarity : 0.004 0.104 9738 Dihedral : 4.916 53.696 7734 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.58 % Favored : 97.25 % Rotamer: Outliers : 1.97 % Allowed : 11.21 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.10), residues: 7026 helix: 0.77 (0.10), residues: 2526 sheet: 0.40 (0.13), residues: 1512 loop : -0.38 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP E 284 HIS 0.012 0.001 HIS G 358 PHE 0.021 0.001 PHE C 152 TYR 0.017 0.001 TYR J 222 ARG 0.008 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 598 time to evaluate : 5.135 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: A 135 ARG cc_start: 0.7942 (mmm160) cc_final: 0.7671 (mmp80) REVERT: A 334 THR cc_start: 0.7822 (m) cc_final: 0.7249 (t) REVERT: A 662 LEU cc_start: 0.7155 (mt) cc_final: 0.6422 (tt) REVERT: A 666 MET cc_start: 0.6395 (ppp) cc_final: 0.6016 (ppp) REVERT: A 691 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7071 (tp30) REVERT: A 699 MET cc_start: 0.6365 (mmt) cc_final: 0.5856 (mmt) REVERT: B 84 MET cc_start: 0.7117 (ttp) cc_final: 0.6876 (ttp) REVERT: C 68 VAL cc_start: 0.8475 (t) cc_final: 0.8199 (p) REVERT: C 179 GLU cc_start: 0.6909 (mp0) cc_final: 0.5492 (tm-30) REVERT: C 316 MET cc_start: 0.2560 (mmp) cc_final: 0.2289 (mmt) REVERT: D 105 ASP cc_start: 0.8155 (t0) cc_final: 0.7896 (t0) REVERT: E 143 TYR cc_start: 0.6656 (p90) cc_final: 0.5803 (p90) REVERT: E 373 MET cc_start: 0.7020 (ttm) cc_final: 0.6625 (mtp) REVERT: E 697 ASN cc_start: 0.6459 (m-40) cc_final: 0.5686 (p0) REVERT: E 699 MET cc_start: 0.3918 (tmm) cc_final: 0.3336 (ttt) REVERT: F 146 ASP cc_start: 0.7345 (m-30) cc_final: 0.6972 (m-30) REVERT: F 333 MET cc_start: 0.7984 (mtt) cc_final: 0.7688 (mtt) REVERT: G 268 ARG cc_start: 0.4594 (mpt180) cc_final: 0.4339 (mpt180) REVERT: G 316 MET cc_start: 0.5222 (mmm) cc_final: 0.4755 (mmm) REVERT: G 350 MET cc_start: 0.6888 (tmm) cc_final: 0.6436 (tmm) REVERT: G 693 MET cc_start: 0.6654 (mtm) cc_final: 0.6161 (ttm) REVERT: I 85 MET cc_start: 0.6656 (mtm) cc_final: 0.6334 (mtm) REVERT: I 270 ILE cc_start: 0.5315 (OUTLIER) cc_final: 0.4960 (pt) REVERT: I 350 MET cc_start: 0.8141 (tpt) cc_final: 0.7675 (tpt) REVERT: K 71 ARG cc_start: 0.6183 (ptm160) cc_final: 0.5973 (ptt180) REVERT: K 177 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6714 (ttmt) REVERT: K 650 MET cc_start: 0.9140 (mmt) cc_final: 0.8852 (mmm) outliers start: 115 outliers final: 68 residues processed: 674 average time/residue: 0.5307 time to fit residues: 604.6817 Evaluate side-chains 595 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 525 time to evaluate : 4.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 642 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 699 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 64 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 471 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 560 optimal weight: 5.9990 chunk 381 optimal weight: 20.0000 chunk 9 optimal weight: 1.9990 chunk 500 optimal weight: 3.9990 chunk 277 optimal weight: 8.9990 chunk 574 optimal weight: 0.9990 chunk 465 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 343 optimal weight: 0.9980 chunk 603 optimal weight: 9.9990 chunk 169 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS E 190 ASN E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN I 140 HIS J 241 GLN J 483 GLN ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 55188 Z= 0.244 Angle : 0.580 17.843 74640 Z= 0.302 Chirality : 0.045 0.203 8478 Planarity : 0.005 0.103 9738 Dihedral : 4.774 59.974 7722 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.22 % Favored : 96.61 % Rotamer: Outliers : 2.24 % Allowed : 11.48 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7026 helix: 0.80 (0.10), residues: 2538 sheet: 0.39 (0.13), residues: 1548 loop : -0.48 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 284 HIS 0.028 0.001 HIS E 269 PHE 0.018 0.002 PHE L 501 TYR 0.023 0.001 TYR H 417 ARG 0.007 0.000 ARG I 399 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 553 time to evaluate : 4.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7495 (ttp80) REVERT: A 334 THR cc_start: 0.7936 (m) cc_final: 0.7327 (t) REVERT: A 662 LEU cc_start: 0.7072 (mt) cc_final: 0.6272 (tt) REVERT: A 691 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.7079 (tp30) REVERT: A 699 MET cc_start: 0.6563 (mmt) cc_final: 0.6147 (mmt) REVERT: B 81 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5495 (tp30) REVERT: C 179 GLU cc_start: 0.6832 (mp0) cc_final: 0.5333 (tm-30) REVERT: C 316 MET cc_start: 0.2604 (mmp) cc_final: 0.2284 (mmt) REVERT: D 105 ASP cc_start: 0.8234 (t0) cc_final: 0.7870 (t0) REVERT: E 143 TYR cc_start: 0.6724 (p90) cc_final: 0.5887 (p90) REVERT: E 369 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7878 (tt) REVERT: E 373 MET cc_start: 0.7053 (ttm) cc_final: 0.6620 (mtp) REVERT: E 697 ASN cc_start: 0.6490 (m-40) cc_final: 0.5688 (p0) REVERT: E 699 MET cc_start: 0.4060 (tmm) cc_final: 0.3501 (ttt) REVERT: F 146 ASP cc_start: 0.7397 (m-30) cc_final: 0.7018 (m-30) REVERT: F 333 MET cc_start: 0.8034 (mtt) cc_final: 0.7761 (mtt) REVERT: G 316 MET cc_start: 0.5615 (mmm) cc_final: 0.4956 (mmm) REVERT: G 350 MET cc_start: 0.7116 (tmm) cc_final: 0.6526 (tmm) REVERT: G 430 ARG cc_start: 0.5666 (ptm160) cc_final: 0.5369 (ptm160) REVERT: G 473 TYR cc_start: 0.6977 (OUTLIER) cc_final: 0.5077 (t80) REVERT: G 693 MET cc_start: 0.6658 (mtm) cc_final: 0.6133 (ttp) REVERT: I 85 MET cc_start: 0.6656 (mtm) cc_final: 0.6407 (mtm) REVERT: I 270 ILE cc_start: 0.5384 (OUTLIER) cc_final: 0.4963 (pt) REVERT: I 350 MET cc_start: 0.8234 (tpt) cc_final: 0.7752 (tpt) REVERT: I 394 TRP cc_start: 0.6695 (t-100) cc_final: 0.6191 (t-100) REVERT: I 695 MET cc_start: 0.6377 (tpp) cc_final: 0.5774 (tpp) REVERT: K 71 ARG cc_start: 0.6255 (ptm160) cc_final: 0.6054 (ptt180) REVERT: K 287 GLU cc_start: 0.6291 (pm20) cc_final: 0.5835 (pm20) REVERT: K 650 MET cc_start: 0.9169 (mmt) cc_final: 0.8933 (mmm) outliers start: 131 outliers final: 94 residues processed: 647 average time/residue: 0.5215 time to fit residues: 571.8862 Evaluate side-chains 605 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 506 time to evaluate : 4.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 190 ASN Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 618 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 304 THR Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 515 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 699 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain H residue 504 ASP Chi-restraints excluded: chain I residue 70 ASN Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 299 VAL Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 636 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 428 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 226 optimal weight: 8.9990 chunk 605 optimal weight: 7.9990 chunk 132 optimal weight: 0.0980 chunk 394 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 673 optimal weight: 0.8980 chunk 559 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 222 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 507 GLN J 147 GLN ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 55188 Z= 0.176 Angle : 0.548 17.333 74640 Z= 0.285 Chirality : 0.044 0.211 8478 Planarity : 0.004 0.102 9738 Dihedral : 4.659 58.892 7722 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.79 % Favored : 97.05 % Rotamer: Outliers : 1.93 % Allowed : 12.00 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.10), residues: 7026 helix: 0.99 (0.11), residues: 2526 sheet: 0.39 (0.13), residues: 1512 loop : -0.43 (0.11), residues: 2988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 284 HIS 0.010 0.001 HIS E 358 PHE 0.026 0.001 PHE E 345 TYR 0.017 0.001 TYR H 417 ARG 0.008 0.000 ARG C 476 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 558 time to evaluate : 4.792 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: A 135 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7540 (ttp80) REVERT: A 334 THR cc_start: 0.7944 (m) cc_final: 0.7312 (t) REVERT: A 662 LEU cc_start: 0.7058 (mt) cc_final: 0.6261 (tt) REVERT: A 666 MET cc_start: 0.6522 (ppp) cc_final: 0.6303 (ppp) REVERT: B 81 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5216 (tp30) REVERT: C 89 THR cc_start: 0.5092 (OUTLIER) cc_final: 0.4691 (p) REVERT: C 179 GLU cc_start: 0.6999 (mp0) cc_final: 0.5522 (tm-30) REVERT: C 316 MET cc_start: 0.2510 (mmp) cc_final: 0.2221 (mmt) REVERT: C 397 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5860 (tt0) REVERT: D 105 ASP cc_start: 0.8188 (t0) cc_final: 0.7936 (t0) REVERT: E 143 TYR cc_start: 0.6626 (p90) cc_final: 0.5747 (p90) REVERT: E 174 MET cc_start: 0.8132 (mpp) cc_final: 0.7925 (mpp) REVERT: E 369 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7907 (tt) REVERT: E 373 MET cc_start: 0.7090 (ttm) cc_final: 0.6687 (mtp) REVERT: E 697 ASN cc_start: 0.6520 (m-40) cc_final: 0.5724 (p0) REVERT: E 699 MET cc_start: 0.4130 (tmm) cc_final: 0.3691 (ttt) REVERT: F 145 MET cc_start: 0.8725 (mtm) cc_final: 0.8416 (mtm) REVERT: F 146 ASP cc_start: 0.7339 (m-30) cc_final: 0.7010 (m-30) REVERT: G 316 MET cc_start: 0.5425 (mmm) cc_final: 0.4752 (mmm) REVERT: G 350 MET cc_start: 0.7370 (tmm) cc_final: 0.6586 (tmm) REVERT: G 367 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6909 (pp) REVERT: G 430 ARG cc_start: 0.5704 (ptm160) cc_final: 0.5446 (ptm160) REVERT: G 473 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.5088 (t80) REVERT: G 693 MET cc_start: 0.6672 (mtm) cc_final: 0.6249 (mtp) REVERT: I 174 MET cc_start: 0.5540 (mpp) cc_final: 0.5309 (mmt) REVERT: I 270 ILE cc_start: 0.5345 (OUTLIER) cc_final: 0.4913 (pt) REVERT: I 350 MET cc_start: 0.8220 (tpt) cc_final: 0.7691 (tpt) REVERT: I 394 TRP cc_start: 0.6563 (OUTLIER) cc_final: 0.6177 (t-100) REVERT: I 496 LYS cc_start: 0.6174 (mmmt) cc_final: 0.5896 (mttm) REVERT: I 695 MET cc_start: 0.6420 (tpp) cc_final: 0.5849 (tpp) REVERT: K 85 MET cc_start: 0.7470 (mtm) cc_final: 0.7206 (mtm) REVERT: K 336 GLU cc_start: 0.6488 (OUTLIER) cc_final: 0.6113 (pt0) REVERT: K 611 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7458 (tp40) REVERT: K 650 MET cc_start: 0.9164 (mmt) cc_final: 0.8914 (mmm) outliers start: 113 outliers final: 83 residues processed: 631 average time/residue: 0.5162 time to fit residues: 551.7889 Evaluate side-chains 608 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 516 time to evaluate : 4.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 602 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 269 HIS Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 425 HIS Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 699 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 394 TRP Chi-restraints excluded: chain I residue 432 ASP Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 428 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 649 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 383 optimal weight: 4.9990 chunk 491 optimal weight: 20.0000 chunk 381 optimal weight: 5.9990 chunk 566 optimal weight: 6.9990 chunk 376 optimal weight: 5.9990 chunk 670 optimal weight: 0.9980 chunk 419 optimal weight: 4.9990 chunk 408 optimal weight: 20.0000 chunk 309 optimal weight: 0.6980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 ASN C 169 HIS C 279 HIS C 371 GLN ** D 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 358 HIS G 102 HIS I 355 GLN ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 55188 Z= 0.310 Angle : 0.615 18.039 74640 Z= 0.319 Chirality : 0.046 0.201 8478 Planarity : 0.005 0.099 9738 Dihedral : 4.888 58.681 7722 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.71 % Favored : 96.16 % Rotamer: Outliers : 2.24 % Allowed : 12.22 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.10), residues: 7026 helix: 0.84 (0.11), residues: 2532 sheet: 0.28 (0.13), residues: 1560 loop : -0.62 (0.12), residues: 2934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E 284 HIS 0.023 0.002 HIS E 269 PHE 0.021 0.002 PHE L 501 TYR 0.016 0.002 TYR F 435 ARG 0.016 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 535 time to evaluate : 4.832 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: A 135 ARG cc_start: 0.8075 (mmm160) cc_final: 0.7548 (ttp80) REVERT: A 334 THR cc_start: 0.7981 (m) cc_final: 0.7349 (t) REVERT: A 662 LEU cc_start: 0.6896 (mt) cc_final: 0.6077 (tt) REVERT: B 81 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5459 (tp30) REVERT: C 89 THR cc_start: 0.5317 (OUTLIER) cc_final: 0.4891 (p) REVERT: C 179 GLU cc_start: 0.6981 (mp0) cc_final: 0.5414 (tm-30) REVERT: C 316 MET cc_start: 0.2461 (mmp) cc_final: 0.2225 (mmt) REVERT: C 397 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5992 (tt0) REVERT: E 143 TYR cc_start: 0.6639 (p90) cc_final: 0.5721 (p90) REVERT: E 269 HIS cc_start: 0.7062 (t70) cc_final: 0.6063 (m-70) REVERT: E 353 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5728 (ptp90) REVERT: E 369 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7982 (tt) REVERT: E 373 MET cc_start: 0.7037 (ttm) cc_final: 0.6651 (mtp) REVERT: E 448 MET cc_start: 0.8520 (tpt) cc_final: 0.7918 (tpt) REVERT: E 697 ASN cc_start: 0.6549 (m-40) cc_final: 0.5764 (p0) REVERT: E 699 MET cc_start: 0.4115 (tmm) cc_final: 0.3690 (ttt) REVERT: F 146 ASP cc_start: 0.7365 (m-30) cc_final: 0.6868 (m-30) REVERT: G 316 MET cc_start: 0.5516 (mmm) cc_final: 0.4830 (mmm) REVERT: G 336 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: G 350 MET cc_start: 0.7237 (tmm) cc_final: 0.6406 (tpp) REVERT: G 430 ARG cc_start: 0.5845 (ptm160) cc_final: 0.5585 (ptm160) REVERT: G 473 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.5077 (t80) REVERT: G 693 MET cc_start: 0.6709 (mtm) cc_final: 0.6300 (mtp) REVERT: H 95 MET cc_start: 0.7875 (mmp) cc_final: 0.7619 (mmt) REVERT: I 270 ILE cc_start: 0.5431 (OUTLIER) cc_final: 0.4787 (pt) REVERT: I 350 MET cc_start: 0.8210 (tpt) cc_final: 0.7633 (tpt) REVERT: I 486 ARG cc_start: 0.7798 (tpt90) cc_final: 0.7589 (ttt-90) REVERT: I 496 LYS cc_start: 0.6259 (mmmt) cc_final: 0.5961 (mttm) REVERT: K 85 MET cc_start: 0.7493 (mtm) cc_final: 0.7226 (mtm) REVERT: K 336 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5948 (mm-30) REVERT: K 650 MET cc_start: 0.9193 (mmt) cc_final: 0.8985 (mmm) outliers start: 131 outliers final: 101 residues processed: 626 average time/residue: 0.5115 time to fit residues: 543.3766 Evaluate side-chains 605 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 495 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 517 CYS Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 178 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 353 ARG Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 425 HIS Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 618 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 627 ILE Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain H residue 504 ASP Chi-restraints excluded: chain H residue 511 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 432 ASP Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 613 THR Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 451 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 415 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 400 optimal weight: 8.9990 chunk 202 optimal weight: 0.0040 chunk 131 optimal weight: 0.7980 chunk 129 optimal weight: 7.9990 chunk 426 optimal weight: 3.9990 chunk 457 optimal weight: 3.9990 chunk 331 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 527 optimal weight: 8.9990 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 ASN C 169 HIS D 58 GLN D 263 ASN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 55188 Z= 0.217 Angle : 0.567 20.441 74640 Z= 0.293 Chirality : 0.044 0.186 8478 Planarity : 0.004 0.094 9738 Dihedral : 4.751 59.812 7722 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.06 % Favored : 96.81 % Rotamer: Outliers : 2.10 % Allowed : 12.80 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.10), residues: 7026 helix: 1.03 (0.11), residues: 2526 sheet: 0.27 (0.13), residues: 1560 loop : -0.59 (0.12), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 284 HIS 0.009 0.001 HIS G 358 PHE 0.022 0.001 PHE E 503 TYR 0.013 0.001 TYR G 401 ARG 0.006 0.000 ARG H 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 537 time to evaluate : 4.874 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: A 135 ARG cc_start: 0.8035 (mmm160) cc_final: 0.7543 (ttp80) REVERT: A 334 THR cc_start: 0.7981 (m) cc_final: 0.7333 (t) REVERT: A 650 MET cc_start: 0.8832 (mmp) cc_final: 0.8048 (mmp) REVERT: A 662 LEU cc_start: 0.6841 (mt) cc_final: 0.6057 (tt) REVERT: B 81 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5259 (tp30) REVERT: C 89 THR cc_start: 0.5216 (OUTLIER) cc_final: 0.4799 (p) REVERT: C 179 GLU cc_start: 0.6921 (mp0) cc_final: 0.5352 (tm-30) REVERT: C 397 GLU cc_start: 0.6389 (OUTLIER) cc_final: 0.5891 (tt0) REVERT: C 420 TYR cc_start: 0.6565 (t80) cc_final: 0.6151 (t80) REVERT: E 143 TYR cc_start: 0.6622 (p90) cc_final: 0.5763 (p90) REVERT: E 174 MET cc_start: 0.8302 (mpp) cc_final: 0.8088 (mpp) REVERT: E 369 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8057 (tt) REVERT: E 373 MET cc_start: 0.7038 (ttm) cc_final: 0.6683 (mtp) REVERT: E 427 PRO cc_start: 0.6809 (Cg_endo) cc_final: 0.6604 (Cg_exo) REVERT: E 448 MET cc_start: 0.8498 (tpt) cc_final: 0.7877 (tpt) REVERT: E 697 ASN cc_start: 0.6577 (m-40) cc_final: 0.5842 (p0) REVERT: E 699 MET cc_start: 0.4343 (tmm) cc_final: 0.4044 (ttt) REVERT: F 145 MET cc_start: 0.8739 (mtm) cc_final: 0.8419 (mtm) REVERT: F 146 ASP cc_start: 0.7352 (m-30) cc_final: 0.6836 (m-30) REVERT: G 316 MET cc_start: 0.5739 (mmm) cc_final: 0.5084 (mmm) REVERT: G 336 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6739 (pm20) REVERT: G 350 MET cc_start: 0.7240 (tmm) cc_final: 0.6843 (tmm) REVERT: G 430 ARG cc_start: 0.5745 (ptm160) cc_final: 0.5542 (ptm160) REVERT: G 473 TYR cc_start: 0.6985 (OUTLIER) cc_final: 0.5161 (t80) REVERT: G 693 MET cc_start: 0.6586 (mtm) cc_final: 0.6274 (mtp) REVERT: H 187 SER cc_start: 0.8997 (t) cc_final: 0.8520 (p) REVERT: I 270 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4814 (pt) REVERT: I 350 MET cc_start: 0.8171 (tpt) cc_final: 0.7572 (tpt) REVERT: I 690 ILE cc_start: 0.7497 (OUTLIER) cc_final: 0.7216 (pt) REVERT: I 726 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.3606 (tp30) REVERT: I 727 LEU cc_start: 0.5845 (tp) cc_final: 0.5321 (tp) REVERT: K 85 MET cc_start: 0.7502 (mtm) cc_final: 0.7274 (mtm) REVERT: K 287 GLU cc_start: 0.6362 (pm20) cc_final: 0.5763 (pm20) REVERT: K 336 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.6284 (pt0) REVERT: K 391 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7824 (mt) REVERT: K 650 MET cc_start: 0.9180 (mmt) cc_final: 0.8971 (mmm) outliers start: 123 outliers final: 98 residues processed: 620 average time/residue: 0.5165 time to fit residues: 547.5141 Evaluate side-chains 605 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 496 time to evaluate : 5.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 273 GLN Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 521 GLU Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 618 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 432 ASP Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 547 SER Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 690 ILE Chi-restraints excluded: chain I residue 693 MET Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 726 GLU Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 435 ILE Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 428 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 610 optimal weight: 3.9990 chunk 642 optimal weight: 1.9990 chunk 586 optimal weight: 0.9980 chunk 625 optimal weight: 0.1980 chunk 376 optimal weight: 0.9980 chunk 272 optimal weight: 0.8980 chunk 490 optimal weight: 8.9990 chunk 191 optimal weight: 3.9990 chunk 564 optimal weight: 2.9990 chunk 591 optimal weight: 0.1980 chunk 622 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS D 58 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 55188 Z= 0.152 Angle : 0.550 20.415 74640 Z= 0.282 Chirality : 0.043 0.185 8478 Planarity : 0.004 0.103 9738 Dihedral : 4.599 59.704 7722 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.51 % Rotamer: Outliers : 1.68 % Allowed : 13.42 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.10), residues: 7026 helix: 1.21 (0.11), residues: 2526 sheet: 0.25 (0.13), residues: 1536 loop : -0.48 (0.12), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP E 284 HIS 0.010 0.001 HIS C 358 PHE 0.018 0.001 PHE K 307 TYR 0.033 0.001 TYR G 401 ARG 0.014 0.000 ARG I 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 558 time to evaluate : 5.052 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: A 135 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7544 (ttp80) REVERT: A 334 THR cc_start: 0.7997 (m) cc_final: 0.7322 (t) REVERT: A 466 MET cc_start: 0.8393 (tpp) cc_final: 0.7640 (tpp) REVERT: A 650 MET cc_start: 0.8790 (mmp) cc_final: 0.7988 (mmp) REVERT: A 662 LEU cc_start: 0.6947 (mt) cc_final: 0.6141 (tt) REVERT: A 696 GLN cc_start: 0.7324 (mp10) cc_final: 0.7017 (mp10) REVERT: B 81 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5190 (tp30) REVERT: C 89 THR cc_start: 0.5271 (OUTLIER) cc_final: 0.4837 (p) REVERT: C 125 ASP cc_start: 0.7126 (t0) cc_final: 0.6903 (t0) REVERT: C 420 TYR cc_start: 0.6457 (t80) cc_final: 0.6062 (t80) REVERT: E 143 TYR cc_start: 0.6604 (p90) cc_final: 0.5792 (p90) REVERT: E 174 MET cc_start: 0.8307 (mpp) cc_final: 0.8063 (mpp) REVERT: E 369 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (tt) REVERT: E 373 MET cc_start: 0.7098 (ttm) cc_final: 0.6719 (mtp) REVERT: E 448 MET cc_start: 0.8522 (tpt) cc_final: 0.7944 (tpt) REVERT: E 697 ASN cc_start: 0.6403 (m-40) cc_final: 0.5656 (p0) REVERT: E 699 MET cc_start: 0.4332 (tmm) cc_final: 0.4026 (ttt) REVERT: F 146 ASP cc_start: 0.7307 (m-30) cc_final: 0.6972 (m-30) REVERT: G 316 MET cc_start: 0.5912 (mmm) cc_final: 0.5258 (mmm) REVERT: G 336 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6645 (pm20) REVERT: G 350 MET cc_start: 0.7279 (tmm) cc_final: 0.6874 (tmm) REVERT: G 451 LYS cc_start: 0.6852 (mmmm) cc_final: 0.6350 (mmtt) REVERT: G 473 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5081 (t80) REVERT: G 693 MET cc_start: 0.6548 (mtm) cc_final: 0.6209 (mtp) REVERT: I 128 MET cc_start: 0.5166 (OUTLIER) cc_final: 0.4106 (ttt) REVERT: I 350 MET cc_start: 0.8221 (tpt) cc_final: 0.7672 (tpt) REVERT: I 397 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: I 690 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7142 (pt) REVERT: K 85 MET cc_start: 0.7443 (mtm) cc_final: 0.7231 (mtm) REVERT: K 287 GLU cc_start: 0.6538 (pm20) cc_final: 0.6006 (pm20) REVERT: K 336 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.6307 (pt0) REVERT: K 391 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7741 (mt) REVERT: K 650 MET cc_start: 0.9168 (mmt) cc_final: 0.8933 (mmm) outliers start: 98 outliers final: 79 residues processed: 619 average time/residue: 0.5545 time to fit residues: 587.4637 Evaluate side-chains 605 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 516 time to evaluate : 4.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 295 SER Chi-restraints excluded: chain D residue 354 ILE Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 425 HIS Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 618 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 335 VAL Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 501 THR Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain G residue 699 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 128 MET Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 432 ASP Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 690 ILE Chi-restraints excluded: chain I residue 693 MET Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 428 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 410 optimal weight: 0.3980 chunk 661 optimal weight: 1.9990 chunk 403 optimal weight: 1.9990 chunk 313 optimal weight: 4.9990 chunk 459 optimal weight: 2.9990 chunk 693 optimal weight: 2.9990 chunk 638 optimal weight: 3.9990 chunk 552 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 426 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS D 58 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 55188 Z= 0.252 Angle : 0.592 21.202 74640 Z= 0.304 Chirality : 0.045 0.228 8478 Planarity : 0.005 0.101 9738 Dihedral : 4.661 55.074 7722 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.54 % Favored : 96.36 % Rotamer: Outliers : 1.69 % Allowed : 13.54 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7026 helix: 1.11 (0.11), residues: 2538 sheet: 0.26 (0.13), residues: 1566 loop : -0.61 (0.12), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 284 HIS 0.009 0.001 HIS I 358 PHE 0.020 0.002 PHE E 337 TYR 0.014 0.001 TYR G 401 ARG 0.010 0.000 ARG H 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14052 Ramachandran restraints generated. 7026 Oldfield, 0 Emsley, 7026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 515 time to evaluate : 4.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8036 (mmm160) cc_final: 0.7552 (ttp80) REVERT: A 334 THR cc_start: 0.7989 (m) cc_final: 0.7325 (t) REVERT: A 650 MET cc_start: 0.8845 (mmp) cc_final: 0.8066 (mmp) REVERT: A 662 LEU cc_start: 0.6858 (mt) cc_final: 0.6050 (tt) REVERT: A 696 GLN cc_start: 0.7359 (mp10) cc_final: 0.7089 (mp10) REVERT: B 81 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5174 (tp30) REVERT: C 89 THR cc_start: 0.5293 (OUTLIER) cc_final: 0.4863 (p) REVERT: C 179 GLU cc_start: 0.6714 (mp0) cc_final: 0.5038 (tm-30) REVERT: C 420 TYR cc_start: 0.6606 (t80) cc_final: 0.6198 (t80) REVERT: C 466 MET cc_start: 0.6468 (tpp) cc_final: 0.6170 (tpp) REVERT: E 143 TYR cc_start: 0.6611 (p90) cc_final: 0.5765 (p90) REVERT: E 174 MET cc_start: 0.8312 (mpp) cc_final: 0.8101 (mpp) REVERT: E 271 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6235 (mt-10) REVERT: E 369 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8064 (tt) REVERT: E 373 MET cc_start: 0.7116 (ttm) cc_final: 0.6710 (mtp) REVERT: E 697 ASN cc_start: 0.6521 (m-40) cc_final: 0.5754 (p0) REVERT: E 699 MET cc_start: 0.4418 (tmm) cc_final: 0.4157 (ttt) REVERT: F 145 MET cc_start: 0.8754 (mtm) cc_final: 0.8398 (mtm) REVERT: F 146 ASP cc_start: 0.7344 (m-30) cc_final: 0.6861 (m-30) REVERT: G 316 MET cc_start: 0.5942 (mmm) cc_final: 0.5263 (mmm) REVERT: G 336 GLU cc_start: 0.7547 (OUTLIER) cc_final: 0.6673 (pm20) REVERT: G 350 MET cc_start: 0.7247 (tmm) cc_final: 0.6842 (tmm) REVERT: G 451 LYS cc_start: 0.6891 (mmmm) cc_final: 0.5989 (mmmt) REVERT: G 473 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5213 (t80) REVERT: G 693 MET cc_start: 0.6531 (mtm) cc_final: 0.6221 (mtp) REVERT: H 187 SER cc_start: 0.9002 (t) cc_final: 0.8477 (p) REVERT: I 350 MET cc_start: 0.8257 (tpt) cc_final: 0.7656 (tpt) REVERT: I 397 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6861 (tm-30) REVERT: I 448 MET cc_start: 0.7390 (tpp) cc_final: 0.6716 (ttt) REVERT: I 449 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8266 (mp) REVERT: I 690 ILE cc_start: 0.7419 (OUTLIER) cc_final: 0.7145 (pt) REVERT: K 85 MET cc_start: 0.7447 (mtm) cc_final: 0.7237 (mtm) REVERT: K 287 GLU cc_start: 0.6526 (pm20) cc_final: 0.6009 (pm20) REVERT: K 336 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6305 (pt0) REVERT: K 345 PHE cc_start: 0.7633 (p90) cc_final: 0.7385 (p90) REVERT: K 391 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7736 (mt) REVERT: K 650 MET cc_start: 0.9174 (mmt) cc_final: 0.8962 (mmm) outliers start: 99 outliers final: 80 residues processed: 582 average time/residue: 0.5156 time to fit residues: 514.0537 Evaluate side-chains 582 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 492 time to evaluate : 4.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 241 GLN Chi-restraints excluded: chain D residue 291 CYS Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 369 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 425 HIS Chi-restraints excluded: chain E residue 565 LEU Chi-restraints excluded: chain E residue 602 LEU Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 618 SER Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain F residue 147 GLN Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 146 LEU Chi-restraints excluded: chain G residue 323 LEU Chi-restraints excluded: chain G residue 336 GLU Chi-restraints excluded: chain G residue 345 PHE Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 565 LEU Chi-restraints excluded: chain G residue 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 128 MET Chi-restraints excluded: chain I residue 191 THR Chi-restraints excluded: chain I residue 216 VAL Chi-restraints excluded: chain I residue 302 GLU Chi-restraints excluded: chain I residue 369 LEU Chi-restraints excluded: chain I residue 376 VAL Chi-restraints excluded: chain I residue 397 GLU Chi-restraints excluded: chain I residue 432 ASP Chi-restraints excluded: chain I residue 449 ILE Chi-restraints excluded: chain I residue 478 VAL Chi-restraints excluded: chain I residue 528 ILE Chi-restraints excluded: chain I residue 566 HIS Chi-restraints excluded: chain I residue 580 VAL Chi-restraints excluded: chain I residue 613 THR Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain I residue 690 ILE Chi-restraints excluded: chain I residue 693 MET Chi-restraints excluded: chain I residue 696 GLN Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 185 LYS Chi-restraints excluded: chain K residue 290 CYS Chi-restraints excluded: chain K residue 321 VAL Chi-restraints excluded: chain K residue 336 GLU Chi-restraints excluded: chain K residue 391 ILE Chi-restraints excluded: chain K residue 414 ILE Chi-restraints excluded: chain K residue 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 580 VAL Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 149 ILE Chi-restraints excluded: chain L residue 197 MET Chi-restraints excluded: chain L residue 281 SER Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 316 MET Chi-restraints excluded: chain L residue 428 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 438 optimal weight: 1.9990 chunk 588 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 509 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 553 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 567 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 101 optimal weight: 0.0670 overall best weight: 0.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS D 58 GLN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 713 GLN ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.162389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.119377 restraints weight = 102972.509| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.34 r_work: 0.3544 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 55188 Z= 0.159 Angle : 0.557 21.135 74640 Z= 0.284 Chirality : 0.044 0.186 8478 Planarity : 0.004 0.103 9738 Dihedral : 4.548 54.823 7722 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.34 % Favored : 96.57 % Rotamer: Outliers : 1.63 % Allowed : 13.72 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.10), residues: 7026 helix: 1.27 (0.11), residues: 2526 sheet: 0.27 (0.13), residues: 1524 loop : -0.52 (0.12), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 284 HIS 0.008 0.001 HIS C 358 PHE 0.027 0.001 PHE I 152 TYR 0.021 0.001 TYR G 401 ARG 0.010 0.000 ARG H 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13123.12 seconds wall clock time: 230 minutes 19.10 seconds (13819.10 seconds total)