Starting phenix.real_space_refine on Thu Jan 16 21:45:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl3_38436/01_2025/8xl3_38436.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl3_38436/01_2025/8xl3_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_38436/01_2025/8xl3_38436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl3_38436/01_2025/8xl3_38436.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl3_38436/01_2025/8xl3_38436.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl3_38436/01_2025/8xl3_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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 23.01, per 1000 atoms: 0.42 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: 10.71 Conformation dependent library (CDL) restraints added in 5.7 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: 6.56 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: 27.13 Time building geometry restraints manager: 12.62 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: 0.34 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: 6.040 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: 0.060 Extract box with map and model: 1.860 Check model and map are aligned: 0.310 Set scattering table: 0.400 Process input model: 104.120 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.590 ------------------------------------------------------------------------------- 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 : 4.851 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: 0.6076 time to fit residues: 1564.7255 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 : 5.730 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.173279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.131313 restraints weight = 104660.428| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.45 r_work: 0.3700 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 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 : 4.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ARG cc_start: 0.6535 (mtm180) cc_final: 0.6308 (mtm180) REVERT: A 334 THR cc_start: 0.8686 (m) cc_final: 0.7735 (t) REVERT: A 382 LEU cc_start: 0.8066 (mt) cc_final: 0.7555 (mp) REVERT: A 403 GLU cc_start: 0.7570 (pt0) cc_final: 0.7260 (mt-10) REVERT: A 466 MET cc_start: 0.8740 (tpp) cc_final: 0.8000 (tpp) REVERT: A 662 LEU cc_start: 0.7026 (mt) cc_final: 0.6375 (tt) REVERT: A 696 GLN cc_start: 0.7756 (mt0) cc_final: 0.7102 (mp10) REVERT: B 253 MET cc_start: 0.8323 (ttt) cc_final: 0.8094 (ttm) REVERT: B 525 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.9013 (tttt) REVERT: C 68 VAL cc_start: 0.8403 (t) cc_final: 0.8091 (p) REVERT: C 84 LYS cc_start: 0.6909 (OUTLIER) cc_final: 0.6234 (tmtt) REVERT: C 179 GLU cc_start: 0.7298 (mp0) cc_final: 0.6050 (tm-30) REVERT: C 272 ILE cc_start: 0.7876 (mt) cc_final: 0.7474 (tt) REVERT: C 584 GLU cc_start: 0.7836 (tt0) cc_final: 0.7528 (tm-30) REVERT: D 40 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8658 (tm-30) REVERT: D 105 ASP cc_start: 0.8006 (t0) cc_final: 0.7467 (t0) REVERT: D 327 ARG cc_start: 0.7303 (ptm160) cc_final: 0.6993 (ttm110) REVERT: E 80 ARG cc_start: 0.8050 (ptp-110) cc_final: 0.7815 (ptm160) REVERT: E 143 TYR cc_start: 0.6148 (p90) cc_final: 0.5415 (p90) REVERT: E 295 ARG cc_start: 0.6930 (mmp80) cc_final: 0.6056 (ptp-170) REVERT: E 358 HIS cc_start: 0.6379 (p-80) cc_final: 0.6175 (p90) REVERT: E 502 LYS cc_start: 0.8067 (mmmm) cc_final: 0.7770 (mmmm) REVERT: E 693 MET cc_start: 0.6644 (mtt) cc_final: 0.6345 (mtp) REVERT: F 333 MET cc_start: 0.8678 (mtt) cc_final: 0.8447 (mtt) REVERT: F 525 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8436 (tttt) REVERT: G 89 THR cc_start: 0.7422 (m) cc_final: 0.6728 (p) REVERT: G 101 VAL cc_start: 0.7862 (t) cc_final: 0.7542 (m) REVERT: G 399 ARG cc_start: 0.7592 (mtm-85) cc_final: 0.6742 (ttp-170) REVERT: G 451 LYS cc_start: 0.7869 (pttt) cc_final: 0.7423 (pttt) REVERT: G 503 PHE cc_start: 0.6073 (t80) cc_final: 0.5852 (t80) REVERT: G 549 MET cc_start: 0.9086 (mmm) cc_final: 0.8798 (mmm) REVERT: G 652 GLU cc_start: 0.6882 (pp20) cc_final: 0.5943 (pm20) REVERT: G 696 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7237 (pt0) REVERT: H 178 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8322 (t0) REVERT: H 248 LYS cc_start: 0.8256 (mmtm) cc_final: 0.8012 (mmmt) REVERT: H 525 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8117 (tttt) REVERT: I 128 MET cc_start: 0.5695 (mtm) cc_final: 0.5379 (mtp) REVERT: I 156 LEU cc_start: 0.6407 (tp) cc_final: 0.5948 (pp) REVERT: I 449 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7817 (mp) REVERT: I 691 GLU cc_start: 0.8163 (pt0) cc_final: 0.7728 (mt-10) REVERT: I 695 MET cc_start: 0.6021 (tpp) cc_final: 0.5583 (tpp) REVERT: J 48 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7199 (mm) REVERT: J 89 ARG cc_start: 0.6855 (mtp85) cc_final: 0.6156 (mtt-85) REVERT: J 518 ASP cc_start: 0.8199 (m-30) cc_final: 0.7879 (m-30) REVERT: J 525 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8841 (tttt) REVERT: K 169 HIS cc_start: 0.8563 (t70) cc_final: 0.7494 (p90) REVERT: K 177 LYS cc_start: 0.7405 (mmtt) cc_final: 0.6824 (ttmt) REVERT: K 351 ASN cc_start: 0.6616 (m-40) cc_final: 0.6218 (m-40) REVERT: K 459 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6959 (ttt-90) outliers start: 112 outliers final: 56 residues processed: 897 average time/residue: 0.5490 time to fit residues: 817.3109 Evaluate side-chains 685 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 619 time to evaluate : 5.003 ------------------------------------------------------------------------------- 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 G residue 696 GLN 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 449 ILE Chi-restraints excluded: chain I residue 614 VAL Chi-restraints excluded: chain I residue 725 VAL Chi-restraints excluded: chain J residue 48 LEU 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 663 optimal weight: 1.9990 chunk 368 optimal weight: 20.0000 chunk 523 optimal weight: 0.1980 chunk 499 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 591 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 637 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** F 88 HIS ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN G 537 GLN G 696 GLN ** H 411 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN I 421 GLN J 41 ASN J 241 GLN J 492 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.163591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.119423 restraints weight = 104725.222| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.68 r_work: 0.3506 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.130 55188 Z= 0.350 Angle : 0.674 18.393 74640 Z= 0.353 Chirality : 0.048 0.249 8478 Planarity : 0.005 0.094 9738 Dihedral : 5.213 58.144 7746 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.00 % Favored : 96.83 % Rotamer: Outliers : 2.36 % Allowed : 9.92 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.10), residues: 7026 helix: 0.54 (0.10), residues: 2532 sheet: 0.38 (0.13), residues: 1566 loop : -0.39 (0.11), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP I 394 HIS 0.047 0.002 HIS H 88 PHE 0.028 0.002 PHE L 501 TYR 0.022 0.002 TYR L 277 ARG 0.012 0.001 ARG K 243 *********************** 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 795 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 657 time to evaluate : 4.923 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 174 MET cc_start: 0.5523 (tpt) cc_final: 0.5263 (tpt) REVERT: A 191 THR cc_start: 0.5428 (OUTLIER) cc_final: 0.4894 (p) REVERT: A 334 THR cc_start: 0.8475 (m) cc_final: 0.7997 (t) REVERT: A 382 LEU cc_start: 0.8036 (mt) cc_final: 0.7801 (mp) REVERT: A 459 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7680 (tmt90) REVERT: A 662 LEU cc_start: 0.7406 (mt) cc_final: 0.6628 (tt) REVERT: A 691 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7004 (tp30) REVERT: B 81 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6502 (tp30) REVERT: C 68 VAL cc_start: 0.8334 (t) cc_final: 0.8054 (p) REVERT: C 179 GLU cc_start: 0.7344 (mp0) cc_final: 0.5938 (tm-30) REVERT: C 271 GLU cc_start: 0.5536 (mt-10) cc_final: 0.5011 (pt0) REVERT: C 272 ILE cc_start: 0.7913 (mt) cc_final: 0.7651 (mt) REVERT: C 290 CYS cc_start: 0.7005 (m) cc_final: 0.6261 (m) REVERT: C 503 PHE cc_start: 0.6666 (t80) cc_final: 0.5720 (t80) REVERT: C 508 TYR cc_start: 0.5329 (m-80) cc_final: 0.5093 (m-10) REVERT: C 577 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8123 (t0) REVERT: C 584 GLU cc_start: 0.7893 (tt0) cc_final: 0.7614 (tm-30) REVERT: C 652 GLU cc_start: 0.6368 (pm20) cc_final: 0.6010 (pt0) REVERT: D 327 ARG cc_start: 0.7283 (ptm160) cc_final: 0.6996 (ttm110) REVERT: E 80 ARG cc_start: 0.8110 (ptp-110) cc_final: 0.7839 (ptt180) REVERT: E 143 TYR cc_start: 0.6569 (p90) cc_final: 0.5541 (p90) REVERT: E 373 MET cc_start: 0.6987 (ttm) cc_final: 0.6780 (mtp) REVERT: E 502 LYS cc_start: 0.8076 (mmmm) cc_final: 0.7705 (mmmm) REVERT: E 697 ASN cc_start: 0.7020 (m-40) cc_final: 0.6127 (p0) REVERT: F 146 ASP cc_start: 0.8423 (m-30) cc_final: 0.8053 (m-30) REVERT: F 333 MET cc_start: 0.8942 (mtt) cc_final: 0.8685 (mtt) REVERT: G 71 ARG cc_start: 0.5862 (OUTLIER) cc_final: 0.5287 (tmm-80) REVERT: G 101 VAL cc_start: 0.8049 (t) cc_final: 0.7747 (m) REVERT: G 124 MET cc_start: 0.7917 (tmm) cc_final: 0.7702 (tmm) REVERT: G 328 LYS cc_start: 0.5941 (mmtt) cc_final: 0.5586 (tptp) REVERT: G 350 MET cc_start: 0.6656 (tmm) cc_final: 0.6313 (tmm) REVERT: G 663 ARG cc_start: 0.5558 (mtt90) cc_final: 0.5298 (mtm180) REVERT: G 666 MET cc_start: 0.3950 (ttt) cc_final: 0.3608 (ttm) REVERT: G 693 MET cc_start: 0.7233 (mtm) cc_final: 0.5953 (ttm) REVERT: H 216 MET cc_start: 0.9090 (ttm) cc_final: 0.8849 (mtp) REVERT: I 65 LYS cc_start: 0.5429 (OUTLIER) cc_final: 0.5071 (ttpt) REVERT: I 156 LEU cc_start: 0.6539 (tp) cc_final: 0.6172 (pp) REVERT: I 350 MET cc_start: 0.7782 (tpt) cc_final: 0.7397 (tpt) REVERT: I 394 TRP cc_start: 0.6646 (t-100) cc_final: 0.5755 (t-100) REVERT: I 449 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7969 (mp) REVERT: I 695 MET cc_start: 0.6427 (tpp) cc_final: 0.5884 (tpp) REVERT: J 48 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7203 (mm) REVERT: J 488 GLU cc_start: 0.7999 (tp30) cc_final: 0.7417 (tm-30) REVERT: J 502 VAL cc_start: 0.8775 (t) cc_final: 0.8520 (m) REVERT: J 504 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8144 (t70) REVERT: K 177 LYS cc_start: 0.7448 (mmtt) cc_final: 0.6841 (ttmt) REVERT: K 287 GLU cc_start: 0.6909 (pm20) cc_final: 0.6490 (pm20) REVERT: L 160 ASP cc_start: 0.7222 (t0) cc_final: 0.6501 (p0) REVERT: L 292 HIS cc_start: 0.8489 (m170) cc_final: 0.8182 (m90) REVERT: L 303 ASP cc_start: 0.8590 (p0) cc_final: 0.8246 (m-30) REVERT: L 486 TYR cc_start: 0.8446 (t80) cc_final: 0.8220 (t80) outliers start: 138 outliers final: 87 residues processed: 761 average time/residue: 0.5321 time to fit residues: 676.5485 Evaluate side-chains 641 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 544 time to evaluate : 4.776 ------------------------------------------------------------------------------- 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 291 CYS Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 310 SER 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 577 ASN Chi-restraints excluded: chain C residue 602 LEU 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 310 SER 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 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 471 ILE Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 345 PHE 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 451 THR Chi-restraints excluded: chain H residue 511 THR 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 449 ILE Chi-restraints excluded: chain I residue 460 THR Chi-restraints excluded: chain I residue 478 VAL 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 48 LEU 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 J residue 504 ASP 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 499 ILE 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 471 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 603 optimal weight: 10.0000 chunk 691 optimal weight: 4.9990 chunk 443 optimal weight: 0.7980 chunk 385 optimal weight: 10.0000 chunk 174 optimal weight: 2.9990 chunk 498 optimal weight: 10.0000 chunk 451 optimal weight: 5.9990 chunk 339 optimal weight: 1.9990 chunk 487 optimal weight: 3.9990 chunk 527 optimal weight: 8.9990 chunk 297 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN I 140 HIS K 140 HIS K 169 HIS ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.160601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116730 restraints weight = 104195.891| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.48 r_work: 0.3480 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 55188 Z= 0.351 Angle : 0.642 16.470 74640 Z= 0.338 Chirality : 0.048 0.224 8478 Planarity : 0.005 0.103 9738 Dihedral : 5.058 50.981 7726 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.20 % Favored : 96.63 % Rotamer: Outliers : 2.75 % Allowed : 10.75 % Favored : 86.50 % 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: -0.08 (0.10), residues: 7026 helix: 0.49 (0.10), residues: 2538 sheet: 0.26 (0.12), residues: 1572 loop : -0.60 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 284 HIS 0.009 0.002 HIS G 358 PHE 0.036 0.002 PHE C 152 TYR 0.020 0.002 TYR F 435 ARG 0.007 0.001 ARG G 399 *********************** 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 762 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 601 time to evaluate : 4.950 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 128 MET cc_start: 0.8557 (mmm) cc_final: 0.8308 (mmp) REVERT: A 135 ARG cc_start: 0.8191 (mmm160) cc_final: 0.7502 (ttp80) REVERT: A 191 THR cc_start: 0.5705 (OUTLIER) cc_final: 0.5173 (p) REVERT: A 334 THR cc_start: 0.8479 (m) cc_final: 0.7977 (t) REVERT: A 403 GLU cc_start: 0.7857 (pt0) cc_final: 0.7291 (mt-10) REVERT: A 459 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7639 (tmt90) REVERT: A 662 LEU cc_start: 0.7420 (mt) cc_final: 0.6557 (tt) REVERT: A 691 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7080 (tp30) REVERT: A 699 MET cc_start: 0.7402 (mmt) cc_final: 0.6831 (mmt) REVERT: B 81 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6515 (tp30) REVERT: B 176 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.6237 (m-10) REVERT: C 179 GLU cc_start: 0.7214 (mp0) cc_final: 0.5755 (tm-30) REVERT: C 584 GLU cc_start: 0.7870 (tt0) cc_final: 0.7516 (tm-30) REVERT: C 615 GLN cc_start: 0.7987 (mt0) cc_final: 0.7402 (tt0) REVERT: E 80 ARG cc_start: 0.8156 (ptp-110) cc_final: 0.7942 (ptt180) REVERT: E 143 TYR cc_start: 0.6626 (p90) cc_final: 0.5595 (p90) REVERT: E 150 LYS cc_start: 0.7391 (mtmm) cc_final: 0.7081 (mmmt) REVERT: E 373 MET cc_start: 0.7307 (ttm) cc_final: 0.6986 (mtp) REVERT: E 545 GLU cc_start: 0.8490 (pm20) cc_final: 0.8201 (tp30) REVERT: E 697 ASN cc_start: 0.7148 (m-40) cc_final: 0.6218 (p0) REVERT: F 146 ASP cc_start: 0.8331 (m-30) cc_final: 0.7820 (m-30) REVERT: F 333 MET cc_start: 0.8939 (mtt) cc_final: 0.8736 (mtm) REVERT: G 71 ARG cc_start: 0.5493 (OUTLIER) cc_final: 0.4985 (tmm-80) REVERT: G 101 VAL cc_start: 0.8122 (t) cc_final: 0.7857 (m) REVERT: G 328 LYS cc_start: 0.5981 (mmtt) cc_final: 0.5449 (tptt) REVERT: G 350 MET cc_start: 0.6762 (tmm) cc_final: 0.6290 (tmm) REVERT: G 397 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: G 399 ARG cc_start: 0.8049 (mtp85) cc_final: 0.7807 (mtp85) REVERT: G 422 GLU cc_start: 0.8339 (pm20) cc_final: 0.8078 (pt0) REVERT: G 430 ARG cc_start: 0.6448 (ptm160) cc_final: 0.6103 (ptm160) REVERT: G 693 MET cc_start: 0.7467 (mtm) cc_final: 0.6020 (ttp) REVERT: H 220 THR cc_start: 0.8676 (m) cc_final: 0.8449 (m) REVERT: H 499 ARG cc_start: 0.6620 (mtt180) cc_final: 0.6311 (mtm180) REVERT: H 518 ASP cc_start: 0.8185 (m-30) cc_final: 0.7764 (m-30) REVERT: I 65 LYS cc_start: 0.5555 (OUTLIER) cc_final: 0.5093 (ttpt) REVERT: I 350 MET cc_start: 0.7794 (tpt) cc_final: 0.7416 (tpt) REVERT: I 351 ASN cc_start: 0.3897 (t0) cc_final: 0.3641 (t0) REVERT: I 357 GLU cc_start: 0.6514 (mp0) cc_final: 0.6274 (mp0) REVERT: I 394 TRP cc_start: 0.6552 (OUTLIER) cc_final: 0.5867 (t-100) REVERT: I 449 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7966 (mp) REVERT: I 567 ASP cc_start: 0.6345 (m-30) cc_final: 0.6091 (p0) REVERT: J 488 GLU cc_start: 0.8124 (tp30) cc_final: 0.7559 (tm-30) REVERT: J 502 VAL cc_start: 0.8915 (t) cc_final: 0.8671 (m) REVERT: J 504 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8253 (t70) REVERT: K 71 ARG cc_start: 0.6636 (ptm160) cc_final: 0.6245 (ptt180) REVERT: K 650 MET cc_start: 0.9252 (mmt) cc_final: 0.9049 (mmm) REVERT: L 303 ASP cc_start: 0.8479 (p0) cc_final: 0.8108 (m-30) outliers start: 161 outliers final: 115 residues processed: 719 average time/residue: 0.5463 time to fit residues: 663.1208 Evaluate side-chains 649 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 523 time to evaluate : 4.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL 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 459 ARG 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 70 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 176 TYR 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 517 CYS 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 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 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 310 SER Chi-restraints excluded: chain D residue 390 THR 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 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 625 MET Chi-restraints excluded: chain E residue 640 THR Chi-restraints excluded: chain E residue 717 THR Chi-restraints excluded: chain F residue 220 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 487 ILE Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 537 ILE Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 131 ILE Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain G residue 367 LEU Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain G residue 397 GLU 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 224 PHE Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 291 CYS 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 65 LYS Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 161 VAL 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 394 TRP Chi-restraints excluded: chain I residue 449 ILE 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 613 THR 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 725 VAL Chi-restraints excluded: chain J residue 78 SER Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 MET Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain J residue 504 ASP 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 321 VAL 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 504 LEU Chi-restraints excluded: chain K residue 552 ILE Chi-restraints excluded: chain K residue 580 VAL 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 304 THR Chi-restraints excluded: chain L residue 306 VAL Chi-restraints excluded: chain L residue 372 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 257 optimal weight: 5.9990 chunk 466 optimal weight: 1.9990 chunk 463 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 chunk 226 optimal weight: 10.0000 chunk 354 optimal weight: 8.9990 chunk 633 optimal weight: 0.8980 chunk 301 optimal weight: 1.9990 chunk 275 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 ASN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 124 GLN F 137 HIS H 507 GLN I 70 ASN J 241 GLN K 169 HIS ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.161025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.117090 restraints weight = 103720.608| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.35 r_work: 0.3513 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3413 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 55188 Z= 0.253 Angle : 0.585 18.152 74640 Z= 0.305 Chirality : 0.045 0.180 8478 Planarity : 0.005 0.088 9738 Dihedral : 4.889 56.860 7726 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.17 % Favored : 96.66 % Rotamer: Outliers : 2.40 % Allowed : 12.11 % Favored : 85.49 % 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: 0.76 (0.10), residues: 2520 sheet: 0.23 (0.13), residues: 1602 loop : -0.63 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP E 284 HIS 0.010 0.001 HIS G 358 PHE 0.018 0.002 PHE I 337 TYR 0.025 0.001 TYR H 417 ARG 0.007 0.000 ARG K 641 *********************** 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 707 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 567 time to evaluate : 4.864 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: 0.8213 (mmm160) cc_final: 0.7520 (ttp80) REVERT: A 191 THR cc_start: 0.5696 (OUTLIER) cc_final: 0.5194 (p) REVERT: A 334 THR cc_start: 0.8506 (m) cc_final: 0.8005 (t) REVERT: A 403 GLU cc_start: 0.7801 (pt0) cc_final: 0.7286 (mt-10) REVERT: A 459 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7430 (tmt90) REVERT: A 662 LEU cc_start: 0.7352 (mt) cc_final: 0.6478 (tt) REVERT: A 666 MET cc_start: 0.6482 (ppp) cc_final: 0.6088 (ppp) REVERT: A 691 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: B 81 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.6283 (tp30) REVERT: C 179 GLU cc_start: 0.7093 (mp0) cc_final: 0.5549 (tm-30) REVERT: C 397 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6354 (tt0) REVERT: C 420 TYR cc_start: 0.6134 (t80) cc_final: 0.5751 (t80) REVERT: C 452 LEU cc_start: 0.7427 (tp) cc_final: 0.7220 (tp) REVERT: C 504 LEU cc_start: 0.6538 (tt) cc_final: 0.6035 (mp) REVERT: C 584 GLU cc_start: 0.7857 (tt0) cc_final: 0.7523 (tm-30) REVERT: C 615 GLN cc_start: 0.8045 (mt0) cc_final: 0.7527 (tt0) REVERT: D 299 VAL cc_start: 0.6758 (OUTLIER) cc_final: 0.6483 (p) REVERT: D 504 ASP cc_start: 0.6676 (t0) cc_final: 0.6347 (m-30) REVERT: E 143 TYR cc_start: 0.6637 (p90) cc_final: 0.5638 (p90) REVERT: E 174 MET cc_start: 0.8321 (mpp) cc_final: 0.8105 (mpp) REVERT: E 373 MET cc_start: 0.7254 (ttm) cc_final: 0.6944 (mtp) REVERT: E 697 ASN cc_start: 0.7108 (m-40) cc_final: 0.6254 (p0) REVERT: E 699 MET cc_start: 0.5145 (tmm) cc_final: 0.4560 (ttt) REVERT: F 146 ASP cc_start: 0.8329 (m-30) cc_final: 0.7764 (m-30) REVERT: G 71 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.4848 (tmm-80) REVERT: G 101 VAL cc_start: 0.8164 (t) cc_final: 0.7897 (m) REVERT: G 174 MET cc_start: 0.5322 (mmt) cc_final: 0.4958 (mmm) REVERT: G 316 MET cc_start: 0.5318 (mmm) cc_final: 0.5039 (mmm) REVERT: G 328 LYS cc_start: 0.6102 (mmtt) cc_final: 0.5528 (tptt) REVERT: G 350 MET cc_start: 0.7182 (tmm) cc_final: 0.6460 (tmm) REVERT: G 367 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7504 (pp) REVERT: G 430 ARG cc_start: 0.6375 (ptm160) cc_final: 0.6055 (ptm160) REVERT: G 473 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5046 (t80) REVERT: G 503 PHE cc_start: 0.6137 (t80) cc_final: 0.5888 (t80) REVERT: G 693 MET cc_start: 0.7422 (mtm) cc_final: 0.6191 (mtp) REVERT: H 187 SER cc_start: 0.9147 (t) cc_final: 0.8786 (p) REVERT: I 350 MET cc_start: 0.7863 (tpt) cc_final: 0.7369 (tpt) REVERT: I 394 TRP cc_start: 0.6642 (OUTLIER) cc_final: 0.5940 (t-100) REVERT: I 449 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8021 (mp) REVERT: I 567 ASP cc_start: 0.6376 (m-30) cc_final: 0.6144 (p0) REVERT: I 691 GLU cc_start: 0.8161 (pt0) cc_final: 0.7451 (mt-10) REVERT: J 89 ARG cc_start: 0.7266 (mtp85) cc_final: 0.7044 (mtt90) REVERT: J 488 GLU cc_start: 0.8014 (tp30) cc_final: 0.7496 (tm-30) REVERT: J 502 VAL cc_start: 0.8969 (t) cc_final: 0.8759 (m) REVERT: J 504 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8199 (t70) REVERT: K 71 ARG cc_start: 0.6583 (ptm160) cc_final: 0.6229 (ptt180) REVERT: K 287 GLU cc_start: 0.7002 (pm20) cc_final: 0.6459 (pm20) REVERT: L 53 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7509 (ttp80) REVERT: L 303 ASP cc_start: 0.8399 (p0) cc_final: 0.8174 (m-30) REVERT: L 382 ASP cc_start: 0.8955 (t0) cc_final: 0.8668 (t0) outliers start: 140 outliers final: 94 residues processed: 669 average time/residue: 0.5217 time to fit residues: 588.4749 Evaluate side-chains 625 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 519 time to evaluate : 4.831 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 459 ARG 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 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 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 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 295 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 310 SER 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 425 HIS 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 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 487 ILE Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 108 GLU Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 146 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 603 LEU Chi-restraints excluded: chain G residue 636 VAL Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 291 CYS 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 537 ILE Chi-restraints excluded: chain I residue 191 THR 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 449 ILE 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 580 VAL Chi-restraints excluded: chain I residue 613 THR 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 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 J residue 504 ASP 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 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 107 VAL 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 471 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 14 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 627 optimal weight: 4.9990 chunk 584 optimal weight: 0.3980 chunk 422 optimal weight: 1.9990 chunk 619 optimal weight: 0.9990 chunk 233 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 420 optimal weight: 0.8980 chunk 592 optimal weight: 7.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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** E 190 ASN ** E 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 344 ASN I 70 ASN I 355 GLN K 169 HIS ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.161731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117724 restraints weight = 103827.779| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.40 r_work: 0.3516 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 55188 Z= 0.195 Angle : 0.559 19.595 74640 Z= 0.290 Chirality : 0.044 0.192 8478 Planarity : 0.004 0.103 9738 Dihedral : 4.765 59.301 7726 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 2.29 % Allowed : 12.56 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.10), residues: 7026 helix: 0.95 (0.11), residues: 2520 sheet: 0.25 (0.13), residues: 1542 loop : -0.55 (0.11), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 284 HIS 0.009 0.001 HIS G 358 PHE 0.028 0.001 PHE E 337 TYR 0.017 0.001 TYR H 417 ARG 0.006 0.000 ARG H 327 *********************** 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 714 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 580 time to evaluate : 4.857 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 124 MET cc_start: 0.7302 (pmm) cc_final: 0.7068 (mtt) REVERT: A 135 ARG cc_start: 0.8246 (mmm160) cc_final: 0.7578 (ttp80) REVERT: A 239 ARG cc_start: 0.6892 (mtm180) cc_final: 0.6667 (mtm180) REVERT: A 334 THR cc_start: 0.8489 (m) cc_final: 0.7956 (t) REVERT: A 403 GLU cc_start: 0.7744 (pt0) cc_final: 0.7189 (mt-10) REVERT: A 662 LEU cc_start: 0.7340 (mt) cc_final: 0.6430 (tt) REVERT: A 691 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7095 (tp30) REVERT: B 81 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6294 (tp30) REVERT: B 253 MET cc_start: 0.8521 (ttt) cc_final: 0.8289 (ttm) REVERT: C 89 THR cc_start: 0.4658 (OUTLIER) cc_final: 0.4190 (p) REVERT: C 179 GLU cc_start: 0.7219 (mp0) cc_final: 0.5690 (tm-30) REVERT: C 420 TYR cc_start: 0.6167 (t80) cc_final: 0.5763 (t80) REVERT: C 504 LEU cc_start: 0.6367 (tt) cc_final: 0.5829 (mp) REVERT: C 505 SER cc_start: 0.5857 (p) cc_final: 0.5634 (p) REVERT: C 584 GLU cc_start: 0.7783 (tt0) cc_final: 0.7453 (tm-30) REVERT: D 299 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6367 (p) REVERT: D 504 ASP cc_start: 0.6771 (t0) cc_final: 0.6405 (m-30) REVERT: E 143 TYR cc_start: 0.6582 (p90) cc_final: 0.5510 (p90) REVERT: E 373 MET cc_start: 0.7247 (ttm) cc_final: 0.6950 (mtp) REVERT: E 697 ASN cc_start: 0.7127 (m-40) cc_final: 0.6339 (p0) REVERT: E 699 MET cc_start: 0.5187 (tmm) cc_final: 0.4764 (ttt) REVERT: F 145 MET cc_start: 0.9025 (mtm) cc_final: 0.8711 (mtm) REVERT: F 146 ASP cc_start: 0.8323 (m-30) cc_final: 0.7895 (m-30) REVERT: G 71 ARG cc_start: 0.5426 (OUTLIER) cc_final: 0.4805 (tmm-80) REVERT: G 101 VAL cc_start: 0.8142 (t) cc_final: 0.7874 (m) REVERT: G 174 MET cc_start: 0.5245 (mmt) cc_final: 0.4711 (mmt) REVERT: G 328 LYS cc_start: 0.6076 (mmtt) cc_final: 0.5473 (tptp) REVERT: G 350 MET cc_start: 0.7097 (tmm) cc_final: 0.6400 (tmm) REVERT: G 367 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7457 (pp) REVERT: G 397 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: G 430 ARG cc_start: 0.6389 (ptm160) cc_final: 0.6007 (ptm160) REVERT: G 473 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.5106 (t80) REVERT: H 95 MET cc_start: 0.8022 (mmp) cc_final: 0.7801 (mmt) REVERT: H 187 SER cc_start: 0.9133 (t) cc_final: 0.8766 (p) REVERT: I 350 MET cc_start: 0.8022 (tpt) cc_final: 0.7534 (tpt) REVERT: I 394 TRP cc_start: 0.6587 (OUTLIER) cc_final: 0.6029 (t-100) REVERT: I 449 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7974 (mp) REVERT: I 486 ARG cc_start: 0.7756 (tpt90) cc_final: 0.7501 (ttt-90) REVERT: I 496 LYS cc_start: 0.7030 (mmmt) cc_final: 0.6409 (mttm) REVERT: I 691 GLU cc_start: 0.8183 (pt0) cc_final: 0.7469 (mt-10) REVERT: J 89 ARG cc_start: 0.7328 (mtp85) cc_final: 0.7053 (mtt90) REVERT: J 253 MET cc_start: 0.8373 (mpp) cc_final: 0.8138 (mmt) REVERT: J 488 GLU cc_start: 0.7906 (tp30) cc_final: 0.7338 (tm-30) REVERT: K 71 ARG cc_start: 0.6563 (ptm160) cc_final: 0.6200 (ptt180) REVERT: K 123 ASN cc_start: 0.7706 (t0) cc_final: 0.7358 (t0) REVERT: K 391 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7748 (mt) REVERT: K 611 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7645 (tp40) REVERT: L 53 ARG cc_start: 0.7927 (ptm-80) cc_final: 0.7565 (ttp80) REVERT: L 303 ASP cc_start: 0.8402 (p0) cc_final: 0.8114 (m-30) REVERT: L 382 ASP cc_start: 0.8922 (t0) cc_final: 0.8633 (t0) outliers start: 134 outliers final: 97 residues processed: 673 average time/residue: 0.5113 time to fit residues: 582.0066 Evaluate side-chains 630 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 522 time to evaluate : 4.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 B residue 479 VAL 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 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 299 VAL Chi-restraints excluded: chain D residue 390 THR Chi-restraints excluded: chain D residue 521 VAL Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain E residue 190 ASN 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 397 GLU 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 640 THR Chi-restraints excluded: chain E residue 717 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 487 ILE Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain G residue 71 ARG Chi-restraints excluded: chain G residue 127 ILE Chi-restraints excluded: chain G residue 299 VAL 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 397 GLU Chi-restraints excluded: chain G residue 418 SER Chi-restraints excluded: chain G residue 473 TYR 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 H residue 178 ASP Chi-restraints excluded: chain H residue 253 MET Chi-restraints excluded: chain H residue 291 CYS Chi-restraints excluded: chain H residue 316 MET Chi-restraints excluded: chain H residue 451 THR 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 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 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 614 VAL 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 J residue 451 THR 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 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 143 LYS 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 316 MET Chi-restraints excluded: chain L residue 428 THR Chi-restraints excluded: chain L residue 471 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 398 optimal weight: 0.0980 chunk 670 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 482 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 72 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 568 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 615 optimal weight: 6.9990 chunk 554 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 GLN K 169 HIS K 319 GLN L 100 ASN L 115 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.163418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120168 restraints weight = 103847.304| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.49 r_work: 0.3529 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3427 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 55188 Z= 0.143 Angle : 0.535 18.824 74640 Z= 0.277 Chirality : 0.043 0.300 8478 Planarity : 0.004 0.100 9738 Dihedral : 4.578 59.613 7722 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.03 % Favored : 96.84 % Rotamer: Outliers : 1.81 % Allowed : 13.31 % Favored : 84.87 % 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: 1.15 (0.11), residues: 2526 sheet: 0.37 (0.13), residues: 1524 loop : -0.48 (0.12), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 284 HIS 0.011 0.001 HIS I 358 PHE 0.024 0.001 PHE G 307 TYR 0.018 0.001 TYR H 417 ARG 0.006 0.000 ARG H 327 *********************** 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 694 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 588 time to evaluate : 4.950 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 124 MET cc_start: 0.7376 (pmm) cc_final: 0.7117 (mtt) REVERT: A 135 ARG cc_start: 0.8279 (mmm160) cc_final: 0.7596 (ttp80) REVERT: A 217 MET cc_start: 0.3317 (ptm) cc_final: 0.2917 (ppp) REVERT: A 334 THR cc_start: 0.8507 (m) cc_final: 0.7925 (t) REVERT: A 403 GLU cc_start: 0.7739 (pt0) cc_final: 0.7141 (mt-10) REVERT: A 650 MET cc_start: 0.8875 (mmp) cc_final: 0.8017 (mmp) REVERT: A 662 LEU cc_start: 0.7336 (mt) cc_final: 0.6435 (tt) REVERT: A 691 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7070 (tp30) REVERT: B 253 MET cc_start: 0.8461 (ttt) cc_final: 0.8187 (ttm) REVERT: C 89 THR cc_start: 0.4568 (OUTLIER) cc_final: 0.4115 (p) REVERT: C 179 GLU cc_start: 0.7290 (mp0) cc_final: 0.5811 (tm-30) REVERT: C 368 ASP cc_start: 0.5540 (p0) cc_final: 0.4778 (p0) REVERT: C 420 TYR cc_start: 0.6176 (t80) cc_final: 0.5766 (t80) REVERT: C 504 LEU cc_start: 0.6232 (tt) cc_final: 0.5777 (mp) REVERT: C 505 SER cc_start: 0.5768 (p) cc_final: 0.5522 (p) REVERT: C 584 GLU cc_start: 0.7853 (tt0) cc_final: 0.7460 (tm-30) REVERT: C 619 ARG cc_start: 0.7166 (tpt90) cc_final: 0.6790 (tpt90) REVERT: D 299 VAL cc_start: 0.6589 (OUTLIER) cc_final: 0.6310 (p) REVERT: E 82 CYS cc_start: 0.8245 (m) cc_final: 0.7920 (m) REVERT: E 143 TYR cc_start: 0.6517 (p90) cc_final: 0.5525 (p90) REVERT: E 174 MET cc_start: 0.8277 (mpp) cc_final: 0.8036 (mpp) REVERT: E 369 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7448 (tt) REVERT: E 373 MET cc_start: 0.7262 (ttm) cc_final: 0.6890 (mtp) REVERT: E 690 ILE cc_start: 0.8279 (mt) cc_final: 0.8000 (mt) REVERT: E 697 ASN cc_start: 0.7080 (m-40) cc_final: 0.6297 (p0) REVERT: E 699 MET cc_start: 0.5187 (tmm) cc_final: 0.4784 (ttt) REVERT: F 145 MET cc_start: 0.9039 (mtm) cc_final: 0.8729 (mtm) REVERT: F 146 ASP cc_start: 0.8288 (m-30) cc_final: 0.7908 (m-30) REVERT: F 347 MET cc_start: 0.8985 (tpp) cc_final: 0.8684 (mmt) REVERT: G 68 VAL cc_start: 0.8275 (t) cc_final: 0.8069 (m) REVERT: G 101 VAL cc_start: 0.8103 (t) cc_final: 0.7849 (m) REVERT: G 174 MET cc_start: 0.5121 (mmt) cc_final: 0.4810 (mmt) REVERT: G 316 MET cc_start: 0.5095 (mmm) cc_final: 0.4861 (mmm) REVERT: G 328 LYS cc_start: 0.5764 (mmtt) cc_final: 0.5254 (tptp) REVERT: G 350 MET cc_start: 0.7062 (tmm) cc_final: 0.6569 (tmm) REVERT: G 367 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7439 (pp) REVERT: G 399 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7715 (mtp85) REVERT: G 430 ARG cc_start: 0.6333 (ptm160) cc_final: 0.6044 (ptm160) REVERT: G 452 LEU cc_start: 0.8907 (tp) cc_final: 0.8644 (tt) REVERT: G 473 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5083 (t80) REVERT: I 350 MET cc_start: 0.7869 (tpt) cc_final: 0.7402 (tpt) REVERT: I 394 TRP cc_start: 0.6449 (OUTLIER) cc_final: 0.5956 (t-100) REVERT: I 449 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.7984 (mp) REVERT: I 486 ARG cc_start: 0.7735 (tpt90) cc_final: 0.7464 (ttt-90) REVERT: I 496 LYS cc_start: 0.7087 (mmmt) cc_final: 0.6440 (mttm) REVERT: I 691 GLU cc_start: 0.8225 (pt0) cc_final: 0.7678 (tt0) REVERT: J 89 ARG cc_start: 0.7407 (mtp85) cc_final: 0.7144 (mtt90) REVERT: J 253 MET cc_start: 0.8361 (mpp) cc_final: 0.8111 (mmt) REVERT: J 488 GLU cc_start: 0.7900 (tp30) cc_final: 0.7324 (tm-30) REVERT: K 71 ARG cc_start: 0.6639 (ptm160) cc_final: 0.6345 (ptt180) REVERT: K 123 ASN cc_start: 0.7621 (t0) cc_final: 0.7252 (t0) REVERT: K 169 HIS cc_start: 0.8385 (OUTLIER) cc_final: 0.7822 (p-80) REVERT: K 287 GLU cc_start: 0.6882 (pm20) cc_final: 0.6316 (pm20) REVERT: L 53 ARG cc_start: 0.7979 (ptm-80) cc_final: 0.7610 (ttp80) REVERT: L 303 ASP cc_start: 0.8474 (p0) cc_final: 0.8030 (m-30) REVERT: L 382 ASP cc_start: 0.8899 (t0) cc_final: 0.8636 (t0) REVERT: L 499 ARG cc_start: 0.8051 (mmt-90) cc_final: 0.7667 (mmt-90) outliers start: 106 outliers final: 74 residues processed: 662 average time/residue: 0.5213 time to fit residues: 582.1188 Evaluate side-chains 624 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 541 time to evaluate : 5.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR 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 A residue 691 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 305 ILE 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 627 ILE Chi-restraints excluded: chain C residue 666 MET 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 299 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 269 HIS 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 425 HIS Chi-restraints excluded: chain E residue 521 GLU 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 F residue 147 GLN Chi-restraints excluded: chain F residue 235 THR 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 527 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 345 PHE Chi-restraints excluded: chain G residue 367 LEU 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 636 VAL Chi-restraints excluded: chain G residue 661 VAL 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 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 449 ILE 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 613 THR Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 169 HIS 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 450 SER Chi-restraints excluded: chain K residue 499 ILE Chi-restraints excluded: chain K residue 724 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 149 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 282 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 376 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 471 optimal weight: 10.0000 chunk 113 optimal weight: 0.0040 chunk 114 optimal weight: 1.9990 chunk 338 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 410 optimal weight: 0.0670 chunk 426 optimal weight: 6.9990 overall best weight: 1.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS C 615 GLN E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN ** I 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 169 HIS ** K 436 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.162381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118507 restraints weight = 104163.873| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.39 r_work: 0.3537 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 55188 Z= 0.188 Angle : 0.551 18.896 74640 Z= 0.284 Chirality : 0.044 0.179 8478 Planarity : 0.004 0.119 9738 Dihedral : 4.571 59.979 7722 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 2.12 % Allowed : 13.36 % Favored : 84.51 % 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: 0.42 (0.10), residues: 7026 helix: 1.18 (0.11), residues: 2526 sheet: 0.35 (0.13), residues: 1524 loop : -0.47 (0.12), residues: 2976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 284 HIS 0.015 0.001 HIS K 169 PHE 0.020 0.001 PHE D 490 TYR 0.014 0.001 TYR H 417 ARG 0.009 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 682 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 558 time to evaluate : 5.856 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 124 MET cc_start: 0.7265 (pmm) cc_final: 0.7002 (mtt) REVERT: A 135 ARG cc_start: 0.8255 (mmm160) cc_final: 0.7613 (ttp80) REVERT: A 217 MET cc_start: 0.3898 (ptm) cc_final: 0.3403 (ppp) REVERT: A 334 THR cc_start: 0.8563 (m) cc_final: 0.8013 (t) REVERT: A 403 GLU cc_start: 0.7722 (pt0) cc_final: 0.7190 (mt-10) REVERT: A 448 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8190 (tmm) REVERT: A 650 MET cc_start: 0.8885 (mmp) cc_final: 0.8045 (mmp) REVERT: A 691 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7123 (tp30) REVERT: C 89 THR cc_start: 0.4578 (OUTLIER) cc_final: 0.4126 (p) REVERT: C 179 GLU cc_start: 0.7214 (mp0) cc_final: 0.5725 (tm-30) REVERT: C 368 ASP cc_start: 0.5489 (p0) cc_final: 0.4776 (p0) REVERT: C 397 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6249 (tt0) REVERT: C 420 TYR cc_start: 0.6203 (t80) cc_final: 0.5724 (t80) REVERT: C 422 GLU cc_start: 0.7928 (pm20) cc_final: 0.7697 (pm20) REVERT: C 504 LEU cc_start: 0.6211 (tt) cc_final: 0.5759 (mp) REVERT: C 584 GLU cc_start: 0.7869 (tt0) cc_final: 0.7515 (tm-30) REVERT: D 299 VAL cc_start: 0.6594 (OUTLIER) cc_final: 0.6319 (p) REVERT: E 82 CYS cc_start: 0.8290 (m) cc_final: 0.7966 (m) REVERT: E 143 TYR cc_start: 0.6520 (p90) cc_final: 0.5540 (p90) REVERT: E 174 MET cc_start: 0.8258 (mpp) cc_final: 0.8042 (mpp) REVERT: E 369 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7870 (tt) REVERT: E 373 MET cc_start: 0.7256 (ttm) cc_final: 0.6920 (mtp) REVERT: E 697 ASN cc_start: 0.7026 (m-40) cc_final: 0.6199 (p0) REVERT: E 699 MET cc_start: 0.5284 (tmm) cc_final: 0.4896 (ttt) REVERT: F 145 MET cc_start: 0.8984 (mtm) cc_final: 0.8701 (mtm) REVERT: F 146 ASP cc_start: 0.8295 (m-30) cc_final: 0.7939 (m-30) REVERT: F 347 MET cc_start: 0.8960 (tpp) cc_final: 0.8662 (mmt) REVERT: G 68 VAL cc_start: 0.8296 (t) cc_final: 0.8093 (m) REVERT: G 101 VAL cc_start: 0.8138 (t) cc_final: 0.7866 (m) REVERT: G 328 LYS cc_start: 0.5877 (mmtt) cc_final: 0.5325 (tptp) REVERT: G 350 MET cc_start: 0.7057 (tmm) cc_final: 0.6168 (tpp) REVERT: G 367 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7474 (pp) REVERT: G 430 ARG cc_start: 0.6287 (ptm160) cc_final: 0.6002 (ptm160) REVERT: G 451 LYS cc_start: 0.7942 (pttp) cc_final: 0.7731 (pttm) REVERT: G 473 TYR cc_start: 0.7094 (OUTLIER) cc_final: 0.5041 (t80) REVERT: I 124 MET cc_start: 0.6929 (mmm) cc_final: 0.6368 (tpp) REVERT: I 350 MET cc_start: 0.8064 (tpt) cc_final: 0.7523 (tpt) REVERT: I 394 TRP cc_start: 0.6363 (OUTLIER) cc_final: 0.5885 (t-100) REVERT: I 449 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7954 (mp) REVERT: I 486 ARG cc_start: 0.7689 (tpt90) cc_final: 0.7397 (ttt-90) REVERT: I 496 LYS cc_start: 0.7037 (mmmt) cc_final: 0.6398 (mttm) REVERT: J 89 ARG cc_start: 0.7387 (mtp85) cc_final: 0.7102 (mtt90) REVERT: J 253 MET cc_start: 0.8366 (mpp) cc_final: 0.8114 (mmt) REVERT: J 451 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8716 (p) REVERT: J 488 GLU cc_start: 0.7942 (tp30) cc_final: 0.7399 (tm-30) REVERT: J 518 ASP cc_start: 0.8444 (m-30) cc_final: 0.8167 (m-30) REVERT: K 71 ARG cc_start: 0.6641 (ptm160) cc_final: 0.6318 (ptt180) REVERT: K 123 ASN cc_start: 0.7647 (t0) cc_final: 0.7264 (t0) REVERT: K 391 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7719 (mt) REVERT: K 611 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7686 (tp40) REVERT: L 53 ARG cc_start: 0.8003 (ptm-80) cc_final: 0.7638 (ttp80) REVERT: L 303 ASP cc_start: 0.8398 (p0) cc_final: 0.8016 (m-30) REVERT: L 382 ASP cc_start: 0.8907 (t0) cc_final: 0.8645 (t0) REVERT: L 499 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7714 (mmt-90) outliers start: 124 outliers final: 91 residues processed: 643 average time/residue: 0.5221 time to fit residues: 571.5483 Evaluate side-chains 639 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 536 time to evaluate : 4.846 ------------------------------------------------------------------------------- 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 448 MET 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 305 ILE Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 168 THR Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET 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 299 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain E residue 105 MET Chi-restraints excluded: chain E residue 216 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 331 SER 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 425 HIS Chi-restraints excluded: chain E residue 521 GLU 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 F residue 147 GLN Chi-restraints excluded: chain F residue 197 MET Chi-restraints excluded: chain F residue 235 THR 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 527 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 345 PHE Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain G residue 367 LEU 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 636 VAL Chi-restraints excluded: chain G residue 661 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 107 VAL 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 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 449 ILE 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 613 THR Chi-restraints excluded: chain I residue 669 VAL Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain J residue 451 THR 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 696 random chunks: chunk 56 optimal weight: 1.9990 chunk 565 optimal weight: 0.3980 chunk 29 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 485 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 334 optimal weight: 4.9990 chunk 351 optimal weight: 10.0000 chunk 191 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS C 279 HIS E 269 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 436 GLN I 70 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.161512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117564 restraints weight = 103995.297| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.39 r_work: 0.3524 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 55188 Z= 0.217 Angle : 0.569 19.237 74640 Z= 0.293 Chirality : 0.044 0.180 8478 Planarity : 0.004 0.115 9738 Dihedral : 4.608 59.259 7722 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.37 % Favored : 96.53 % Rotamer: Outliers : 2.16 % Allowed : 13.45 % Favored : 84.39 % 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: 0.36 (0.10), residues: 7026 helix: 1.14 (0.11), residues: 2538 sheet: 0.31 (0.13), residues: 1578 loop : -0.52 (0.12), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 284 HIS 0.017 0.001 HIS E 269 PHE 0.023 0.001 PHE E 337 TYR 0.026 0.001 TYR L 405 ARG 0.010 0.000 ARG H 327 *********************** 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 673 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 547 time to evaluate : 4.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.8271 (mmm160) cc_final: 0.7616 (ttp80) REVERT: A 217 MET cc_start: 0.3640 (ptm) cc_final: 0.3434 (ppp) REVERT: A 334 THR cc_start: 0.8553 (m) cc_final: 0.8009 (t) REVERT: A 403 GLU cc_start: 0.7756 (pt0) cc_final: 0.7241 (mt-10) REVERT: A 448 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8404 (tmm) REVERT: A 466 MET cc_start: 0.8785 (tpp) cc_final: 0.8029 (tpp) REVERT: A 650 MET cc_start: 0.8908 (mmp) cc_final: 0.8060 (mmp) REVERT: A 691 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7154 (tp30) REVERT: C 89 THR cc_start: 0.4637 (OUTLIER) cc_final: 0.4170 (p) REVERT: C 368 ASP cc_start: 0.5474 (p0) cc_final: 0.4741 (p0) REVERT: C 397 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: C 420 TYR cc_start: 0.6273 (t80) cc_final: 0.5791 (t80) REVERT: C 422 GLU cc_start: 0.7847 (pm20) cc_final: 0.7608 (pm20) REVERT: C 504 LEU cc_start: 0.6258 (tt) cc_final: 0.5729 (mp) REVERT: C 584 GLU cc_start: 0.7870 (tt0) cc_final: 0.7501 (tm-30) REVERT: D 299 VAL cc_start: 0.6502 (OUTLIER) cc_final: 0.6199 (p) REVERT: E 143 TYR cc_start: 0.6504 (p90) cc_final: 0.5498 (p90) REVERT: E 271 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6303 (mp0) REVERT: E 369 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7981 (tt) REVERT: E 373 MET cc_start: 0.7271 (ttm) cc_final: 0.6930 (mtp) REVERT: E 697 ASN cc_start: 0.7087 (m-40) cc_final: 0.6274 (p0) REVERT: E 699 MET cc_start: 0.5321 (tmm) cc_final: 0.4943 (ttt) REVERT: F 146 ASP cc_start: 0.8317 (m-30) cc_final: 0.7950 (m-30) REVERT: G 68 VAL cc_start: 0.8285 (t) cc_final: 0.8068 (m) REVERT: G 101 VAL cc_start: 0.8162 (t) cc_final: 0.7899 (m) REVERT: G 316 MET cc_start: 0.5048 (mmm) cc_final: 0.4833 (mmm) REVERT: G 328 LYS cc_start: 0.5929 (mmtt) cc_final: 0.5335 (tptp) REVERT: G 350 MET cc_start: 0.7116 (tmm) cc_final: 0.6486 (tmm) REVERT: G 397 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: G 430 ARG cc_start: 0.6322 (ptm160) cc_final: 0.6057 (ptm160) REVERT: G 440 ASP cc_start: 0.7472 (t0) cc_final: 0.6920 (p0) REVERT: G 473 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.5104 (t80) REVERT: G 693 MET cc_start: 0.7232 (mtm) cc_final: 0.6235 (mtm) REVERT: H 187 SER cc_start: 0.9132 (t) cc_final: 0.8726 (p) REVERT: I 124 MET cc_start: 0.6772 (mmm) cc_final: 0.6345 (tpp) REVERT: I 350 MET cc_start: 0.8078 (tpt) cc_final: 0.7561 (tpt) REVERT: I 394 TRP cc_start: 0.6377 (OUTLIER) cc_final: 0.6084 (t-100) REVERT: I 397 GLU cc_start: 0.8035 (tt0) cc_final: 0.7361 (tp30) REVERT: I 449 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7968 (mp) REVERT: I 486 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7408 (ttt-90) REVERT: I 496 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6322 (mttm) REVERT: J 89 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7047 (mtt90) REVERT: J 253 MET cc_start: 0.8390 (mpp) cc_final: 0.8131 (mmt) REVERT: J 488 GLU cc_start: 0.7952 (tp30) cc_final: 0.7400 (tm-30) REVERT: J 518 ASP cc_start: 0.8448 (m-30) cc_final: 0.8187 (m-30) REVERT: K 71 ARG cc_start: 0.6746 (ptm160) cc_final: 0.6405 (ptt180) REVERT: K 123 ASN cc_start: 0.7785 (t0) cc_final: 0.7377 (t0) REVERT: K 287 GLU cc_start: 0.6927 (pm20) cc_final: 0.6302 (pm20) REVERT: K 391 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7682 (mt) REVERT: K 611 GLN cc_start: 0.8085 (tm-30) cc_final: 0.7733 (tp40) REVERT: L 53 ARG cc_start: 0.8054 (ptm-80) cc_final: 0.7643 (ttp80) REVERT: L 303 ASP cc_start: 0.8362 (p0) cc_final: 0.8094 (m-30) REVERT: L 382 ASP cc_start: 0.8952 (t0) cc_final: 0.8744 (t70) REVERT: L 499 ARG cc_start: 0.8060 (mmt-90) cc_final: 0.7758 (mmt-90) outliers start: 126 outliers final: 101 residues processed: 629 average time/residue: 0.5151 time to fit residues: 552.1644 Evaluate side-chains 638 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 526 time to evaluate : 4.836 ------------------------------------------------------------------------------- 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 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 448 MET 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 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 180 SER Chi-restraints excluded: chain C residue 397 GLU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 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 295 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 527 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 331 SER 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 425 HIS Chi-restraints excluded: chain E residue 521 GLU 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 F residue 147 GLN Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 235 THR 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 527 VAL Chi-restraints excluded: chain F residue 537 ILE 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 345 PHE Chi-restraints excluded: chain G residue 349 GLU Chi-restraints excluded: chain G residue 397 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 661 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 107 VAL 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 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 449 ILE 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 613 THR 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 J residue 451 THR 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 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 36 optimal weight: 0.3980 chunk 308 optimal weight: 0.9990 chunk 593 optimal weight: 0.0010 chunk 516 optimal weight: 8.9990 chunk 578 optimal weight: 0.9980 chunk 476 optimal weight: 7.9990 chunk 305 optimal weight: 0.7980 chunk 603 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 685 optimal weight: 0.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 70 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.163585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.120052 restraints weight = 103974.485| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.39 r_work: 0.3558 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 55188 Z= 0.149 Angle : 0.546 19.095 74640 Z= 0.280 Chirality : 0.043 0.182 8478 Planarity : 0.004 0.113 9738 Dihedral : 4.505 59.144 7722 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 1.69 % Allowed : 14.15 % Favored : 84.15 % 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: 0.49 (0.10), residues: 7026 helix: 1.28 (0.11), residues: 2526 sheet: 0.34 (0.13), residues: 1536 loop : -0.44 (0.12), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 284 HIS 0.008 0.001 HIS G 358 PHE 0.016 0.001 PHE J 122 TYR 0.014 0.001 TYR H 417 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 691 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 592 time to evaluate : 4.985 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: 0.8303 (mmm160) cc_final: 0.7654 (ttp80) REVERT: A 334 THR cc_start: 0.8568 (m) cc_final: 0.8245 (t) REVERT: A 403 GLU cc_start: 0.7704 (pt0) cc_final: 0.7175 (mt-10) REVERT: A 448 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8339 (tmm) REVERT: A 691 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7157 (tp30) REVERT: A 696 GLN cc_start: 0.7995 (mt0) cc_final: 0.7602 (mp10) REVERT: B 253 MET cc_start: 0.8356 (ttm) cc_final: 0.8145 (ttt) REVERT: B 517 CYS cc_start: 0.8855 (m) cc_final: 0.8429 (p) REVERT: C 89 THR cc_start: 0.4713 (OUTLIER) cc_final: 0.4249 (p) REVERT: C 368 ASP cc_start: 0.5403 (p0) cc_final: 0.4683 (p0) REVERT: C 397 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: C 420 TYR cc_start: 0.6236 (t80) cc_final: 0.5719 (t80) REVERT: C 504 LEU cc_start: 0.6430 (tt) cc_final: 0.5931 (mp) REVERT: C 584 GLU cc_start: 0.7877 (tt0) cc_final: 0.7498 (tm-30) REVERT: D 238 ASP cc_start: 0.7993 (t0) cc_final: 0.7707 (t0) REVERT: D 299 VAL cc_start: 0.6555 (OUTLIER) cc_final: 0.6290 (p) REVERT: E 82 CYS cc_start: 0.8238 (m) cc_final: 0.7853 (m) REVERT: E 143 TYR cc_start: 0.6511 (p90) cc_final: 0.5575 (p90) REVERT: E 174 MET cc_start: 0.8333 (mpp) cc_final: 0.8129 (mpp) REVERT: E 271 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6262 (mt-10) REVERT: E 369 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7433 (tt) REVERT: E 373 MET cc_start: 0.7271 (ttm) cc_final: 0.6900 (mtp) REVERT: E 697 ASN cc_start: 0.7056 (m-40) cc_final: 0.6292 (p0) REVERT: E 699 MET cc_start: 0.5320 (tmm) cc_final: 0.4932 (ttt) REVERT: F 146 ASP cc_start: 0.8239 (m-30) cc_final: 0.7865 (m-30) REVERT: G 68 VAL cc_start: 0.8290 (t) cc_final: 0.8083 (m) REVERT: G 101 VAL cc_start: 0.8181 (t) cc_final: 0.7920 (m) REVERT: G 328 LYS cc_start: 0.5920 (mmtt) cc_final: 0.5364 (tptp) REVERT: G 350 MET cc_start: 0.7137 (tmm) cc_final: 0.6494 (tmm) REVERT: G 367 LEU cc_start: 0.8175 (mp) cc_final: 0.7868 (tp) REVERT: G 399 ARG cc_start: 0.7968 (mtp180) cc_final: 0.7440 (ptm160) REVERT: G 401 TYR cc_start: 0.7690 (m-80) cc_final: 0.7310 (m-80) REVERT: G 430 ARG cc_start: 0.6309 (ptm160) cc_final: 0.6073 (ptm160) REVERT: G 440 ASP cc_start: 0.7435 (t0) cc_final: 0.6890 (p0) REVERT: G 473 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.5122 (t80) REVERT: G 653 LYS cc_start: 0.6180 (mttt) cc_final: 0.5934 (mttt) REVERT: G 693 MET cc_start: 0.7056 (mtm) cc_final: 0.5992 (mtp) REVERT: H 187 SER cc_start: 0.9058 (t) cc_final: 0.8610 (p) REVERT: I 350 MET cc_start: 0.8045 (tpt) cc_final: 0.7553 (tpt) REVERT: I 397 GLU cc_start: 0.7946 (tt0) cc_final: 0.7259 (tp30) REVERT: I 449 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.8003 (mp) REVERT: I 486 ARG cc_start: 0.7767 (tpt90) cc_final: 0.7551 (ttt-90) REVERT: I 496 LYS cc_start: 0.6902 (mmmt) cc_final: 0.6339 (mttm) REVERT: J 89 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7056 (mtt90) REVERT: J 253 MET cc_start: 0.8344 (mpp) cc_final: 0.8091 (mmt) REVERT: J 488 GLU cc_start: 0.7954 (tp30) cc_final: 0.7438 (tm-30) REVERT: J 518 ASP cc_start: 0.8434 (m-30) cc_final: 0.8164 (m-30) REVERT: K 71 ARG cc_start: 0.6670 (ptm160) cc_final: 0.6356 (ptt180) REVERT: K 123 ASN cc_start: 0.7641 (t0) cc_final: 0.7223 (t0) REVERT: K 287 GLU cc_start: 0.6962 (pm20) cc_final: 0.6376 (pm20) REVERT: K 345 PHE cc_start: 0.7582 (p90) cc_final: 0.7127 (p90) REVERT: K 391 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7643 (mt) REVERT: K 611 GLN cc_start: 0.8076 (tm-30) cc_final: 0.7701 (tp40) REVERT: K 639 LEU cc_start: 0.9053 (mt) cc_final: 0.8809 (mp) REVERT: L 33 THR cc_start: 0.7759 (m) cc_final: 0.7547 (t) REVERT: L 53 ARG cc_start: 0.8014 (ptm-80) cc_final: 0.7694 (ttp80) REVERT: L 303 ASP cc_start: 0.8386 (p0) cc_final: 0.8167 (m-30) REVERT: L 382 ASP cc_start: 0.8843 (t0) cc_final: 0.8602 (t0) REVERT: L 480 GLU cc_start: 0.7670 (mp0) cc_final: 0.7053 (mp0) REVERT: L 499 ARG cc_start: 0.8059 (mmt-90) cc_final: 0.7719 (mmt-90) outliers start: 99 outliers final: 77 residues processed: 656 average time/residue: 0.5278 time to fit residues: 583.4058 Evaluate side-chains 638 residues out of total 5844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 552 time to evaluate : 4.811 ------------------------------------------------------------------------------- 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 335 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 448 MET 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 305 ILE 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 453 ILE Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 603 LEU Chi-restraints excluded: chain C residue 627 ILE Chi-restraints excluded: chain C residue 666 MET 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 299 VAL Chi-restraints excluded: chain D residue 403 GLN Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain E residue 216 VAL Chi-restraints excluded: chain E residue 290 CYS Chi-restraints excluded: chain E residue 331 SER 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 425 HIS 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 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 71 ARG 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 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 636 VAL Chi-restraints excluded: chain G residue 695 MET Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 291 CYS 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 369 LEU Chi-restraints excluded: chain I residue 376 VAL 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 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 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 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 347 optimal weight: 0.9990 chunk 497 optimal weight: 20.0000 chunk 70 optimal weight: 0.2980 chunk 552 optimal weight: 5.9990 chunk 563 optimal weight: 0.9990 chunk 644 optimal weight: 0.5980 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 0.0970 chunk 221 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 692 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 169 HIS I 70 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.163905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.120638 restraints weight = 104083.495| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.37 r_work: 0.3565 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.6055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 55188 Z= 0.151 Angle : 0.554 19.227 74640 Z= 0.283 Chirality : 0.043 0.219 8478 Planarity : 0.004 0.110 9738 Dihedral : 4.422 59.770 7722 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 1.63 % Allowed : 14.29 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.10), residues: 7026 helix: 1.31 (0.11), residues: 2538 sheet: 0.37 (0.13), residues: 1536 loop : -0.43 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP I 394 HIS 0.007 0.001 HIS C 169 PHE 0.015 0.001 PHE J 122 TYR 0.018 0.001 TYR L 405 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: 36837.29 seconds wall clock time: 629 minutes 35.09 seconds (37775.09 seconds total)