Starting phenix.real_space_refine on Sat Mar 7 01:58:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.map" model { file = "/net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ybp_10770/03_2026/6ybp_10770.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 157 5.16 5 C 22970 2.51 5 N 6423 2.21 5 O 6842 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 189 residue(s): 0.06s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36410 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "B" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "C" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "D" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "E" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "F" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3910 Classifications: {'peptide': 506} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 484} Chain: "G" Number of atoms: 2135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2135 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 18, 'TRANS': 264} Chain breaks: 5 Chain: "H" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1565 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 11, 'TRANS': 196} Chain: "I" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2183 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 17, 'TRANS': 270} Chain breaks: 4 Chain: "J" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2305 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 20, 'TRANS': 282} Chain breaks: 3 Chain: "K" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2217 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 18, 'TRANS': 274} Chain breaks: 4 Chain: "L" Number of atoms: 2208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2208 Classifications: {'peptide': 291} Link IDs: {'PTRANS': 18, 'TRANS': 272} Chain breaks: 4 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.26, per 1000 atoms: 0.23 Number of scatterers: 36410 At special positions: 0 Unit cell: (160.48, 160.48, 175.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 157 16.00 P 18 15.00 O 6842 8.00 N 6423 7.00 C 22970 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: 3.00 Conformation dependent library (CDL) restraints added in 1.5 seconds 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8554 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 55 sheets defined 39.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 3.655A pdb=" N GLU A 9 " --> pdb=" O LEU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.597A pdb=" N ARG A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 95 through 99 Processing helix chain 'A' and resid 101 through 119 Processing helix chain 'A' and resid 132 through 135 Processing helix chain 'A' and resid 136 through 154 removed outlier: 4.122A pdb=" N LEU A 140 " --> pdb=" O GLY A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.639A pdb=" N ALA A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 177' Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 213 through 220 Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.868A pdb=" N ASP A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 3.603A pdb=" N LEU A 269 " --> pdb=" O ASP A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 291 removed outlier: 4.021A pdb=" N LEU A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 Processing helix chain 'A' and resid 334 through 351 removed outlier: 3.610A pdb=" N PHE A 351 " --> pdb=" O PHE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 374 through 389 removed outlier: 3.950A pdb=" N LEU A 382 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA A 389 " --> pdb=" O ALA A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 Processing helix chain 'A' and resid 411 through 415 Processing helix chain 'A' and resid 431 through 440 Processing helix chain 'A' and resid 441 through 444 removed outlier: 4.101A pdb=" N ILE A 444 " --> pdb=" O ARG A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 441 through 444' Processing helix chain 'A' and resid 446 through 462 Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.535A pdb=" N ALA A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 removed outlier: 3.951A pdb=" N GLY A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET A 492 " --> pdb=" O ARG A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 16 Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 63 through 67 removed outlier: 3.748A pdb=" N LYS B 66 " --> pdb=" O GLY B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.524A pdb=" N GLU B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 136 through 154 removed outlier: 4.104A pdb=" N LEU B 140 " --> pdb=" O GLY B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.580A pdb=" N MET B 177 " --> pdb=" O TYR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 213 through 220 Processing helix chain 'B' and resid 230 through 243 removed outlier: 3.874A pdb=" N ASP B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 272 removed outlier: 3.634A pdb=" N LEU B 269 " --> pdb=" O ASP B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 291 removed outlier: 4.014A pdb=" N LEU B 286 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 Processing helix chain 'B' and resid 334 through 351 Processing helix chain 'B' and resid 367 through 374 removed outlier: 3.521A pdb=" N GLU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 removed outlier: 3.542A pdb=" N HIS B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 382 " --> pdb=" O HIS B 378 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 383 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 389 " --> pdb=" O ALA B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 Processing helix chain 'B' and resid 411 through 415 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 447 through 462 Processing helix chain 'B' and resid 464 through 470 Processing helix chain 'B' and resid 478 through 480 No H-bonds generated for 'chain 'B' and resid 478 through 480' Processing helix chain 'B' and resid 481 through 494 removed outlier: 3.669A pdb=" N GLY B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 16 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 63 through 67 removed outlier: 3.683A pdb=" N LYS C 66 " --> pdb=" O GLY C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 101 through 119 Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 154 removed outlier: 4.223A pdb=" N LEU C 140 " --> pdb=" O GLY C 136 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.559A pdb=" N ALA C 176 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N MET C 177 " --> pdb=" O TYR C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 177' Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 207 through 213 Processing helix chain 'C' and resid 213 through 220 Processing helix chain 'C' and resid 230 through 242 Processing helix chain 'C' and resid 267 through 272 Processing helix chain 'C' and resid 282 through 291 removed outlier: 3.897A pdb=" N LEU C 286 " --> pdb=" O ASP C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 Processing helix chain 'C' and resid 334 through 351 Processing helix chain 'C' and resid 367 through 374 removed outlier: 3.530A pdb=" N GLU C 371 " --> pdb=" O GLY C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 389 removed outlier: 3.542A pdb=" N HIS C 378 " --> pdb=" O GLY C 374 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 382 " --> pdb=" O HIS C 378 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU C 383 " --> pdb=" O GLY C 379 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA C 389 " --> pdb=" O ALA C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.526A pdb=" N VAL C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 415 removed outlier: 3.532A pdb=" N GLY C 415 " --> pdb=" O LYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 440 Processing helix chain 'C' and resid 441 through 444 Processing helix chain 'C' and resid 447 through 462 Processing helix chain 'C' and resid 464 through 470 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 481 through 493 removed outlier: 3.708A pdb=" N GLY C 491 " --> pdb=" O ALA C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'D' and resid 6 through 16 Processing helix chain 'D' and resid 20 through 30 Processing helix chain 'D' and resid 34 through 43 Processing helix chain 'D' and resid 60 through 67 removed outlier: 4.402A pdb=" N GLY D 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N GLU D 65 " --> pdb=" O PHE D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 99 Processing helix chain 'D' and resid 101 through 119 removed outlier: 3.730A pdb=" N LYS D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 108 " --> pdb=" O HIS D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 135 Processing helix chain 'D' and resid 136 through 154 removed outlier: 4.003A pdb=" N LEU D 140 " --> pdb=" O GLY D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 removed outlier: 4.189A pdb=" N ASP D 171 " --> pdb=" O ALA D 168 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 207 through 213 Processing helix chain 'D' and resid 213 through 220 Processing helix chain 'D' and resid 230 through 243 removed outlier: 3.999A pdb=" N ASP D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 272 removed outlier: 3.549A pdb=" N LEU D 269 " --> pdb=" O ASP D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 291 removed outlier: 4.149A pdb=" N LEU D 286 " --> pdb=" O ASP D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 Processing helix chain 'D' and resid 334 through 351 removed outlier: 3.639A pdb=" N PHE D 351 " --> pdb=" O PHE D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 374 removed outlier: 3.615A pdb=" N GLU D 371 " --> pdb=" O GLY D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 removed outlier: 3.586A pdb=" N HIS D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU D 382 " --> pdb=" O HIS D 378 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 383 " --> pdb=" O GLY D 379 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 388 " --> pdb=" O PHE D 384 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA D 389 " --> pdb=" O ALA D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.538A pdb=" N VAL D 408 " --> pdb=" O GLY D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 440 Processing helix chain 'D' and resid 441 through 444 removed outlier: 3.805A pdb=" N ILE D 444 " --> pdb=" O ARG D 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 441 through 444' Processing helix chain 'D' and resid 447 through 462 Processing helix chain 'D' and resid 464 through 470 removed outlier: 3.612A pdb=" N ARG D 470 " --> pdb=" O VAL D 466 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 480 No H-bonds generated for 'chain 'D' and resid 478 through 480' Processing helix chain 'D' and resid 481 through 493 removed outlier: 3.603A pdb=" N GLY D 491 " --> pdb=" O ALA D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'E' and resid 6 through 16 Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 95 through 99 Processing helix chain 'E' and resid 101 through 119 removed outlier: 3.732A pdb=" N LYS E 107 " --> pdb=" O ALA E 103 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE E 108 " --> pdb=" O HIS E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 Processing helix chain 'E' and resid 136 through 154 removed outlier: 4.299A pdb=" N LEU E 140 " --> pdb=" O GLY E 136 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY E 141 " --> pdb=" O VAL E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.633A pdb=" N MET E 177 " --> pdb=" O TYR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 207 through 213 Processing helix chain 'E' and resid 213 through 220 Processing helix chain 'E' and resid 230 through 243 removed outlier: 3.695A pdb=" N ASP E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 272 removed outlier: 3.523A pdb=" N LEU E 269 " --> pdb=" O ASP E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 291 removed outlier: 4.031A pdb=" N LEU E 286 " --> pdb=" O ASP E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 332 Processing helix chain 'E' and resid 334 through 351 Processing helix chain 'E' and resid 367 through 373 removed outlier: 3.621A pdb=" N GLU E 371 " --> pdb=" O GLY E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 removed outlier: 4.103A pdb=" N LEU E 382 " --> pdb=" O HIS E 378 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU E 383 " --> pdb=" O GLY E 379 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA E 389 " --> pdb=" O ALA E 385 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 411 through 415 Processing helix chain 'E' and resid 431 through 440 Processing helix chain 'E' and resid 441 through 444 Processing helix chain 'E' and resid 447 through 462 Processing helix chain 'E' and resid 464 through 470 Processing helix chain 'E' and resid 478 through 480 No H-bonds generated for 'chain 'E' and resid 478 through 480' Processing helix chain 'E' and resid 481 through 493 Processing helix chain 'E' and resid 494 through 496 No H-bonds generated for 'chain 'E' and resid 494 through 496' Processing helix chain 'F' and resid 6 through 16 Processing helix chain 'F' and resid 20 through 30 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 63 through 67 removed outlier: 3.699A pdb=" N LYS F 66 " --> pdb=" O GLY F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 101 through 119 Processing helix chain 'F' and resid 132 through 134 No H-bonds generated for 'chain 'F' and resid 132 through 134' Processing helix chain 'F' and resid 135 through 154 removed outlier: 4.106A pdb=" N LEU F 140 " --> pdb=" O GLY F 136 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 177 removed outlier: 3.743A pdb=" N ALA F 176 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET F 177 " --> pdb=" O TYR F 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 177' Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 207 through 213 Processing helix chain 'F' and resid 213 through 220 Processing helix chain 'F' and resid 230 through 243 removed outlier: 3.849A pdb=" N ASP F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 272 Processing helix chain 'F' and resid 282 through 291 removed outlier: 4.012A pdb=" N LEU F 286 " --> pdb=" O ASP F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 332 Processing helix chain 'F' and resid 334 through 351 Processing helix chain 'F' and resid 367 through 373 removed outlier: 3.585A pdb=" N GLU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 removed outlier: 3.523A pdb=" N HIS F 378 " --> pdb=" O GLY F 374 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 382 " --> pdb=" O HIS F 378 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU F 383 " --> pdb=" O GLY F 379 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 389 " --> pdb=" O ALA F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 409 removed outlier: 3.604A pdb=" N VAL F 408 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 415 Processing helix chain 'F' and resid 431 through 440 Processing helix chain 'F' and resid 441 through 444 Processing helix chain 'F' and resid 447 through 462 removed outlier: 3.525A pdb=" N LEU F 462 " --> pdb=" O GLU F 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 470 Processing helix chain 'F' and resid 478 through 480 No H-bonds generated for 'chain 'F' and resid 478 through 480' Processing helix chain 'F' and resid 481 through 493 removed outlier: 3.914A pdb=" N GLY F 491 " --> pdb=" O ALA F 487 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 496 No H-bonds generated for 'chain 'F' and resid 494 through 496' Processing helix chain 'G' and resid 401 through 412 Processing helix chain 'G' and resid 424 through 430 Processing helix chain 'G' and resid 460 through 483 Processing helix chain 'G' and resid 579 through 587 Processing helix chain 'H' and resid 460 through 483 Processing helix chain 'H' and resid 579 through 587 Processing helix chain 'I' and resid 401 through 414 Processing helix chain 'I' and resid 423 through 430 Processing helix chain 'I' and resid 460 through 483 removed outlier: 3.773A pdb=" N ARG I 466 " --> pdb=" O PRO I 462 " (cutoff:3.500A) Processing helix chain 'I' and resid 491 through 495 removed outlier: 3.740A pdb=" N LEU I 494 " --> pdb=" O ASP I 491 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU I 495 " --> pdb=" O PRO I 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 491 through 495' Processing helix chain 'I' and resid 580 through 587 removed outlier: 3.620A pdb=" N ASP I 587 " --> pdb=" O ALA I 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 402 through 415 Processing helix chain 'J' and resid 423 through 433 Processing helix chain 'J' and resid 460 through 483 Processing helix chain 'J' and resid 579 through 586 Processing helix chain 'K' and resid 401 through 415 Processing helix chain 'K' and resid 423 through 433 Processing helix chain 'K' and resid 460 through 483 removed outlier: 4.184A pdb=" N HIS K 465 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG K 466 " --> pdb=" O PRO K 462 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL K 470 " --> pdb=" O ARG K 466 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP K 475 " --> pdb=" O ALA K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 491 through 495 removed outlier: 3.649A pdb=" N LEU K 494 " --> pdb=" O ASP K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 579 through 587 removed outlier: 3.812A pdb=" N ASP K 587 " --> pdb=" O ALA K 583 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 413 removed outlier: 3.699A pdb=" N ILE L 405 " --> pdb=" O ARG L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 432 Processing helix chain 'L' and resid 460 through 483 Processing helix chain 'L' and resid 491 through 495 removed outlier: 3.683A pdb=" N LEU L 494 " --> pdb=" O ASP L 491 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU L 495 " --> pdb=" O PRO L 492 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 491 through 495' Processing helix chain 'L' and resid 579 through 588 removed outlier: 3.913A pdb=" N LEU L 588 " --> pdb=" O GLU L 584 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 4.811A pdb=" N THR A 76 " --> pdb=" O PHE A 51 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A 180 " --> pdb=" O GLN A 159 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N PHE A 228 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N MET A 183 " --> pdb=" O PHE A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 6.741A pdb=" N CYS A 167 " --> pdb=" O PHE A 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 5.564A pdb=" N ASP A 360 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL A 361 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A 400 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLN A 426 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ARG A 399 " --> pdb=" O GLN A 426 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA A 428 " --> pdb=" O ARG A 399 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA A 401 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 5.564A pdb=" N ASP A 360 " --> pdb=" O ASN A 324 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N VAL A 361 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LYS A 400 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LEU A 393 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N TYR A 420 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR A 395 " --> pdb=" O TYR A 420 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 475 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 50 removed outlier: 6.288A pdb=" N ILE B 122 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N VAL B 162 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY B 124 " --> pdb=" O VAL B 162 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 180 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 184 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 226 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.796A pdb=" N CYS B 167 " --> pdb=" O PHE B 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 297 through 298 removed outlier: 8.578A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL B 361 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS B 400 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ALA B 428 " --> pdb=" O ARG B 399 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ALA B 401 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 297 through 298 removed outlier: 8.578A pdb=" N VAL B 356 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLY B 320 " --> pdb=" O VAL B 356 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N PHE B 358 " --> pdb=" O GLY B 320 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 322 " --> pdb=" O PHE B 358 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP B 360 " --> pdb=" O VAL B 322 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASN B 324 " --> pdb=" O ASP B 360 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N VAL B 361 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS B 400 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU B 393 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 8.297A pdb=" N TYR B 420 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B 395 " --> pdb=" O TYR B 420 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU B 475 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 49 through 50 removed outlier: 3.651A pdb=" N PHE C 180 " --> pdb=" O GLN C 159 " (cutoff:3.500A) removed outlier: 9.163A pdb=" N PHE C 228 " --> pdb=" O ILE C 181 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N MET C 183 " --> pdb=" O PHE C 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 297 through 298 removed outlier: 8.563A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL C 361 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS C 400 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN C 426 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG C 399 " --> pdb=" O GLN C 426 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ALA C 428 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA C 401 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 297 through 298 removed outlier: 8.563A pdb=" N VAL C 356 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY C 320 " --> pdb=" O VAL C 356 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N PHE C 358 " --> pdb=" O GLY C 320 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL C 322 " --> pdb=" O PHE C 358 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N ASP C 360 " --> pdb=" O VAL C 322 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASN C 324 " --> pdb=" O ASP C 360 " (cutoff:3.500A) removed outlier: 8.805A pdb=" N VAL C 361 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS C 400 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU C 393 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N TYR C 420 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR C 395 " --> pdb=" O TYR C 420 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU C 475 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.738A pdb=" N THR D 76 " --> pdb=" O PHE D 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE D 180 " --> pdb=" O GLN D 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 184 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N PHE D 228 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET D 183 " --> pdb=" O PHE D 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 297 through 298 removed outlier: 5.492A pdb=" N ASP D 360 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL D 361 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS D 400 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN D 426 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG D 399 " --> pdb=" O GLN D 426 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ALA D 428 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA D 401 " --> pdb=" O ALA D 428 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 297 through 298 removed outlier: 5.492A pdb=" N ASP D 360 " --> pdb=" O ASN D 324 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL D 361 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LYS D 400 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU D 393 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N TYR D 420 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR D 395 " --> pdb=" O TYR D 420 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU D 475 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 49 through 51 removed outlier: 4.796A pdb=" N THR E 76 " --> pdb=" O PHE E 51 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE E 122 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N VAL E 162 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY E 124 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE E 180 " --> pdb=" O GLN E 159 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL E 184 " --> pdb=" O ILE E 163 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 226 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 166 through 168 removed outlier: 4.111A pdb=" N PHE E 191 " --> pdb=" O CYS E 167 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 297 through 298 removed outlier: 8.591A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL E 361 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS E 400 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N GLN E 426 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ARG E 399 " --> pdb=" O GLN E 426 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA E 428 " --> pdb=" O ARG E 399 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA E 401 " --> pdb=" O ALA E 428 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 297 through 298 removed outlier: 8.591A pdb=" N VAL E 356 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY E 320 " --> pdb=" O VAL E 356 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE E 358 " --> pdb=" O GLY E 320 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL E 322 " --> pdb=" O PHE E 358 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ASP E 360 " --> pdb=" O VAL E 322 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N ASN E 324 " --> pdb=" O ASP E 360 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL E 361 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N LYS E 400 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU E 393 " --> pdb=" O LEU E 418 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N TYR E 420 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 395 " --> pdb=" O TYR E 420 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU E 475 " --> pdb=" O ASN E 419 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 49 through 50 removed outlier: 3.757A pdb=" N PHE F 180 " --> pdb=" O GLN F 159 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N PHE F 228 " --> pdb=" O ILE F 181 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N MET F 183 " --> pdb=" O PHE F 228 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 166 through 168 removed outlier: 6.716A pdb=" N CYS F 167 " --> pdb=" O PHE F 191 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 297 through 298 removed outlier: 5.384A pdb=" N ASP F 360 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL F 361 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS F 400 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N ALA F 428 " --> pdb=" O ARG F 399 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ALA F 401 " --> pdb=" O ALA F 428 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 297 through 298 removed outlier: 5.384A pdb=" N ASP F 360 " --> pdb=" O ASN F 324 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N VAL F 361 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LYS F 400 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 393 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N TYR F 420 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR F 395 " --> pdb=" O TYR F 420 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 475 " --> pdb=" O ASN F 419 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 335 through 339 removed outlier: 3.798A pdb=" N VAL G 335 " --> pdb=" O THR G 396 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR G 396 " --> pdb=" O VAL G 335 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 357 through 359 removed outlier: 4.068A pdb=" N THR G 357 " --> pdb=" O GLU G 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU G 418 " --> pdb=" O THR G 357 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 508 through 513 removed outlier: 3.574A pdb=" N GLN G 508 " --> pdb=" O LEU G 505 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP G 517 " --> pdb=" O ASP G 520 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 600 through 602 removed outlier: 3.891A pdb=" N LEU G 664 " --> pdb=" O LEU G 601 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU G 665 " --> pdb=" O LYS G 648 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LYS G 648 " --> pdb=" O GLU G 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 609 through 612 removed outlier: 6.692A pdb=" N ILE G 628 " --> pdb=" O LYS G 610 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 500 through 505 removed outlier: 3.673A pdb=" N GLN H 508 " --> pdb=" O LEU H 505 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 600 through 602 removed outlier: 3.574A pdb=" N LEU H 664 " --> pdb=" O LEU H 601 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 637 through 639 removed outlier: 6.841A pdb=" N LEU H 638 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N LEU H 626 " --> pdb=" O ILE H 612 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE H 612 " --> pdb=" O LEU H 626 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE H 628 " --> pdb=" O LYS H 610 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY H 607 " --> pdb=" O LEU H 657 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 619 through 620 removed outlier: 3.643A pdb=" N GLY H 644 " --> pdb=" O VAL H 620 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 336 through 340 removed outlier: 4.504A pdb=" N ALA I 392 " --> pdb=" O VAL I 339 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 357 through 359 removed outlier: 3.569A pdb=" N ALA I 416 " --> pdb=" O GLN I 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 501 through 504 Processing sheet with id=AD8, first strand: chain 'I' and resid 608 through 609 removed outlier: 3.962A pdb=" N ALA I 627 " --> pdb=" O LEU I 638 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 648 through 649 removed outlier: 3.765A pdb=" N LYS I 648 " --> pdb=" O GLU I 665 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU I 665 " --> pdb=" O LYS I 648 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'J' and resid 336 through 340 removed outlier: 4.328A pdb=" N ALA J 392 " --> pdb=" O VAL J 339 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 342 through 343 Processing sheet with id=AE3, first strand: chain 'J' and resid 357 through 359 removed outlier: 3.745A pdb=" N THR J 357 " --> pdb=" O GLU J 418 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 500 through 504 Processing sheet with id=AE5, first strand: chain 'J' and resid 619 through 620 removed outlier: 3.628A pdb=" N GLY J 644 " --> pdb=" O VAL J 620 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 625 through 630 removed outlier: 4.290A pdb=" N ALA J 627 " --> pdb=" O LEU J 638 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 648 through 649 removed outlier: 3.675A pdb=" N LYS J 648 " --> pdb=" O GLU J 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 336 through 339 Processing sheet with id=AE9, first strand: chain 'K' and resid 357 through 358 removed outlier: 3.564A pdb=" N THR K 357 " --> pdb=" O GLU K 418 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 530 through 531 removed outlier: 3.792A pdb=" N VAL K 523 " --> pdb=" O ALA K 531 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 600 through 602 removed outlier: 4.067A pdb=" N LEU K 664 " --> pdb=" O LEU K 601 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 608 through 612 removed outlier: 6.884A pdb=" N ILE K 628 " --> pdb=" O LYS K 610 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ILE K 612 " --> pdb=" O LEU K 626 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LEU K 626 " --> pdb=" O ILE K 612 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA K 627 " --> pdb=" O LEU K 638 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 619 through 620 removed outlier: 3.996A pdb=" N VAL K 620 " --> pdb=" O GLY K 644 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY K 644 " --> pdb=" O VAL K 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 336 through 340 removed outlier: 7.205A pdb=" N SER L 337 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS L 393 " --> pdb=" O SER L 337 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL L 339 " --> pdb=" O ILE L 391 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 357 through 359 removed outlier: 3.607A pdb=" N THR L 357 " --> pdb=" O GLU L 418 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 520 through 524 removed outlier: 3.709A pdb=" N GLN L 508 " --> pdb=" O LEU L 505 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL L 548 " --> pdb=" O GLN L 551 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG L 534 " --> pdb=" O THR L 547 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 600 through 602 removed outlier: 4.385A pdb=" N LEU L 664 " --> pdb=" O LEU L 601 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 608 through 612 removed outlier: 6.469A pdb=" N ILE L 628 " --> pdb=" O LYS L 610 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 619 through 620 removed outlier: 3.522A pdb=" N VAL L 620 " --> pdb=" O GLY L 644 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY L 644 " --> pdb=" O VAL L 620 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 1664 hydrogen bonds defined for protein. 4572 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: 9.44 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6263 1.31 - 1.44: 9116 1.44 - 1.57: 21376 1.57 - 1.70: 30 1.70 - 1.83: 293 Bond restraints: 37078 Sorted by residual: bond pdb=" C9P COA A 601 " pdb=" N8P COA A 601 " ideal model delta sigma weight residual 1.340 1.485 -0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" C9P COA B 601 " pdb=" N8P COA B 601 " ideal model delta sigma weight residual 1.340 1.483 -0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" C9P COA F 601 " pdb=" N8P COA F 601 " ideal model delta sigma weight residual 1.340 1.482 -0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C5P COA F 601 " pdb=" N4P COA F 601 " ideal model delta sigma weight residual 1.348 1.477 -0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" C5P COA A 601 " pdb=" N4P COA A 601 " ideal model delta sigma weight residual 1.348 1.475 -0.127 2.00e-02 2.50e+03 4.03e+01 ... (remaining 37073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 49900 4.16 - 8.32: 207 8.32 - 12.47: 57 12.47 - 16.63: 2 16.63 - 20.79: 12 Bond angle restraints: 50178 Sorted by residual: angle pdb=" O4A COA A 601 " pdb=" P2A COA A 601 " pdb=" O5A COA A 601 " ideal model delta sigma weight residual 120.51 99.72 20.79 3.00e+00 1.11e-01 4.80e+01 angle pdb=" O1A COA A 601 " pdb=" P1A COA A 601 " pdb=" O2A COA A 601 " ideal model delta sigma weight residual 120.41 100.22 20.19 3.00e+00 1.11e-01 4.53e+01 angle pdb=" O4A COA C 601 " pdb=" P2A COA C 601 " pdb=" O5A COA C 601 " ideal model delta sigma weight residual 120.51 100.68 19.83 3.00e+00 1.11e-01 4.37e+01 angle pdb=" O4A COA D 601 " pdb=" P2A COA D 601 " pdb=" O5A COA D 601 " ideal model delta sigma weight residual 120.51 100.75 19.76 3.00e+00 1.11e-01 4.34e+01 angle pdb=" O1A COA D 601 " pdb=" P1A COA D 601 " pdb=" O2A COA D 601 " ideal model delta sigma weight residual 120.41 100.91 19.50 3.00e+00 1.11e-01 4.23e+01 ... (remaining 50173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 19986 18.03 - 36.06: 2128 36.06 - 54.09: 383 54.09 - 72.12: 94 72.12 - 90.15: 40 Dihedral angle restraints: 22631 sinusoidal: 9328 harmonic: 13303 Sorted by residual: dihedral pdb=" CA ASP C 127 " pdb=" C ASP C 127 " pdb=" N ALA C 128 " pdb=" CA ALA C 128 " ideal model delta harmonic sigma weight residual -180.00 -156.82 -23.18 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA PHE E 51 " pdb=" C PHE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta harmonic sigma weight residual 180.00 158.46 21.54 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA PHE H 578 " pdb=" C PHE H 578 " pdb=" N THR H 579 " pdb=" CA THR H 579 " ideal model delta harmonic sigma weight residual 180.00 159.51 20.49 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 22628 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 4345 0.061 - 0.122: 1162 0.122 - 0.183: 117 0.183 - 0.244: 7 0.244 - 0.304: 4 Chirality restraints: 5635 Sorted by residual: chirality pdb=" C2 BTI L 701 " pdb=" C4 BTI L 701 " pdb=" C7 BTI L 701 " pdb=" S1 BTI L 701 " both_signs ideal model delta sigma weight residual False 3.11 3.41 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C3B COA D 601 " pdb=" C2B COA D 601 " pdb=" C4B COA D 601 " pdb=" O3B COA D 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA LYS J 633 " pdb=" N LYS J 633 " pdb=" C LYS J 633 " pdb=" CB LYS J 633 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 5632 not shown) Planarity restraints: 6569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 BTI G 701 " 0.078 2.00e-02 2.50e+03 2.06e-01 6.39e+02 pdb=" C4 BTI G 701 " -0.096 2.00e-02 2.50e+03 pdb=" C5 BTI G 701 " -0.228 2.00e-02 2.50e+03 pdb=" N2 BTI G 701 " 0.190 2.00e-02 2.50e+03 pdb=" N3 BTI G 701 " 0.302 2.00e-02 2.50e+03 pdb=" O3 BTI G 701 " -0.247 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI L 701 " -0.066 2.00e-02 2.50e+03 1.84e-01 5.10e+02 pdb=" C4 BTI L 701 " 0.159 2.00e-02 2.50e+03 pdb=" C5 BTI L 701 " 0.137 2.00e-02 2.50e+03 pdb=" N2 BTI L 701 " -0.237 2.00e-02 2.50e+03 pdb=" N3 BTI L 701 " -0.219 2.00e-02 2.50e+03 pdb=" O3 BTI L 701 " 0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 BTI J 701 " 0.065 2.00e-02 2.50e+03 1.84e-01 5.06e+02 pdb=" C4 BTI J 701 " -0.046 2.00e-02 2.50e+03 pdb=" C5 BTI J 701 " -0.231 2.00e-02 2.50e+03 pdb=" N2 BTI J 701 " 0.137 2.00e-02 2.50e+03 pdb=" N3 BTI J 701 " 0.283 2.00e-02 2.50e+03 pdb=" O3 BTI J 701 " -0.209 2.00e-02 2.50e+03 ... (remaining 6566 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4801 2.74 - 3.28: 34780 3.28 - 3.82: 54151 3.82 - 4.36: 61139 4.36 - 4.90: 112566 Nonbonded interactions: 267437 Sorted by model distance: nonbonded pdb=" NZ LYS B 381 " pdb=" OXT LEU B 510 " model vdw 2.201 3.120 nonbonded pdb=" OG SER D 99 " pdb=" O GLY D 130 " model vdw 2.206 3.040 nonbonded pdb=" OG1 THR D 34 " pdb=" OE1 GLU D 37 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLU E 475 " pdb=" NH1 ARG E 485 " model vdw 2.211 3.120 nonbonded pdb=" OG1 THR A 34 " pdb=" OE1 GLU A 37 " model vdw 2.213 3.040 ... (remaining 267432 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 510 or (resid 601 and (name C1B or name C2A or n \ ame C2B or name C3B or name C4A or name C4B or name C5A or name C5B or name C6A \ or name C8A or name N1A or name N3A or name N6A or name N7A or name N9A or name \ O1A or name O2A or name O2B or name O3A or name O3B or name O4A or name O4B or n \ ame O5A or name O5B or name O6A or name O7A or name O8A or name O9A or name P1A \ or name P2A or name P3B)))) selection = (chain 'B' and (resid 5 through 510 or (resid 601 and (name C1B or name C2A or n \ ame C2B or name C3B or name C4A or name C4B or name C5A or name C5B or name C6A \ or name C8A or name N1A or name N3A or name N6A or name N7A or name N9A or name \ O1A or name O2A or name O2B or name O3A or name O3B or name O4A or name O4B or n \ ame O5A or name O5B or name O6A or name O7A or name O8A or name O9A or name P1A \ or name P2A or name P3B)))) selection = (chain 'C' and (resid 5 through 510 or (resid 601 and (name C1B or name C2A or n \ ame C2B or name C3B or name C4A or name C4B or name C5A or name C5B or name C6A \ or name C8A or name N1A or name N3A or name N6A or name N7A or name N9A or name \ O1A or name O2A or name O2B or name O3A or name O3B or name O4A or name O4B or n \ ame O5A or name O5B or name O6A or name O7A or name O8A or name O9A or name P1A \ or name P2A or name P3B)))) selection = (chain 'D' and (resid 5 through 510 or (resid 601 and (name C1B or name C2A or n \ ame C2B or name C3B or name C4A or name C4B or name C5A or name C5B or name C6A \ or name C8A or name N1A or name N3A or name N6A or name N7A or name N9A or name \ O1A or name O2A or name O2B or name O3A or name O3B or name O4A or name O4B or n \ ame O5A or name O5B or name O6A or name O7A or name O8A or name O9A or name P1A \ or name P2A or name P3B)))) selection = chain 'E' selection = (chain 'F' and (resid 5 through 510 or (resid 601 and (name C1B or name C2A or n \ ame C2B or name C3B or name C4A or name C4B or name C5A or name C5B or name C6A \ or name C8A or name N1A or name N3A or name N6A or name N7A or name N9A or name \ O1A or name O2A or name O2B or name O3A or name O3B or name O4A or name O4B or n \ ame O5A or name O5B or name O6A or name O7A or name O8A or name O9A or name P1A \ or name P2A or name P3B)))) } ncs_group { reference = (chain 'G' and (resid 334 through 339 or resid 354 through 396 or resid 401 thro \ ugh 431 or resid 456 through 701)) selection = (chain 'I' and (resid 334 through 339 or resid 354 through 382 or resid 389 thro \ ugh 396 or resid 401 through 431 or resid 456 through 701)) selection = (chain 'J' and (resid 334 through 339 or resid 354 through 361 or resid 370 thro \ ugh 382 or resid 389 through 431 or resid 456 through 701)) selection = (chain 'K' and (resid 334 through 339 or resid 354 through 361 or resid 370 thro \ ugh 382 or resid 389 through 396 or resid 401 through 431 or resid 456 through 7 \ 01)) selection = (chain 'L' and (resid 334 through 339 or resid 354 through 382 or resid 389 thro \ ugh 396 or resid 401 through 431 or resid 456 through 701)) } 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: 1.180 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 33.910 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.080 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.009 0.145 37084 Z= 0.415 Angle : 0.942 20.790 50178 Z= 0.473 Chirality : 0.052 0.304 5635 Planarity : 0.008 0.206 6569 Dihedral : 15.459 90.151 14077 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.10), residues: 4638 helix: -1.46 (0.11), residues: 1547 sheet: -0.75 (0.17), residues: 766 loop : -2.39 (0.11), residues: 2325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 481 TYR 0.017 0.002 TYR D 173 PHE 0.027 0.002 PHE B 384 TRP 0.023 0.002 TRP J 537 HIS 0.008 0.002 HIS C 378 Details of bonding type rmsd covalent geometry : bond 0.00923 (37078) covalent geometry : angle 0.94231 (50178) hydrogen bonds : bond 0.18709 ( 1562) hydrogen bonds : angle 7.12621 ( 4572) Misc. bond : bond 0.08902 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 1.715 Fit side-chains REVERT: C 177 MET cc_start: 0.8991 (mtm) cc_final: 0.8775 (mtp) REVERT: E 243 ASP cc_start: 0.8342 (m-30) cc_final: 0.7873 (t0) REVERT: E 497 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7721 (mt-10) REVERT: F 255 GLU cc_start: 0.8442 (pp20) cc_final: 0.8176 (pp20) REVERT: F 449 LYS cc_start: 0.7932 (tppp) cc_final: 0.7404 (tptp) REVERT: F 452 GLU cc_start: 0.8639 (tt0) cc_final: 0.8395 (tm-30) REVERT: I 390 MET cc_start: 0.7662 (mpp) cc_final: 0.7383 (mpp) REVERT: I 599 LYS cc_start: 0.7686 (mppt) cc_final: 0.7431 (mmtm) REVERT: I 632 MET cc_start: 0.9123 (mtt) cc_final: 0.8826 (mtt) REVERT: J 390 MET cc_start: 0.7822 (ttm) cc_final: 0.7119 (mmp) REVERT: J 589 MET cc_start: 0.8762 (mmp) cc_final: 0.8551 (mmp) REVERT: K 386 HIS cc_start: 0.7955 (m-70) cc_final: 0.7644 (m170) REVERT: K 393 LYS cc_start: 0.8211 (mttt) cc_final: 0.7692 (mtmt) REVERT: K 482 LYS cc_start: 0.8973 (ttpt) cc_final: 0.8757 (tmmt) REVERT: K 613 MET cc_start: 0.7723 (ptp) cc_final: 0.7416 (mmp) REVERT: K 634 MET cc_start: 0.7968 (ttm) cc_final: 0.7305 (tpp) REVERT: L 610 LYS cc_start: 0.8720 (mtpp) cc_final: 0.8253 (mtpp) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2361 time to fit residues: 113.0560 Evaluate side-chains 240 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 7.9990 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 HIS A 217 HIS A 237 GLN A 325 GLN A 349 ASN A 378 HIS A 388 GLN A 413 HIS B 57 HIS B 104 HIS B 217 HIS B 325 GLN B 378 HIS B 388 GLN B 413 HIS C 57 HIS ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 278 ASN C 325 GLN C 388 GLN C 413 HIS C 480 HIS D 217 HIS D 278 ASN D 325 GLN D 349 ASN D 413 HIS D 480 HIS E 57 HIS ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 217 HIS E 388 GLN E 480 HIS F 57 HIS F 104 HIS F 217 HIS F 349 ASN F 388 GLN F 413 HIS G 611 GLN H 479 ASN H 562 ASN H 594 ASN H 618 GLN I 386 HIS I 488 GLN I 618 GLN J 359 GLN J 567 GLN J 622 ASN K 373 ASN L 408 GLN L 488 GLN L 498 GLN Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.072514 restraints weight = 68777.576| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.77 r_work: 0.2839 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 37084 Z= 0.175 Angle : 0.592 8.157 50178 Z= 0.314 Chirality : 0.046 0.164 5635 Planarity : 0.005 0.067 6569 Dihedral : 9.254 89.427 5504 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.54 % Allowed : 13.10 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.12), residues: 4638 helix: 0.17 (0.13), residues: 1633 sheet: -0.18 (0.18), residues: 774 loop : -1.96 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 485 TYR 0.013 0.001 TYR G 358 PHE 0.016 0.001 PHE L 578 TRP 0.018 0.002 TRP J 544 HIS 0.005 0.001 HIS C 104 Details of bonding type rmsd covalent geometry : bond 0.00422 (37078) covalent geometry : angle 0.59166 (50178) hydrogen bonds : bond 0.05335 ( 1562) hydrogen bonds : angle 5.16270 ( 4572) Misc. bond : bond 0.00049 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.8128 (ttm) REVERT: B 127 ASP cc_start: 0.8565 (t0) cc_final: 0.7885 (t0) REVERT: C 177 MET cc_start: 0.9039 (mtm) cc_final: 0.8786 (mtp) REVERT: C 217 HIS cc_start: 0.9095 (OUTLIER) cc_final: 0.8858 (m-70) REVERT: C 500 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8325 (mt0) REVERT: D 64 MET cc_start: 0.7971 (tpp) cc_final: 0.7706 (ttt) REVERT: D 293 GLU cc_start: 0.8977 (mp0) cc_final: 0.8600 (mp0) REVERT: D 409 MET cc_start: 0.9111 (mmm) cc_final: 0.8678 (mmt) REVERT: E 243 ASP cc_start: 0.8705 (m-30) cc_final: 0.7983 (t0) REVERT: E 458 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8280 (tm-30) REVERT: E 497 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8229 (mt-10) REVERT: F 217 HIS cc_start: 0.9231 (OUTLIER) cc_final: 0.8934 (m-70) REVERT: F 255 GLU cc_start: 0.8682 (pp20) cc_final: 0.8373 (pp20) REVERT: F 449 LYS cc_start: 0.7786 (tppp) cc_final: 0.7313 (tptp) REVERT: F 452 GLU cc_start: 0.8689 (tt0) cc_final: 0.8381 (tm-30) REVERT: G 613 MET cc_start: 0.8850 (ptp) cc_final: 0.8267 (pmm) REVERT: G 634 MET cc_start: 0.7107 (tpp) cc_final: 0.6264 (tpp) REVERT: H 535 SER cc_start: 0.8240 (m) cc_final: 0.7998 (m) REVERT: H 633 LYS cc_start: 0.8462 (mttp) cc_final: 0.8201 (mttp) REVERT: I 421 ARG cc_start: 0.6689 (ttp-170) cc_final: 0.6399 (tmm-80) REVERT: I 599 LYS cc_start: 0.7453 (mppt) cc_final: 0.6916 (mtpt) REVERT: I 632 MET cc_start: 0.9057 (mtt) cc_final: 0.8713 (mtt) REVERT: I 634 MET cc_start: 0.7912 (tpp) cc_final: 0.7449 (tpp) REVERT: J 634 MET cc_start: 0.8319 (tpp) cc_final: 0.7832 (tpp) REVERT: K 386 HIS cc_start: 0.8155 (m-70) cc_final: 0.7827 (m170) REVERT: K 390 MET cc_start: 0.7493 (ttp) cc_final: 0.6894 (tpp) REVERT: K 393 LYS cc_start: 0.8131 (mttt) cc_final: 0.7529 (mtmt) REVERT: K 613 MET cc_start: 0.7957 (ptp) cc_final: 0.7312 (mmp) REVERT: K 634 MET cc_start: 0.7960 (ttm) cc_final: 0.6980 (tpp) REVERT: L 426 PHE cc_start: 0.7314 (t80) cc_final: 0.7086 (t80) REVERT: L 610 LYS cc_start: 0.8477 (mtpp) cc_final: 0.8020 (mtpp) outliers start: 58 outliers final: 26 residues processed: 307 average time/residue: 0.2087 time to fit residues: 108.3421 Evaluate side-chains 268 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 217 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 513 THR Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 475 ASP Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 504 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain K residue 373 ASN Chi-restraints excluded: chain K residue 375 THR Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 161 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 274 optimal weight: 9.9990 chunk 343 optimal weight: 0.9990 chunk 50 optimal weight: 10.0000 chunk 191 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 140 optimal weight: 0.9990 chunk 395 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 388 GLN ** C 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN D 57 HIS E 82 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS H 562 ASN I 373 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.075125 restraints weight = 68293.696| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.77 r_work: 0.2891 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 37084 Z= 0.093 Angle : 0.497 6.486 50178 Z= 0.262 Chirality : 0.043 0.143 5635 Planarity : 0.004 0.047 6569 Dihedral : 8.286 87.321 5504 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.60 % Allowed : 14.64 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.12), residues: 4638 helix: 0.88 (0.13), residues: 1633 sheet: 0.20 (0.18), residues: 761 loop : -1.69 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 372 TYR 0.014 0.001 TYR G 358 PHE 0.008 0.001 PHE F 351 TRP 0.015 0.001 TRP J 544 HIS 0.013 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00200 (37078) covalent geometry : angle 0.49695 (50178) hydrogen bonds : bond 0.03794 ( 1562) hydrogen bonds : angle 4.64323 ( 4572) Misc. bond : bond 0.00029 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 277 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8148 (tt) cc_final: 0.7846 (mm) REVERT: A 64 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: A 498 MET cc_start: 0.8620 (ptp) cc_final: 0.8294 (ptm) REVERT: B 127 ASP cc_start: 0.8420 (t0) cc_final: 0.7958 (t0) REVERT: C 177 MET cc_start: 0.9035 (mtm) cc_final: 0.8803 (mtp) REVERT: C 409 MET cc_start: 0.9122 (mmt) cc_final: 0.8726 (mmt) REVERT: C 500 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8263 (mt0) REVERT: D 64 MET cc_start: 0.7896 (tpp) cc_final: 0.7620 (ttt) REVERT: D 293 GLU cc_start: 0.8821 (mp0) cc_final: 0.8600 (mp0) REVERT: D 409 MET cc_start: 0.9114 (mmm) cc_final: 0.8824 (mmt) REVERT: E 243 ASP cc_start: 0.8538 (m-30) cc_final: 0.7960 (t0) REVERT: E 458 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8158 (tm-30) REVERT: E 497 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8173 (mt-10) REVERT: F 217 HIS cc_start: 0.9085 (OUTLIER) cc_final: 0.8848 (m-70) REVERT: F 255 GLU cc_start: 0.8653 (pp20) cc_final: 0.8265 (pp20) REVERT: F 449 LYS cc_start: 0.7676 (tppp) cc_final: 0.7178 (tptp) REVERT: F 452 GLU cc_start: 0.8646 (tt0) cc_final: 0.8354 (tm-30) REVERT: G 613 MET cc_start: 0.8847 (ptp) cc_final: 0.8202 (pmm) REVERT: H 535 SER cc_start: 0.8239 (m) cc_final: 0.7951 (m) REVERT: H 633 LYS cc_start: 0.8463 (mttp) cc_final: 0.8206 (mttp) REVERT: I 599 LYS cc_start: 0.7598 (mppt) cc_final: 0.6992 (mtpt) REVERT: I 632 MET cc_start: 0.8976 (mtt) cc_final: 0.8576 (mtt) REVERT: I 634 MET cc_start: 0.7846 (tpp) cc_final: 0.7515 (tpp) REVERT: J 634 MET cc_start: 0.8223 (tpp) cc_final: 0.8020 (tpp) REVERT: K 373 ASN cc_start: 0.8505 (p0) cc_final: 0.8283 (p0) REVERT: K 390 MET cc_start: 0.7331 (ttp) cc_final: 0.6870 (tpp) REVERT: K 393 LYS cc_start: 0.8087 (mttt) cc_final: 0.7546 (mtmt) REVERT: K 479 ASN cc_start: 0.8500 (t0) cc_final: 0.8251 (t0) REVERT: K 605 MET cc_start: 0.6358 (tpt) cc_final: 0.5972 (tpt) REVERT: K 613 MET cc_start: 0.7998 (ptp) cc_final: 0.7250 (mmp) REVERT: K 634 MET cc_start: 0.7926 (ttm) cc_final: 0.6968 (tpp) REVERT: L 390 MET cc_start: 0.8147 (tmm) cc_final: 0.7935 (tmm) REVERT: L 426 PHE cc_start: 0.7317 (t80) cc_final: 0.7075 (t80) REVERT: L 610 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8135 (mtpp) REVERT: L 634 MET cc_start: 0.7054 (tpp) cc_final: 0.6653 (tpp) outliers start: 60 outliers final: 31 residues processed: 323 average time/residue: 0.2116 time to fit residues: 115.4785 Evaluate side-chains 280 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 137 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 190 MET Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 511 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 226 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 378 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 184 optimal weight: 0.7980 chunk 459 optimal weight: 20.0000 chunk 396 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 434 optimal weight: 10.0000 chunk 394 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 217 HIS C 278 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN ** F 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN L 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.073753 restraints weight = 68310.380| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.83 r_work: 0.2863 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 37084 Z= 0.116 Angle : 0.491 8.374 50178 Z= 0.258 Chirality : 0.043 0.143 5635 Planarity : 0.004 0.043 6569 Dihedral : 7.936 89.962 5504 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.21 % Allowed : 15.73 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.12), residues: 4638 helix: 1.08 (0.13), residues: 1634 sheet: 0.30 (0.18), residues: 771 loop : -1.65 (0.12), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.013 0.001 TYR L 358 PHE 0.013 0.001 PHE L 578 TRP 0.013 0.001 TRP J 544 HIS 0.013 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00276 (37078) covalent geometry : angle 0.49082 (50178) hydrogen bonds : bond 0.04101 ( 1562) hydrogen bonds : angle 4.48874 ( 4572) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 256 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8164 (tt) cc_final: 0.7854 (mm) REVERT: A 64 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7941 (ttm) REVERT: A 148 ARG cc_start: 0.8771 (ttp80) cc_final: 0.8499 (ttp80) REVERT: B 127 ASP cc_start: 0.8610 (t0) cc_final: 0.8185 (t0) REVERT: B 492 MET cc_start: 0.8664 (tmm) cc_final: 0.8343 (tmm) REVERT: B 495 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8549 (t) REVERT: C 53 MET cc_start: 0.8797 (ttm) cc_final: 0.8373 (ttm) REVERT: C 171 ASP cc_start: 0.8152 (t0) cc_final: 0.7943 (t0) REVERT: D 293 GLU cc_start: 0.8783 (mp0) cc_final: 0.8564 (mp0) REVERT: D 409 MET cc_start: 0.9145 (mmm) cc_final: 0.8627 (mmt) REVERT: E 243 ASP cc_start: 0.8501 (m-30) cc_final: 0.7981 (t0) REVERT: E 458 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8213 (tm-30) REVERT: F 255 GLU cc_start: 0.8667 (pp20) cc_final: 0.8334 (pp20) REVERT: F 449 LYS cc_start: 0.7699 (tppp) cc_final: 0.7298 (tptp) REVERT: F 452 GLU cc_start: 0.8670 (tt0) cc_final: 0.8382 (tm-30) REVERT: G 390 MET cc_start: 0.6254 (tmm) cc_final: 0.5939 (tmm) REVERT: G 613 MET cc_start: 0.8911 (ptp) cc_final: 0.8275 (pmm) REVERT: H 535 SER cc_start: 0.8344 (m) cc_final: 0.8042 (m) REVERT: H 633 LYS cc_start: 0.8505 (mttp) cc_final: 0.8246 (mttp) REVERT: I 494 LEU cc_start: 0.7576 (mp) cc_final: 0.7305 (pt) REVERT: I 599 LYS cc_start: 0.7589 (mppt) cc_final: 0.6996 (mtpt) REVERT: I 618 GLN cc_start: 0.6715 (tt0) cc_final: 0.6503 (tt0) REVERT: I 632 MET cc_start: 0.9063 (mtt) cc_final: 0.8634 (mtt) REVERT: I 634 MET cc_start: 0.7964 (tpp) cc_final: 0.7561 (tpp) REVERT: J 479 ASN cc_start: 0.8815 (t0) cc_final: 0.8374 (m110) REVERT: J 634 MET cc_start: 0.8372 (tpp) cc_final: 0.8141 (tpp) REVERT: K 373 ASN cc_start: 0.8502 (p0) cc_final: 0.8222 (p0) REVERT: K 390 MET cc_start: 0.7306 (ttp) cc_final: 0.6838 (tpp) REVERT: K 393 LYS cc_start: 0.8039 (mttt) cc_final: 0.7500 (mtmt) REVERT: K 422 HIS cc_start: 0.8136 (p-80) cc_final: 0.7568 (p90) REVERT: K 479 ASN cc_start: 0.8538 (t0) cc_final: 0.8271 (t0) REVERT: K 497 PHE cc_start: 0.7832 (t80) cc_final: 0.7631 (t80) REVERT: K 605 MET cc_start: 0.6376 (tpt) cc_final: 0.5903 (tpt) REVERT: K 613 MET cc_start: 0.8001 (ptp) cc_final: 0.7220 (mmp) REVERT: K 634 MET cc_start: 0.7965 (ttm) cc_final: 0.6955 (tpp) REVERT: L 426 PHE cc_start: 0.7156 (t80) cc_final: 0.6880 (t80) REVERT: L 610 LYS cc_start: 0.8444 (mtpp) cc_final: 0.8100 (mtpp) REVERT: L 634 MET cc_start: 0.6954 (tpp) cc_final: 0.6405 (tpp) outliers start: 83 outliers final: 54 residues processed: 320 average time/residue: 0.1874 time to fit residues: 104.1942 Evaluate side-chains 300 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 562 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 461 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 401 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 416 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 177 optimal weight: 0.9990 chunk 423 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 394 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS H 562 ASN H 618 GLN K 562 ASN L 562 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.106831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074740 restraints weight = 67877.568| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.78 r_work: 0.2889 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 37084 Z= 0.100 Angle : 0.473 7.251 50178 Z= 0.248 Chirality : 0.043 0.141 5635 Planarity : 0.004 0.039 6569 Dihedral : 7.586 88.561 5504 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.29 % Allowed : 16.13 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4638 helix: 1.26 (0.13), residues: 1628 sheet: 0.44 (0.19), residues: 723 loop : -1.53 (0.12), residues: 2287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 317 TYR 0.012 0.001 TYR L 358 PHE 0.010 0.001 PHE L 578 TRP 0.013 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00235 (37078) covalent geometry : angle 0.47329 (50178) hydrogen bonds : bond 0.03729 ( 1562) hydrogen bonds : angle 4.34872 ( 4572) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 260 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 24 LEU cc_start: 0.8197 (tt) cc_final: 0.7886 (mm) REVERT: A 64 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: A 148 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8453 (ttp80) REVERT: B 127 ASP cc_start: 0.8615 (t0) cc_final: 0.8299 (t0) REVERT: B 492 MET cc_start: 0.8680 (tmm) cc_final: 0.8309 (tmm) REVERT: B 495 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8598 (t) REVERT: C 53 MET cc_start: 0.8816 (ttm) cc_final: 0.8357 (ttm) REVERT: C 171 ASP cc_start: 0.8068 (t0) cc_final: 0.7793 (t0) REVERT: D 164 MET cc_start: 0.9134 (mtt) cc_final: 0.8891 (mtt) REVERT: D 409 MET cc_start: 0.9178 (mmm) cc_final: 0.8689 (mmt) REVERT: E 243 ASP cc_start: 0.8461 (m-30) cc_final: 0.7990 (t0) REVERT: E 458 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8213 (tm-30) REVERT: F 217 HIS cc_start: 0.9139 (OUTLIER) cc_final: 0.8829 (m-70) REVERT: F 255 GLU cc_start: 0.8642 (pp20) cc_final: 0.8318 (pp20) REVERT: F 449 LYS cc_start: 0.7696 (tppp) cc_final: 0.7279 (tptp) REVERT: F 452 GLU cc_start: 0.8660 (tt0) cc_final: 0.8423 (tm-30) REVERT: G 613 MET cc_start: 0.8845 (ptp) cc_final: 0.8168 (pmm) REVERT: H 535 SER cc_start: 0.8412 (m) cc_final: 0.8104 (m) REVERT: H 611 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7284 (tm-30) REVERT: H 613 MET cc_start: 0.7668 (mmt) cc_final: 0.7350 (mmp) REVERT: I 494 LEU cc_start: 0.7600 (mp) cc_final: 0.7297 (pt) REVERT: I 599 LYS cc_start: 0.7634 (mppt) cc_final: 0.7038 (mtpt) REVERT: I 618 GLN cc_start: 0.6681 (tt0) cc_final: 0.6452 (tt0) REVERT: I 632 MET cc_start: 0.8985 (mtt) cc_final: 0.8607 (mtt) REVERT: I 634 MET cc_start: 0.7995 (tpp) cc_final: 0.7588 (tpp) REVERT: J 479 ASN cc_start: 0.8792 (t0) cc_final: 0.8412 (m110) REVERT: J 634 MET cc_start: 0.8437 (tpp) cc_final: 0.8014 (tpp) REVERT: K 373 ASN cc_start: 0.8506 (p0) cc_final: 0.8225 (p0) REVERT: K 390 MET cc_start: 0.7337 (ttp) cc_final: 0.6835 (tpp) REVERT: K 422 HIS cc_start: 0.8159 (p-80) cc_final: 0.7589 (p90) REVERT: K 479 ASN cc_start: 0.8551 (t0) cc_final: 0.8296 (t0) REVERT: K 497 PHE cc_start: 0.7847 (t80) cc_final: 0.7637 (t80) REVERT: K 562 ASN cc_start: 0.7992 (m-40) cc_final: 0.7738 (m110) REVERT: K 605 MET cc_start: 0.6449 (tpt) cc_final: 0.5982 (tpt) REVERT: K 613 MET cc_start: 0.8001 (ptp) cc_final: 0.7204 (mmp) REVERT: K 632 MET cc_start: 0.7648 (mmt) cc_final: 0.7319 (mtt) REVERT: K 634 MET cc_start: 0.7965 (ttm) cc_final: 0.6770 (tpp) REVERT: L 426 PHE cc_start: 0.7166 (t80) cc_final: 0.6877 (t80) REVERT: L 610 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8095 (ttmm) REVERT: L 634 MET cc_start: 0.7079 (tpp) cc_final: 0.6523 (tpp) outliers start: 86 outliers final: 56 residues processed: 332 average time/residue: 0.1867 time to fit residues: 107.1471 Evaluate side-chains 306 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 217 HIS Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 388 GLN Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 217 HIS Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain I residue 609 VAL Chi-restraints excluded: chain J residue 426 PHE Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 251 optimal weight: 5.9990 chunk 257 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 377 optimal weight: 2.9990 chunk 221 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 chunk 463 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 ASN ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 HIS F 278 ASN H 562 ASN H 594 ASN H 618 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.103888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.071827 restraints weight = 68612.902| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.75 r_work: 0.2823 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 37084 Z= 0.200 Angle : 0.548 6.795 50178 Z= 0.288 Chirality : 0.045 0.146 5635 Planarity : 0.004 0.044 6569 Dihedral : 7.604 88.429 5504 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.74 % Allowed : 16.74 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4638 helix: 1.13 (0.13), residues: 1628 sheet: 0.38 (0.18), residues: 763 loop : -1.60 (0.12), residues: 2247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 317 TYR 0.009 0.001 TYR L 358 PHE 0.021 0.001 PHE L 578 TRP 0.012 0.001 TRP J 544 HIS 0.019 0.001 HIS F 217 Details of bonding type rmsd covalent geometry : bond 0.00494 (37078) covalent geometry : angle 0.54772 (50178) hydrogen bonds : bond 0.05210 ( 1562) hydrogen bonds : angle 4.54607 ( 4572) Misc. bond : bond 0.00032 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 244 time to evaluate : 1.393 Fit side-chains revert: symmetry clash REVERT: A 64 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: A 148 ARG cc_start: 0.8844 (ttp80) cc_final: 0.8542 (ttp80) REVERT: B 127 ASP cc_start: 0.8715 (t0) cc_final: 0.8181 (t0) REVERT: B 492 MET cc_start: 0.8764 (tmm) cc_final: 0.8302 (tmm) REVERT: B 495 THR cc_start: 0.9078 (OUTLIER) cc_final: 0.8564 (t) REVERT: C 171 ASP cc_start: 0.8266 (t0) cc_final: 0.7986 (t0) REVERT: C 500 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: D 164 MET cc_start: 0.9226 (mtt) cc_final: 0.8946 (mtt) REVERT: D 409 MET cc_start: 0.9226 (mmm) cc_final: 0.8893 (mmt) REVERT: E 243 ASP cc_start: 0.8530 (m-30) cc_final: 0.7945 (t0) REVERT: E 458 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8199 (tm-30) REVERT: F 255 GLU cc_start: 0.8600 (pp20) cc_final: 0.8317 (pp20) REVERT: F 449 LYS cc_start: 0.7710 (tppp) cc_final: 0.7276 (tptp) REVERT: F 452 GLU cc_start: 0.8709 (tt0) cc_final: 0.8395 (tm-30) REVERT: G 390 MET cc_start: 0.6226 (tmm) cc_final: 0.5954 (tmm) REVERT: G 613 MET cc_start: 0.8995 (ptp) cc_final: 0.8263 (pmm) REVERT: H 535 SER cc_start: 0.8397 (m) cc_final: 0.8148 (m) REVERT: H 600 GLN cc_start: 0.7744 (mt0) cc_final: 0.7521 (mt0) REVERT: I 478 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7479 (mt) REVERT: I 599 LYS cc_start: 0.7534 (mppt) cc_final: 0.6950 (mtpt) REVERT: I 618 GLN cc_start: 0.6726 (tt0) cc_final: 0.6481 (tt0) REVERT: I 632 MET cc_start: 0.9017 (mtt) cc_final: 0.8588 (mtt) REVERT: I 634 MET cc_start: 0.8000 (tpp) cc_final: 0.7480 (tpp) REVERT: J 634 MET cc_start: 0.8360 (tpp) cc_final: 0.7886 (tpp) REVERT: K 373 ASN cc_start: 0.8449 (p0) cc_final: 0.8212 (p0) REVERT: K 390 MET cc_start: 0.7325 (ttp) cc_final: 0.6923 (tpp) REVERT: K 613 MET cc_start: 0.7968 (ptp) cc_final: 0.7207 (mmp) REVERT: K 634 MET cc_start: 0.8020 (ttm) cc_final: 0.6984 (tpp) REVERT: L 610 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8064 (ttmm) REVERT: L 634 MET cc_start: 0.6921 (tpp) cc_final: 0.6374 (tpp) outliers start: 103 outliers final: 76 residues processed: 326 average time/residue: 0.1898 time to fit residues: 107.7054 Evaluate side-chains 316 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 236 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 454 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 266 ASP Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 408 VAL Chi-restraints excluded: chain G residue 394 LEU Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 591 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 637 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 553 VAL Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 460 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 22 optimal weight: 6.9990 chunk 414 optimal weight: 0.0970 chunk 296 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 chunk 434 optimal weight: 0.0170 overall best weight: 1.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN E 378 HIS ** E 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN K 562 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.107022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.074929 restraints weight = 67993.426| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 2.78 r_work: 0.2894 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37084 Z= 0.093 Angle : 0.469 8.238 50178 Z= 0.244 Chirality : 0.043 0.139 5635 Planarity : 0.004 0.042 6569 Dihedral : 7.168 89.375 5504 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.48 % Allowed : 17.03 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.12), residues: 4638 helix: 1.35 (0.13), residues: 1628 sheet: 0.48 (0.18), residues: 727 loop : -1.44 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 490 TYR 0.012 0.001 TYR L 358 PHE 0.009 0.001 PHE F 351 TRP 0.013 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00213 (37078) covalent geometry : angle 0.46908 (50178) hydrogen bonds : bond 0.03434 ( 1562) hydrogen bonds : angle 4.26588 ( 4572) Misc. bond : bond 0.00016 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 262 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7958 (ttm) REVERT: A 148 ARG cc_start: 0.8767 (ttp80) cc_final: 0.8442 (ttp80) REVERT: A 221 SER cc_start: 0.9401 (m) cc_final: 0.9170 (p) REVERT: A 260 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7830 (t0) REVERT: B 113 ASP cc_start: 0.8655 (t0) cc_final: 0.8101 (t0) REVERT: B 127 ASP cc_start: 0.8573 (t0) cc_final: 0.8229 (t0) REVERT: B 492 MET cc_start: 0.8615 (tmm) cc_final: 0.8179 (tmm) REVERT: C 53 MET cc_start: 0.8808 (ttp) cc_final: 0.8509 (ttm) REVERT: C 171 ASP cc_start: 0.8080 (t0) cc_final: 0.7808 (t0) REVERT: C 500 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: D 164 MET cc_start: 0.9125 (mtt) cc_final: 0.8923 (mtt) REVERT: D 409 MET cc_start: 0.9247 (mmm) cc_final: 0.8827 (mmt) REVERT: E 243 ASP cc_start: 0.8410 (m-30) cc_final: 0.8032 (t0) REVERT: E 458 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8202 (tm-30) REVERT: E 492 MET cc_start: 0.9292 (tmm) cc_final: 0.8973 (tmm) REVERT: F 255 GLU cc_start: 0.8607 (pp20) cc_final: 0.8321 (pp20) REVERT: F 449 LYS cc_start: 0.7678 (tppp) cc_final: 0.7371 (tptp) REVERT: F 452 GLU cc_start: 0.8665 (tt0) cc_final: 0.8418 (tm-30) REVERT: G 390 MET cc_start: 0.6334 (tmm) cc_final: 0.6064 (tmm) REVERT: G 613 MET cc_start: 0.8905 (ptp) cc_final: 0.8297 (pmm) REVERT: H 535 SER cc_start: 0.8489 (m) cc_final: 0.8186 (m) REVERT: H 605 MET cc_start: 0.8283 (ttm) cc_final: 0.7954 (tpp) REVERT: I 599 LYS cc_start: 0.7638 (mppt) cc_final: 0.7076 (mtpt) REVERT: I 613 MET cc_start: 0.7682 (ptp) cc_final: 0.7237 (pmm) REVERT: I 618 GLN cc_start: 0.6728 (tt0) cc_final: 0.6509 (tt0) REVERT: I 634 MET cc_start: 0.8113 (tpp) cc_final: 0.7646 (tpp) REVERT: J 479 ASN cc_start: 0.8818 (t0) cc_final: 0.8430 (m110) REVERT: J 634 MET cc_start: 0.8348 (tpp) cc_final: 0.7902 (tpp) REVERT: K 373 ASN cc_start: 0.8427 (p0) cc_final: 0.8190 (p0) REVERT: K 390 MET cc_start: 0.7382 (ttp) cc_final: 0.7012 (tpp) REVERT: K 479 ASN cc_start: 0.8553 (t0) cc_final: 0.8307 (t0) REVERT: K 562 ASN cc_start: 0.7932 (m-40) cc_final: 0.7718 (m110) REVERT: K 605 MET cc_start: 0.6165 (tpt) cc_final: 0.5619 (tpt) REVERT: K 613 MET cc_start: 0.7915 (ptp) cc_final: 0.7145 (mmp) REVERT: K 634 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7108 (tpp) REVERT: L 610 LYS cc_start: 0.8545 (mtpp) cc_final: 0.8223 (ttmm) REVERT: L 634 MET cc_start: 0.7022 (tpp) cc_final: 0.6480 (tpp) outliers start: 93 outliers final: 70 residues processed: 336 average time/residue: 0.1875 time to fit residues: 109.3292 Evaluate side-chains 323 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 562 ASN Chi-restraints excluded: chain H residue 603 CYS Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 637 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 634 MET Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 216 optimal weight: 5.9990 chunk 197 optimal weight: 0.5980 chunk 139 optimal weight: 0.0030 chunk 124 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 436 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 291 optimal weight: 2.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 413 HIS E 500 GLN H 562 ASN H 618 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.106946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.074725 restraints weight = 67624.799| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.78 r_work: 0.2884 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 37084 Z= 0.096 Angle : 0.467 7.101 50178 Z= 0.244 Chirality : 0.043 0.139 5635 Planarity : 0.004 0.060 6569 Dihedral : 6.934 89.723 5504 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.50 % Allowed : 17.33 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.12), residues: 4638 helix: 1.45 (0.13), residues: 1630 sheet: 0.58 (0.18), residues: 727 loop : -1.39 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.010 0.001 TYR L 358 PHE 0.010 0.001 PHE L 578 TRP 0.012 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00222 (37078) covalent geometry : angle 0.46679 (50178) hydrogen bonds : bond 0.03578 ( 1562) hydrogen bonds : angle 4.22241 ( 4572) Misc. bond : bond 0.00017 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 254 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7906 (ttm) REVERT: A 148 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8458 (ttp80) REVERT: A 260 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.7831 (t70) REVERT: B 113 ASP cc_start: 0.8641 (t0) cc_final: 0.8068 (t0) REVERT: B 127 ASP cc_start: 0.8576 (t0) cc_final: 0.7990 (t0) REVERT: B 492 MET cc_start: 0.8596 (tmm) cc_final: 0.8128 (tmm) REVERT: B 495 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8686 (t) REVERT: C 171 ASP cc_start: 0.7939 (t0) cc_final: 0.7650 (t0) REVERT: D 164 MET cc_start: 0.9125 (mtt) cc_final: 0.8882 (mtt) REVERT: D 409 MET cc_start: 0.9240 (mmm) cc_final: 0.8769 (mmt) REVERT: E 243 ASP cc_start: 0.8462 (m-30) cc_final: 0.8087 (t0) REVERT: E 458 GLU cc_start: 0.8618 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 492 MET cc_start: 0.9308 (tmm) cc_final: 0.8979 (tmm) REVERT: F 255 GLU cc_start: 0.8587 (pp20) cc_final: 0.8289 (pp20) REVERT: F 449 LYS cc_start: 0.7661 (tppp) cc_final: 0.7309 (tptp) REVERT: F 452 GLU cc_start: 0.8668 (tt0) cc_final: 0.8415 (tm-30) REVERT: G 390 MET cc_start: 0.6183 (tmm) cc_final: 0.5931 (tmm) REVERT: G 613 MET cc_start: 0.8975 (ptp) cc_final: 0.8313 (pmm) REVERT: H 535 SER cc_start: 0.8426 (m) cc_final: 0.8136 (m) REVERT: I 599 LYS cc_start: 0.7578 (mppt) cc_final: 0.7033 (mtpt) REVERT: I 613 MET cc_start: 0.7638 (ptp) cc_final: 0.7171 (pmm) REVERT: I 618 GLN cc_start: 0.6673 (tt0) cc_final: 0.6456 (tt0) REVERT: I 634 MET cc_start: 0.8035 (tpp) cc_final: 0.7609 (tpp) REVERT: I 652 LYS cc_start: 0.7967 (tptt) cc_final: 0.7340 (pttm) REVERT: J 479 ASN cc_start: 0.8779 (t0) cc_final: 0.8409 (m110) REVERT: J 634 MET cc_start: 0.8246 (tpp) cc_final: 0.7761 (tpp) REVERT: K 373 ASN cc_start: 0.8429 (p0) cc_final: 0.8174 (p0) REVERT: K 390 MET cc_start: 0.7338 (ttp) cc_final: 0.6963 (tpp) REVERT: K 479 ASN cc_start: 0.8516 (t0) cc_final: 0.8252 (t0) REVERT: K 562 ASN cc_start: 0.7842 (m-40) cc_final: 0.7626 (m110) REVERT: K 605 MET cc_start: 0.6171 (tpt) cc_final: 0.5635 (tpt) REVERT: K 634 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7234 (tpp) REVERT: L 393 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.7881 (mmmt) REVERT: L 426 PHE cc_start: 0.7327 (t80) cc_final: 0.6711 (t80) REVERT: L 610 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8171 (ttmm) REVERT: L 634 MET cc_start: 0.7039 (tpp) cc_final: 0.6474 (tpp) outliers start: 94 outliers final: 75 residues processed: 328 average time/residue: 0.1901 time to fit residues: 108.5037 Evaluate side-chains 325 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 245 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 251 GLU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain E residue 500 GLN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain G residue 431 MET Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 562 ASN Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 335 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 637 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 634 MET Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Chi-restraints excluded: chain L residue 588 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 68 optimal weight: 0.5980 chunk 432 optimal weight: 6.9990 chunk 365 optimal weight: 0.9990 chunk 261 optimal weight: 0.0570 chunk 409 optimal weight: 4.9990 chunk 444 optimal weight: 0.9980 chunk 451 optimal weight: 0.0980 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 367 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.109791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.077093 restraints weight = 67699.667| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.84 r_work: 0.2931 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 37084 Z= 0.080 Angle : 0.456 8.865 50178 Z= 0.236 Chirality : 0.042 0.158 5635 Planarity : 0.004 0.050 6569 Dihedral : 6.694 88.884 5504 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.13 % Allowed : 17.73 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4638 helix: 1.53 (0.13), residues: 1629 sheet: 0.69 (0.19), residues: 727 loop : -1.30 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 490 TYR 0.011 0.001 TYR L 358 PHE 0.008 0.001 PHE D 89 TRP 0.012 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00171 (37078) covalent geometry : angle 0.45647 (50178) hydrogen bonds : bond 0.03016 ( 1562) hydrogen bonds : angle 4.12315 ( 4572) Misc. bond : bond 0.00017 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 261 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7731 (ttm) REVERT: A 148 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8325 (ttp80) REVERT: B 113 ASP cc_start: 0.8576 (t0) cc_final: 0.8010 (t0) REVERT: B 127 ASP cc_start: 0.8591 (t0) cc_final: 0.7965 (t0) REVERT: B 492 MET cc_start: 0.8565 (tmm) cc_final: 0.8147 (tmm) REVERT: B 495 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8503 (t) REVERT: C 53 MET cc_start: 0.8773 (ttp) cc_final: 0.8492 (ttm) REVERT: D 164 MET cc_start: 0.9126 (mtt) cc_final: 0.8903 (mtt) REVERT: D 409 MET cc_start: 0.9171 (mmm) cc_final: 0.8774 (mmt) REVERT: E 243 ASP cc_start: 0.8425 (m-30) cc_final: 0.8048 (t0) REVERT: E 458 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8157 (tm-30) REVERT: E 492 MET cc_start: 0.9282 (tmm) cc_final: 0.8962 (tmm) REVERT: F 255 GLU cc_start: 0.8622 (pp20) cc_final: 0.8271 (pp20) REVERT: F 449 LYS cc_start: 0.7615 (tppp) cc_final: 0.7258 (tptp) REVERT: F 452 GLU cc_start: 0.8660 (tt0) cc_final: 0.8389 (tm-30) REVERT: G 390 MET cc_start: 0.6126 (tmm) cc_final: 0.5862 (tmm) REVERT: G 613 MET cc_start: 0.8914 (ptp) cc_final: 0.8240 (pmm) REVERT: H 535 SER cc_start: 0.8364 (m) cc_final: 0.8053 (m) REVERT: I 357 THR cc_start: 0.8506 (m) cc_final: 0.8001 (p) REVERT: I 599 LYS cc_start: 0.7501 (mppt) cc_final: 0.6985 (mtpt) REVERT: I 613 MET cc_start: 0.7615 (ptp) cc_final: 0.7163 (pmm) REVERT: I 618 GLN cc_start: 0.6604 (tt0) cc_final: 0.6388 (tt0) REVERT: I 634 MET cc_start: 0.8006 (tpp) cc_final: 0.7624 (tpp) REVERT: I 652 LYS cc_start: 0.7960 (tptt) cc_final: 0.7269 (pttm) REVERT: J 479 ASN cc_start: 0.8624 (t0) cc_final: 0.8269 (m110) REVERT: J 634 MET cc_start: 0.8087 (tpp) cc_final: 0.7754 (tpp) REVERT: K 373 ASN cc_start: 0.8415 (p0) cc_final: 0.8157 (p0) REVERT: K 386 HIS cc_start: 0.8198 (m-70) cc_final: 0.7937 (m170) REVERT: K 390 MET cc_start: 0.7292 (ttp) cc_final: 0.6940 (tpp) REVERT: K 479 ASN cc_start: 0.8359 (t0) cc_final: 0.8115 (t0) REVERT: K 562 ASN cc_start: 0.7920 (m-40) cc_final: 0.7702 (m110) REVERT: K 605 MET cc_start: 0.6216 (tpt) cc_final: 0.5801 (tpp) REVERT: K 613 MET cc_start: 0.7895 (ptp) cc_final: 0.7681 (ppp) REVERT: K 634 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7274 (tpp) REVERT: L 393 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7866 (mmmt) REVERT: L 426 PHE cc_start: 0.7247 (t80) cc_final: 0.6623 (t80) REVERT: L 610 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8204 (ttmm) REVERT: L 634 MET cc_start: 0.6797 (tpp) cc_final: 0.6232 (tpp) outliers start: 80 outliers final: 64 residues processed: 324 average time/residue: 0.1887 time to fit residues: 106.0009 Evaluate side-chains 315 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 217 HIS Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain H residue 603 CYS Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 426 PHE Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 634 MET Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 393 LYS Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 24 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 250 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 438 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 238 optimal weight: 0.1980 chunk 418 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN ** L 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.074973 restraints weight = 67993.664| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.84 r_work: 0.2883 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37084 Z= 0.117 Angle : 0.478 8.112 50178 Z= 0.249 Chirality : 0.043 0.183 5635 Planarity : 0.004 0.048 6569 Dihedral : 6.639 88.107 5504 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.02 % Allowed : 18.15 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.12), residues: 4638 helix: 1.52 (0.13), residues: 1630 sheet: 0.71 (0.18), residues: 727 loop : -1.31 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 317 TYR 0.009 0.001 TYR I 340 PHE 0.013 0.001 PHE L 578 TRP 0.010 0.001 TRP K 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00283 (37078) covalent geometry : angle 0.47849 (50178) hydrogen bonds : bond 0.03799 ( 1562) hydrogen bonds : angle 4.17957 ( 4572) Misc. bond : bond 0.00019 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9276 Ramachandran restraints generated. 4638 Oldfield, 0 Emsley, 4638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 248 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.8749 (ttp80) cc_final: 0.8403 (ttp80) REVERT: B 127 ASP cc_start: 0.8625 (t0) cc_final: 0.8007 (t0) REVERT: B 492 MET cc_start: 0.8577 (tmm) cc_final: 0.8091 (tmm) REVERT: B 495 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8662 (t) REVERT: C 53 MET cc_start: 0.8817 (ttp) cc_final: 0.8528 (ttm) REVERT: C 386 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7520 (t80) REVERT: D 164 MET cc_start: 0.9167 (mtt) cc_final: 0.8892 (mtt) REVERT: D 409 MET cc_start: 0.9215 (mmm) cc_final: 0.8804 (mmt) REVERT: E 243 ASP cc_start: 0.8546 (m-30) cc_final: 0.8032 (t0) REVERT: E 458 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8129 (tm-30) REVERT: F 255 GLU cc_start: 0.8614 (pp20) cc_final: 0.8257 (pp20) REVERT: F 449 LYS cc_start: 0.7617 (tppp) cc_final: 0.7238 (tptp) REVERT: F 452 GLU cc_start: 0.8671 (tt0) cc_final: 0.8390 (tm-30) REVERT: G 390 MET cc_start: 0.6080 (tmm) cc_final: 0.5813 (tmm) REVERT: G 613 MET cc_start: 0.8973 (ptp) cc_final: 0.8259 (pmm) REVERT: H 535 SER cc_start: 0.8382 (m) cc_final: 0.8070 (m) REVERT: I 599 LYS cc_start: 0.7460 (mppt) cc_final: 0.6969 (mtpt) REVERT: I 605 MET cc_start: 0.8401 (pmm) cc_final: 0.7380 (ttm) REVERT: I 613 MET cc_start: 0.7564 (ptp) cc_final: 0.7103 (pmm) REVERT: I 618 GLN cc_start: 0.6601 (tt0) cc_final: 0.6376 (tt0) REVERT: I 634 MET cc_start: 0.7864 (tpp) cc_final: 0.7387 (tpp) REVERT: I 652 LYS cc_start: 0.7947 (tptt) cc_final: 0.7239 (pttm) REVERT: J 479 ASN cc_start: 0.8702 (t0) cc_final: 0.8335 (m110) REVERT: J 634 MET cc_start: 0.8018 (tpp) cc_final: 0.7630 (tpp) REVERT: K 373 ASN cc_start: 0.8419 (p0) cc_final: 0.8191 (p0) REVERT: K 386 HIS cc_start: 0.8216 (m-70) cc_final: 0.7954 (m170) REVERT: K 390 MET cc_start: 0.7215 (ttp) cc_final: 0.6785 (tpp) REVERT: K 479 ASN cc_start: 0.8389 (t0) cc_final: 0.8108 (t0) REVERT: K 562 ASN cc_start: 0.7828 (m-40) cc_final: 0.7602 (m110) REVERT: K 605 MET cc_start: 0.6245 (tpt) cc_final: 0.5838 (tpp) REVERT: K 634 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7177 (tpp) REVERT: L 393 LYS cc_start: 0.8446 (mmtm) cc_final: 0.7850 (mmmt) REVERT: L 426 PHE cc_start: 0.7291 (t80) cc_final: 0.6673 (t80) REVERT: L 605 MET cc_start: 0.7460 (mtt) cc_final: 0.7225 (mtm) REVERT: L 610 LYS cc_start: 0.8448 (mtpp) cc_final: 0.8151 (ttmm) REVERT: L 634 MET cc_start: 0.6783 (tpp) cc_final: 0.6264 (tpp) outliers start: 76 outliers final: 68 residues processed: 311 average time/residue: 0.1920 time to fit residues: 103.2651 Evaluate side-chains 316 residues out of total 3757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 245 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 495 THR Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 386 TYR Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 85 THR Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 309 THR Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 478 MET Chi-restraints excluded: chain E residue 495 THR Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 172 VAL Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 218 THR Chi-restraints excluded: chain F residue 266 ASP Chi-restraints excluded: chain F residue 463 SER Chi-restraints excluded: chain G residue 548 VAL Chi-restraints excluded: chain G residue 557 VAL Chi-restraints excluded: chain G residue 632 MET Chi-restraints excluded: chain H residue 504 VAL Chi-restraints excluded: chain H residue 506 SER Chi-restraints excluded: chain H residue 511 ASN Chi-restraints excluded: chain H residue 514 VAL Chi-restraints excluded: chain H residue 523 VAL Chi-restraints excluded: chain H residue 530 THR Chi-restraints excluded: chain I residue 455 ILE Chi-restraints excluded: chain I residue 478 LEU Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 514 VAL Chi-restraints excluded: chain I residue 548 VAL Chi-restraints excluded: chain I residue 557 VAL Chi-restraints excluded: chain J residue 480 ILE Chi-restraints excluded: chain J residue 557 VAL Chi-restraints excluded: chain J residue 577 VAL Chi-restraints excluded: chain J residue 578 PHE Chi-restraints excluded: chain J residue 591 VAL Chi-restraints excluded: chain J residue 637 VAL Chi-restraints excluded: chain K residue 426 PHE Chi-restraints excluded: chain K residue 433 HIS Chi-restraints excluded: chain K residue 504 VAL Chi-restraints excluded: chain K residue 512 VAL Chi-restraints excluded: chain K residue 634 MET Chi-restraints excluded: chain K residue 652 LYS Chi-restraints excluded: chain L residue 340 TYR Chi-restraints excluded: chain L residue 429 THR Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 511 ASN Chi-restraints excluded: chain L residue 577 VAL Chi-restraints excluded: chain L residue 578 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 179 optimal weight: 0.9980 chunk 413 optimal weight: 7.9990 chunk 409 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 chunk 282 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 189 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 chunk 369 optimal weight: 7.9990 chunk 386 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 278 ASN ** E 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 ASN H 618 GLN I 636 ASN ** L 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.107891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075072 restraints weight = 67211.422| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.82 r_work: 0.2893 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37084 Z= 0.111 Angle : 0.480 8.842 50178 Z= 0.248 Chirality : 0.043 0.138 5635 Planarity : 0.004 0.044 6569 Dihedral : 6.571 87.484 5504 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.08 % Allowed : 18.29 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.12), residues: 4638 helix: 1.51 (0.13), residues: 1630 sheet: 0.69 (0.18), residues: 727 loop : -1.29 (0.12), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 16 TYR 0.009 0.001 TYR L 358 PHE 0.011 0.001 PHE L 578 TRP 0.010 0.001 TRP J 544 HIS 0.005 0.001 HIS B 104 Details of bonding type rmsd covalent geometry : bond 0.00267 (37078) covalent geometry : angle 0.47975 (50178) hydrogen bonds : bond 0.03731 ( 1562) hydrogen bonds : angle 4.17111 ( 4572) Misc. bond : bond 0.00018 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6693.10 seconds wall clock time: 115 minutes 27.66 seconds (6927.66 seconds total)