Starting phenix.real_space_refine on Sat Mar 7 04:40:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.map" model { file = "/net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rvs_10011/03_2026/6rvs_10011.cif" } resolution = 3.59 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 144 5.16 5 C 24708 2.51 5 N 6564 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.04s 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: 38388 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3199 Classifications: {'peptide': 397} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 378} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 4.41, per 1000 atoms: 0.11 Number of scatterers: 38388 At special positions: 0 Unit cell: (157.94, 157.94, 133.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 6972 8.00 N 6564 7.00 C 24708 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=0, symmetry=0 Time building additional restraints: 3.11 Conformation dependent library (CDL) restraints added in 1.7 seconds 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9168 Finding SS restraints... Secondary structure from input PDB file: 216 helices and 48 sheets defined 58.4% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 33 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 removed outlier: 3.610A pdb=" N THR A 45 " --> pdb=" O GLN A 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 51 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 90 Processing helix chain 'A' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG A 128 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 124 through 129' Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 164 " --> pdb=" O GLN A 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 273 " --> pdb=" O GLU A 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 276 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 278 " --> pdb=" O CYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER A 452 " --> pdb=" O ASN A 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA A 453 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER A 454 " --> pdb=" O PRO A 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 454' Processing helix chain 'A' and resid 480 through 498 Processing helix chain 'A' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR A 545 " --> pdb=" O ASP A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE A 552 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU A 554 " --> pdb=" O GLU A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE A 563 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A 564 " --> pdb=" O ARG A 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 568 " --> pdb=" O TYR A 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU B 32 " --> pdb=" O VAL B 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 33 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 3.609A pdb=" N THR B 45 " --> pdb=" O GLN B 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG B 51 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 90 Processing helix chain 'B' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL B 129 " --> pdb=" O ASN B 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 124 through 129' Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 142 " --> pdb=" O TYR B 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 177 removed outlier: 3.934A pdb=" N HIS B 163 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B 164 " --> pdb=" O GLN B 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS B 175 " --> pdb=" O ASP B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG B 185 " --> pdb=" O GLU B 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 267 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 273 " --> pdb=" O GLU B 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 276 " --> pdb=" O LYS B 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 278 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 449 through 454 removed outlier: 6.284A pdb=" N SER B 452 " --> pdb=" O ASN B 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER B 454 " --> pdb=" O PRO B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 454' Processing helix chain 'B' and resid 480 through 498 Processing helix chain 'B' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 521 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE B 552 " --> pdb=" O ILE B 548 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 554 " --> pdb=" O GLU B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE B 563 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU B 568 " --> pdb=" O TYR B 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU C 32 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 33 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU C 34 " --> pdb=" O LEU C 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 35 " --> pdb=" O PHE C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 3.611A pdb=" N THR C 45 " --> pdb=" O GLN C 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG C 51 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 removed outlier: 3.743A pdb=" N HIS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 90 Processing helix chain 'C' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL C 129 " --> pdb=" O ASN C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 129' Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.732A pdb=" N TYR C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL C 142 " --> pdb=" O TYR C 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP C 144 " --> pdb=" O ARG C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS C 163 " --> pdb=" O THR C 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 164 " --> pdb=" O GLN C 160 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS C 175 " --> pdb=" O ASP C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG C 185 " --> pdb=" O GLU C 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 186 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 278 removed outlier: 3.720A pdb=" N PHE C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR C 267 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE C 273 " --> pdb=" O GLU C 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 276 " --> pdb=" O LYS C 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 278 " --> pdb=" O CYS C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 448 Processing helix chain 'C' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER C 452 " --> pdb=" O ASN C 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA C 453 " --> pdb=" O SER C 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER C 454 " --> pdb=" O PRO C 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 454' Processing helix chain 'C' and resid 480 through 498 Processing helix chain 'C' and resid 516 through 523 removed outlier: 3.520A pdb=" N SER C 520 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 521 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 528 Processing helix chain 'C' and resid 540 through 545 removed outlier: 4.622A pdb=" N THR C 545 " --> pdb=" O ASP C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE C 552 " --> pdb=" O ILE C 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 554 " --> pdb=" O GLU C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE C 563 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR C 564 " --> pdb=" O ARG C 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 568 " --> pdb=" O TYR C 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE D 33 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN D 35 " --> pdb=" O PHE D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 51 removed outlier: 3.611A pdb=" N THR D 45 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 51 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.741A pdb=" N HIS D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 90 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG D 128 " --> pdb=" O THR D 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 129 " --> pdb=" O ASN D 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 124 through 129' Processing helix chain 'D' and resid 137 through 146 removed outlier: 3.732A pdb=" N TYR D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 142 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP D 144 " --> pdb=" O ARG D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS D 163 " --> pdb=" O THR D 159 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER D 164 " --> pdb=" O GLN D 160 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS D 175 " --> pdb=" O ASP D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER D 186 " --> pdb=" O ARG D 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR D 267 " --> pdb=" O MET D 263 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 273 " --> pdb=" O GLU D 269 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN D 278 " --> pdb=" O CYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER D 452 " --> pdb=" O ASN D 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA D 453 " --> pdb=" O SER D 450 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER D 454 " --> pdb=" O PRO D 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 449 through 454' Processing helix chain 'D' and resid 480 through 498 Processing helix chain 'D' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER D 520 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 521 " --> pdb=" O ASP D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 Processing helix chain 'D' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR D 545 " --> pdb=" O ASP D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE D 552 " --> pdb=" O ILE D 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 554 " --> pdb=" O GLU D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE D 563 " --> pdb=" O SER D 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR D 564 " --> pdb=" O ARG D 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU D 568 " --> pdb=" O TYR D 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 removed outlier: 3.573A pdb=" N GLU E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE E 33 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU E 34 " --> pdb=" O LEU E 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 35 " --> pdb=" O PHE E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 51 removed outlier: 3.610A pdb=" N THR E 45 " --> pdb=" O GLN E 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG E 51 " --> pdb=" O ALA E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 90 Processing helix chain 'E' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 129 " --> pdb=" O ASN E 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 124 through 129' Processing helix chain 'E' and resid 137 through 146 removed outlier: 3.732A pdb=" N TYR E 141 " --> pdb=" O SER E 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 142 " --> pdb=" O TYR E 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP E 144 " --> pdb=" O ARG E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS E 163 " --> pdb=" O THR E 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER E 164 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS E 175 " --> pdb=" O ASP E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER E 186 " --> pdb=" O ARG E 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER E 201 " --> pdb=" O GLU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS E 272 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN E 278 " --> pdb=" O CYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 448 Processing helix chain 'E' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER E 452 " --> pdb=" O ASN E 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA E 453 " --> pdb=" O SER E 450 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER E 454 " --> pdb=" O PRO E 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 449 through 454' Processing helix chain 'E' and resid 480 through 498 Processing helix chain 'E' and resid 516 through 523 removed outlier: 3.520A pdb=" N SER E 520 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR E 545 " --> pdb=" O ASP E 541 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE E 552 " --> pdb=" O ILE E 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU E 554 " --> pdb=" O GLU E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE E 563 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR E 564 " --> pdb=" O ARG E 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU E 568 " --> pdb=" O TYR E 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU F 32 " --> pdb=" O VAL F 28 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE F 33 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 35 " --> pdb=" O PHE F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 51 removed outlier: 3.611A pdb=" N THR F 45 " --> pdb=" O GLN F 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG F 51 " --> pdb=" O ALA F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.743A pdb=" N HIS F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 90 Processing helix chain 'F' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG F 128 " --> pdb=" O THR F 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL F 129 " --> pdb=" O ASN F 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 124 through 129' Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR F 141 " --> pdb=" O SER F 137 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 142 " --> pdb=" O TYR F 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP F 144 " --> pdb=" O ARG F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS F 163 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER F 164 " --> pdb=" O GLN F 160 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS F 175 " --> pdb=" O ASP F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER F 201 " --> pdb=" O GLU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 278 removed outlier: 3.720A pdb=" N PHE F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR F 267 " --> pdb=" O MET F 263 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS F 272 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE F 273 " --> pdb=" O GLU F 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN F 278 " --> pdb=" O CYS F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 448 Processing helix chain 'F' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER F 452 " --> pdb=" O ASN F 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 453 " --> pdb=" O SER F 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER F 454 " --> pdb=" O PRO F 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 449 through 454' Processing helix chain 'F' and resid 480 through 498 Processing helix chain 'F' and resid 516 through 523 removed outlier: 3.520A pdb=" N SER F 520 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 521 " --> pdb=" O ASP F 517 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR F 545 " --> pdb=" O ASP F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE F 552 " --> pdb=" O ILE F 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU F 554 " --> pdb=" O GLU F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE F 563 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR F 564 " --> pdb=" O ARG F 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 568 " --> pdb=" O TYR F 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU G 32 " --> pdb=" O VAL G 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU G 34 " --> pdb=" O LEU G 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN G 35 " --> pdb=" O PHE G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 51 removed outlier: 3.610A pdb=" N THR G 45 " --> pdb=" O GLN G 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG G 51 " --> pdb=" O ALA G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 71 removed outlier: 3.741A pdb=" N HIS G 71 " --> pdb=" O ARG G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 90 Processing helix chain 'G' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 removed outlier: 3.894A pdb=" N ARG G 128 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL G 129 " --> pdb=" O ASN G 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 124 through 129' Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR G 141 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL G 142 " --> pdb=" O TYR G 138 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP G 144 " --> pdb=" O ARG G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS G 163 " --> pdb=" O THR G 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER G 164 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N CYS G 175 " --> pdb=" O ASP G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG G 185 " --> pdb=" O GLU G 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER G 186 " --> pdb=" O ARG G 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER G 201 " --> pdb=" O GLU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR G 267 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS G 270 " --> pdb=" O ARG G 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS G 272 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE G 273 " --> pdb=" O GLU G 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 276 " --> pdb=" O LYS G 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 278 " --> pdb=" O CYS G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 441 through 448 Processing helix chain 'G' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER G 452 " --> pdb=" O ASN G 449 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALA G 453 " --> pdb=" O SER G 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER G 454 " --> pdb=" O PRO G 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 449 through 454' Processing helix chain 'G' and resid 480 through 498 Processing helix chain 'G' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER G 520 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 521 " --> pdb=" O ASP G 517 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 Processing helix chain 'G' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR G 545 " --> pdb=" O ASP G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE G 552 " --> pdb=" O ILE G 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU G 554 " --> pdb=" O GLU G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE G 563 " --> pdb=" O SER G 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR G 564 " --> pdb=" O ARG G 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU G 568 " --> pdb=" O TYR G 564 " (cutoff:3.500A) Processing helix chain 'H' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU H 32 " --> pdb=" O VAL H 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE H 33 " --> pdb=" O ARG H 29 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU H 34 " --> pdb=" O LEU H 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN H 35 " --> pdb=" O PHE H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.611A pdb=" N THR H 45 " --> pdb=" O GLN H 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG H 51 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS H 71 " --> pdb=" O ARG H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 90 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR H 106 " --> pdb=" O PHE H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG H 128 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL H 129 " --> pdb=" O ASN H 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 124 through 129' Processing helix chain 'H' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR H 141 " --> pdb=" O SER H 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL H 142 " --> pdb=" O TYR H 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP H 144 " --> pdb=" O ARG H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS H 163 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER H 164 " --> pdb=" O GLN H 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG H 185 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER H 186 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER H 201 " --> pdb=" O GLU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 278 removed outlier: 3.720A pdb=" N PHE H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR H 267 " --> pdb=" O MET H 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS H 270 " --> pdb=" O ARG H 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE H 273 " --> pdb=" O GLU H 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 276 " --> pdb=" O LYS H 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN H 278 " --> pdb=" O CYS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 441 through 448 Processing helix chain 'H' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER H 452 " --> pdb=" O ASN H 449 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA H 453 " --> pdb=" O SER H 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER H 454 " --> pdb=" O PRO H 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 449 through 454' Processing helix chain 'H' and resid 480 through 498 Processing helix chain 'H' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER H 520 " --> pdb=" O SER H 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE H 521 " --> pdb=" O ASP H 517 " (cutoff:3.500A) Processing helix chain 'H' and resid 523 through 528 Processing helix chain 'H' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR H 545 " --> pdb=" O ASP H 541 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 558 removed outlier: 3.525A pdb=" N ILE H 552 " --> pdb=" O ILE H 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU H 554 " --> pdb=" O GLU H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE H 563 " --> pdb=" O SER H 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR H 564 " --> pdb=" O ARG H 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU H 568 " --> pdb=" O TYR H 564 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE I 33 " --> pdb=" O ARG I 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 removed outlier: 3.609A pdb=" N THR I 45 " --> pdb=" O GLN I 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG I 51 " --> pdb=" O ALA I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 54 through 71 removed outlier: 3.741A pdb=" N HIS I 71 " --> pdb=" O ARG I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 90 Processing helix chain 'I' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR I 106 " --> pdb=" O PHE I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG I 128 " --> pdb=" O THR I 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL I 129 " --> pdb=" O ASN I 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 124 through 129' Processing helix chain 'I' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR I 141 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL I 142 " --> pdb=" O TYR I 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP I 143 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP I 144 " --> pdb=" O ARG I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER I 164 " --> pdb=" O GLN I 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG I 185 " --> pdb=" O GLU I 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER I 186 " --> pdb=" O ARG I 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER I 201 " --> pdb=" O GLU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 278 removed outlier: 3.718A pdb=" N PHE I 262 " --> pdb=" O TYR I 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR I 267 " --> pdb=" O MET I 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS I 270 " --> pdb=" O ARG I 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS I 272 " --> pdb=" O LEU I 268 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE I 273 " --> pdb=" O GLU I 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU I 276 " --> pdb=" O LYS I 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN I 278 " --> pdb=" O CYS I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 441 through 448 Processing helix chain 'I' and resid 449 through 454 removed outlier: 6.284A pdb=" N SER I 452 " --> pdb=" O ASN I 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA I 453 " --> pdb=" O SER I 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER I 454 " --> pdb=" O PRO I 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 449 through 454' Processing helix chain 'I' and resid 480 through 498 Processing helix chain 'I' and resid 516 through 523 removed outlier: 3.520A pdb=" N SER I 520 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE I 521 " --> pdb=" O ASP I 517 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 Processing helix chain 'I' and resid 540 through 545 removed outlier: 4.622A pdb=" N THR I 545 " --> pdb=" O ASP I 541 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE I 552 " --> pdb=" O ILE I 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU I 554 " --> pdb=" O GLU I 550 " (cutoff:3.500A) Processing helix chain 'I' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE I 563 " --> pdb=" O SER I 559 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR I 564 " --> pdb=" O ARG I 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU I 568 " --> pdb=" O TYR I 564 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 36 removed outlier: 3.573A pdb=" N GLU J 32 " --> pdb=" O VAL J 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE J 33 " --> pdb=" O ARG J 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU J 34 " --> pdb=" O LEU J 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN J 35 " --> pdb=" O PHE J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 51 removed outlier: 3.610A pdb=" N THR J 45 " --> pdb=" O GLN J 42 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG J 51 " --> pdb=" O ALA J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 54 through 71 removed outlier: 3.743A pdb=" N HIS J 71 " --> pdb=" O ARG J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 74 through 90 Processing helix chain 'J' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR J 106 " --> pdb=" O PHE J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG J 128 " --> pdb=" O THR J 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL J 129 " --> pdb=" O ASN J 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 124 through 129' Processing helix chain 'J' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR J 141 " --> pdb=" O SER J 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL J 142 " --> pdb=" O TYR J 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP J 143 " --> pdb=" O GLU J 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP J 144 " --> pdb=" O ARG J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 177 removed outlier: 3.934A pdb=" N HIS J 163 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER J 164 " --> pdb=" O GLN J 160 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS J 175 " --> pdb=" O ASP J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 202 removed outlier: 4.010A pdb=" N ARG J 185 " --> pdb=" O GLU J 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER J 186 " --> pdb=" O ARG J 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER J 201 " --> pdb=" O GLU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 257 through 278 removed outlier: 3.720A pdb=" N PHE J 262 " --> pdb=" O TYR J 258 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR J 267 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS J 270 " --> pdb=" O ARG J 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS J 272 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE J 273 " --> pdb=" O GLU J 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 276 " --> pdb=" O LYS J 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN J 278 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 441 through 448 Processing helix chain 'J' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER J 452 " --> pdb=" O ASN J 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA J 453 " --> pdb=" O SER J 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER J 454 " --> pdb=" O PRO J 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 449 through 454' Processing helix chain 'J' and resid 480 through 497 Processing helix chain 'J' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER J 520 " --> pdb=" O SER J 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE J 521 " --> pdb=" O ASP J 517 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 528 Processing helix chain 'J' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR J 545 " --> pdb=" O ASP J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE J 552 " --> pdb=" O ILE J 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU J 554 " --> pdb=" O GLU J 550 " (cutoff:3.500A) Processing helix chain 'J' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE J 563 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR J 564 " --> pdb=" O ARG J 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU J 568 " --> pdb=" O TYR J 564 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE K 33 " --> pdb=" O ARG K 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU K 34 " --> pdb=" O LEU K 30 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN K 35 " --> pdb=" O PHE K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 51 removed outlier: 3.610A pdb=" N THR K 45 " --> pdb=" O GLN K 42 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG K 51 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.742A pdb=" N HIS K 71 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 74 through 90 Processing helix chain 'K' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR K 106 " --> pdb=" O PHE K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 124 through 129 removed outlier: 3.896A pdb=" N ARG K 128 " --> pdb=" O THR K 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL K 129 " --> pdb=" O ASN K 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 124 through 129' Processing helix chain 'K' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR K 141 " --> pdb=" O SER K 137 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL K 142 " --> pdb=" O TYR K 138 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP K 143 " --> pdb=" O GLU K 139 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TRP K 144 " --> pdb=" O ARG K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER K 164 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS K 175 " --> pdb=" O ASP K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG K 185 " --> pdb=" O GLU K 181 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER K 186 " --> pdb=" O ARG K 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER K 201 " --> pdb=" O GLU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE K 262 " --> pdb=" O TYR K 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR K 267 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS K 270 " --> pdb=" O ARG K 266 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS K 272 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE K 273 " --> pdb=" O GLU K 269 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 276 " --> pdb=" O LYS K 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN K 278 " --> pdb=" O CYS K 274 " (cutoff:3.500A) Processing helix chain 'K' and resid 441 through 448 Processing helix chain 'K' and resid 449 through 454 removed outlier: 6.283A pdb=" N SER K 452 " --> pdb=" O ASN K 449 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA K 453 " --> pdb=" O SER K 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER K 454 " --> pdb=" O PRO K 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 449 through 454' Processing helix chain 'K' and resid 480 through 498 Processing helix chain 'K' and resid 516 through 523 removed outlier: 3.521A pdb=" N SER K 520 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE K 521 " --> pdb=" O ASP K 517 " (cutoff:3.500A) Processing helix chain 'K' and resid 523 through 528 Processing helix chain 'K' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR K 545 " --> pdb=" O ASP K 541 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 558 removed outlier: 3.525A pdb=" N ILE K 552 " --> pdb=" O ILE K 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU K 554 " --> pdb=" O GLU K 550 " (cutoff:3.500A) Processing helix chain 'K' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE K 563 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR K 564 " --> pdb=" O ARG K 560 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU K 568 " --> pdb=" O TYR K 564 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 36 removed outlier: 3.572A pdb=" N GLU L 32 " --> pdb=" O VAL L 28 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE L 33 " --> pdb=" O ARG L 29 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU L 34 " --> pdb=" O LEU L 30 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN L 35 " --> pdb=" O PHE L 31 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 51 removed outlier: 3.611A pdb=" N THR L 45 " --> pdb=" O GLN L 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG L 51 " --> pdb=" O ALA L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 54 through 71 removed outlier: 3.741A pdb=" N HIS L 71 " --> pdb=" O ARG L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 74 through 90 Processing helix chain 'L' and resid 100 through 121 removed outlier: 3.546A pdb=" N THR L 106 " --> pdb=" O PHE L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.895A pdb=" N ARG L 128 " --> pdb=" O THR L 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL L 129 " --> pdb=" O ASN L 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 124 through 129' Processing helix chain 'L' and resid 137 through 146 removed outlier: 3.733A pdb=" N TYR L 141 " --> pdb=" O SER L 137 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL L 142 " --> pdb=" O TYR L 138 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP L 143 " --> pdb=" O GLU L 139 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP L 144 " --> pdb=" O ARG L 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 177 removed outlier: 3.935A pdb=" N HIS L 163 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER L 164 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N CYS L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 202 removed outlier: 4.011A pdb=" N ARG L 185 " --> pdb=" O GLU L 181 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER L 186 " --> pdb=" O ARG L 182 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR L 189 " --> pdb=" O ARG L 185 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER L 201 " --> pdb=" O GLU L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 278 removed outlier: 3.719A pdb=" N PHE L 262 " --> pdb=" O TYR L 258 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N THR L 267 " --> pdb=" O MET L 263 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS L 270 " --> pdb=" O ARG L 266 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS L 272 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE L 273 " --> pdb=" O GLU L 269 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 276 " --> pdb=" O LYS L 272 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN L 278 " --> pdb=" O CYS L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 441 through 448 Processing helix chain 'L' and resid 449 through 454 removed outlier: 6.284A pdb=" N SER L 452 " --> pdb=" O ASN L 449 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA L 453 " --> pdb=" O SER L 450 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N SER L 454 " --> pdb=" O PRO L 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 449 through 454' Processing helix chain 'L' and resid 480 through 498 Processing helix chain 'L' and resid 516 through 523 removed outlier: 3.520A pdb=" N SER L 520 " --> pdb=" O SER L 516 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE L 521 " --> pdb=" O ASP L 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 523 through 528 Processing helix chain 'L' and resid 540 through 545 removed outlier: 4.623A pdb=" N THR L 545 " --> pdb=" O ASP L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 558 removed outlier: 3.524A pdb=" N ILE L 552 " --> pdb=" O ILE L 548 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU L 554 " --> pdb=" O GLU L 550 " (cutoff:3.500A) Processing helix chain 'L' and resid 559 through 568 removed outlier: 4.133A pdb=" N ILE L 563 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR L 564 " --> pdb=" O ARG L 560 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU L 568 " --> pdb=" O TYR L 564 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE A 19 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 217 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 214 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 218 " --> pdb=" O GLU A 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU A 223 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR A 224 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU A 235 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA A 226 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG A 232 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS A 155 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG A 234 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 243 Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 457 removed outlier: 3.552A pdb=" N LEU A 455 " --> pdb=" O LEU A 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 457 " --> pdb=" O ALA A 284 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASN L 468 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 471 removed outlier: 3.924A pdb=" N ASN A 468 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 455 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 457 " --> pdb=" O ALA B 284 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR A 500 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE B 19 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B 217 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 214 " --> pdb=" O TYR B 227 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 218 " --> pdb=" O GLU B 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU B 223 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR B 224 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU B 235 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA B 226 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG B 232 " --> pdb=" O LYS B 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS B 155 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG B 234 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 243 Processing sheet with id=AA8, first strand: chain 'B' and resid 466 through 471 removed outlier: 3.964A pdb=" N ASN B 468 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 455 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 457 " --> pdb=" O ALA C 284 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR B 500 " --> pdb=" O ARG B 513 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE C 19 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR C 217 " --> pdb=" O ILE C 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 214 " --> pdb=" O TYR C 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU C 218 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 223 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR C 224 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU C 235 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA C 226 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG C 232 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS C 155 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 234 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AB3, first strand: chain 'C' and resid 466 through 471 removed outlier: 3.964A pdb=" N ASN C 468 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 455 " --> pdb=" O LEU D 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 457 " --> pdb=" O ALA D 284 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR C 500 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE D 19 " --> pdb=" O TYR D 217 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR D 217 " --> pdb=" O ILE D 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR D 214 " --> pdb=" O TYR D 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D 218 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 223 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR D 224 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU D 235 " --> pdb=" O TYR D 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA D 226 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG D 232 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS D 155 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG D 234 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 242 through 243 Processing sheet with id=AB7, first strand: chain 'D' and resid 466 through 471 removed outlier: 3.962A pdb=" N ASN D 468 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU E 455 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 457 " --> pdb=" O ALA E 284 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR D 500 " --> pdb=" O ARG D 513 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE E 19 " --> pdb=" O TYR E 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR E 217 " --> pdb=" O ILE E 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 214 " --> pdb=" O TYR E 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E 218 " --> pdb=" O GLU E 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU E 223 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR E 224 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU E 235 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA E 226 " --> pdb=" O ILE E 233 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG E 232 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS E 155 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG E 234 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 242 through 243 Processing sheet with id=AC2, first strand: chain 'E' and resid 466 through 471 removed outlier: 3.963A pdb=" N ASN E 468 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU F 455 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA F 457 " --> pdb=" O ALA F 284 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR E 500 " --> pdb=" O ARG E 513 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE F 19 " --> pdb=" O TYR F 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR F 217 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR F 214 " --> pdb=" O TYR F 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU F 218 " --> pdb=" O GLU F 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU F 223 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TYR F 224 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU F 235 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA F 226 " --> pdb=" O ILE F 233 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG F 232 " --> pdb=" O LYS F 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS F 155 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 234 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 242 through 243 Processing sheet with id=AC6, first strand: chain 'F' and resid 466 through 471 removed outlier: 3.963A pdb=" N ASN F 468 " --> pdb=" O ILE G 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU G 455 " --> pdb=" O LEU G 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 457 " --> pdb=" O ALA G 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR F 500 " --> pdb=" O ARG F 513 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE G 19 " --> pdb=" O TYR G 217 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR G 217 " --> pdb=" O ILE G 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR G 214 " --> pdb=" O TYR G 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU G 218 " --> pdb=" O GLU G 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU G 223 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR G 224 " --> pdb=" O LEU G 235 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU G 235 " --> pdb=" O TYR G 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA G 226 " --> pdb=" O ILE G 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG G 232 " --> pdb=" O LYS G 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS G 155 " --> pdb=" O ARG G 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG G 234 " --> pdb=" O ALA G 153 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 242 through 243 Processing sheet with id=AD1, first strand: chain 'G' and resid 466 through 471 removed outlier: 3.963A pdb=" N ASN G 468 " --> pdb=" O ILE H 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU H 455 " --> pdb=" O LEU H 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 457 " --> pdb=" O ALA H 284 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR G 500 " --> pdb=" O ARG G 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 19 through 20 removed outlier: 3.532A pdb=" N ILE H 19 " --> pdb=" O TYR H 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR H 217 " --> pdb=" O ILE H 19 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR H 214 " --> pdb=" O TYR H 227 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU H 218 " --> pdb=" O GLU H 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU H 223 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR H 224 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU H 235 " --> pdb=" O TYR H 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA H 226 " --> pdb=" O ILE H 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG H 232 " --> pdb=" O LYS H 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS H 155 " --> pdb=" O ARG H 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG H 234 " --> pdb=" O ALA H 153 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 242 through 243 Processing sheet with id=AD5, first strand: chain 'H' and resid 466 through 471 removed outlier: 3.963A pdb=" N ASN H 468 " --> pdb=" O ILE I 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU I 455 " --> pdb=" O LEU I 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA I 457 " --> pdb=" O ALA I 284 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR H 500 " --> pdb=" O ARG H 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE I 19 " --> pdb=" O TYR I 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR I 217 " --> pdb=" O ILE I 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR I 214 " --> pdb=" O TYR I 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU I 218 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU I 223 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR I 224 " --> pdb=" O LEU I 235 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU I 235 " --> pdb=" O TYR I 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA I 226 " --> pdb=" O ILE I 233 " (cutoff:3.500A) removed outlier: 10.679A pdb=" N ARG I 232 " --> pdb=" O LYS I 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS I 155 " --> pdb=" O ARG I 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG I 234 " --> pdb=" O ALA I 153 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 242 through 243 Processing sheet with id=AD9, first strand: chain 'I' and resid 466 through 471 removed outlier: 3.964A pdb=" N ASN I 468 " --> pdb=" O ILE J 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU J 455 " --> pdb=" O LEU J 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA J 457 " --> pdb=" O ALA J 284 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR I 500 " --> pdb=" O ARG I 513 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE J 19 " --> pdb=" O TYR J 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR J 217 " --> pdb=" O ILE J 19 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR J 214 " --> pdb=" O TYR J 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU J 218 " --> pdb=" O GLU J 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU J 223 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TYR J 224 " --> pdb=" O LEU J 235 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU J 235 " --> pdb=" O TYR J 224 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ALA J 226 " --> pdb=" O ILE J 233 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG J 232 " --> pdb=" O LYS J 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS J 155 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG J 234 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 242 through 243 Processing sheet with id=AE4, first strand: chain 'J' and resid 466 through 471 removed outlier: 3.963A pdb=" N ASN J 468 " --> pdb=" O ILE K 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU K 455 " --> pdb=" O LEU K 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA K 457 " --> pdb=" O ALA K 284 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR J 500 " --> pdb=" O ARG J 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE K 19 " --> pdb=" O TYR K 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR K 217 " --> pdb=" O ILE K 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR K 214 " --> pdb=" O TYR K 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU K 218 " --> pdb=" O GLU K 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU K 223 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR K 224 " --> pdb=" O LEU K 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU K 235 " --> pdb=" O TYR K 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA K 226 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG K 232 " --> pdb=" O LYS K 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS K 155 " --> pdb=" O ARG K 232 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG K 234 " --> pdb=" O ALA K 153 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 242 through 243 Processing sheet with id=AE8, first strand: chain 'K' and resid 466 through 471 removed outlier: 3.964A pdb=" N ASN K 468 " --> pdb=" O ILE L 285 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 455 " --> pdb=" O LEU L 282 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA L 457 " --> pdb=" O ALA L 284 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR K 500 " --> pdb=" O ARG K 513 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 19 through 20 removed outlier: 3.531A pdb=" N ILE L 19 " --> pdb=" O TYR L 217 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR L 217 " --> pdb=" O ILE L 19 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR L 214 " --> pdb=" O TYR L 227 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU L 218 " --> pdb=" O GLU L 223 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU L 223 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N TYR L 224 " --> pdb=" O LEU L 235 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU L 235 " --> pdb=" O TYR L 224 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA L 226 " --> pdb=" O ILE L 233 " (cutoff:3.500A) removed outlier: 10.678A pdb=" N ARG L 232 " --> pdb=" O LYS L 155 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N LYS L 155 " --> pdb=" O ARG L 232 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG L 234 " --> pdb=" O ALA L 153 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 242 through 243 Processing sheet with id=AF3, first strand: chain 'L' and resid 500 through 502 removed outlier: 3.520A pdb=" N THR L 500 " --> pdb=" O ARG L 513 " (cutoff:3.500A) 1691 hydrogen bonds defined for protein. 4785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12146 1.34 - 1.46: 8661 1.46 - 1.58: 18265 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 39264 Sorted by residual: bond pdb=" C LYS C 483 " pdb=" O LYS C 483 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.16e-02 7.43e+03 1.06e+01 bond pdb=" C LYS F 483 " pdb=" O LYS F 483 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.16e-02 7.43e+03 1.06e+01 bond pdb=" C LYS K 483 " pdb=" O LYS K 483 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.16e-02 7.43e+03 1.06e+01 bond pdb=" C LYS B 483 " pdb=" O LYS B 483 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.16e-02 7.43e+03 1.06e+01 bond pdb=" C LYS E 483 " pdb=" O LYS E 483 " ideal model delta sigma weight residual 1.237 1.274 -0.038 1.16e-02 7.43e+03 1.06e+01 ... (remaining 39259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 50023 2.02 - 4.05: 2870 4.05 - 6.07: 322 6.07 - 8.10: 77 8.10 - 10.12: 36 Bond angle restraints: 53328 Sorted by residual: angle pdb=" C SER K 439 " pdb=" N THR K 440 " pdb=" CA THR K 440 " ideal model delta sigma weight residual 121.54 131.51 -9.97 1.91e+00 2.74e-01 2.72e+01 angle pdb=" C SER F 439 " pdb=" N THR F 440 " pdb=" CA THR F 440 " ideal model delta sigma weight residual 121.54 131.46 -9.92 1.91e+00 2.74e-01 2.70e+01 angle pdb=" C SER C 439 " pdb=" N THR C 440 " pdb=" CA THR C 440 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C SER G 439 " pdb=" N THR G 440 " pdb=" CA THR G 440 " ideal model delta sigma weight residual 121.54 131.45 -9.91 1.91e+00 2.74e-01 2.69e+01 angle pdb=" C SER B 439 " pdb=" N THR B 440 " pdb=" CA THR B 440 " ideal model delta sigma weight residual 121.54 131.44 -9.90 1.91e+00 2.74e-01 2.69e+01 ... (remaining 53323 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 20813 17.87 - 35.75: 2236 35.75 - 53.62: 423 53.62 - 71.50: 24 71.50 - 89.37: 48 Dihedral angle restraints: 23544 sinusoidal: 9408 harmonic: 14136 Sorted by residual: dihedral pdb=" CA SER L 515 " pdb=" C SER L 515 " pdb=" N SER L 516 " pdb=" CA SER L 516 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA SER J 515 " pdb=" C SER J 515 " pdb=" N SER J 516 " pdb=" CA SER J 516 " ideal model delta harmonic sigma weight residual -180.00 -152.35 -27.65 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA SER H 515 " pdb=" C SER H 515 " pdb=" N SER H 516 " pdb=" CA SER H 516 " ideal model delta harmonic sigma weight residual -180.00 -152.37 -27.63 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 23541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4132 0.053 - 0.107: 1533 0.107 - 0.160: 402 0.160 - 0.214: 77 0.214 - 0.267: 24 Chirality restraints: 6168 Sorted by residual: chirality pdb=" CB ILE C 19 " pdb=" CA ILE C 19 " pdb=" CG1 ILE C 19 " pdb=" CG2 ILE C 19 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE G 19 " pdb=" CA ILE G 19 " pdb=" CG1 ILE G 19 " pdb=" CG2 ILE G 19 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE F 19 " pdb=" CA ILE F 19 " pdb=" CG1 ILE F 19 " pdb=" CG2 ILE F 19 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 6165 not shown) Planarity restraints: 6648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR J 24 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO J 25 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO J 25 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 25 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 24 " -0.039 5.00e-02 4.00e+02 5.87e-02 5.51e+00 pdb=" N PRO G 25 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 25 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 25 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 24 " 0.039 5.00e-02 4.00e+02 5.87e-02 5.50e+00 pdb=" N PRO C 25 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 25 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 25 " 0.033 5.00e-02 4.00e+02 ... (remaining 6645 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 12174 2.83 - 3.34: 34984 3.34 - 3.86: 59726 3.86 - 4.38: 68454 4.38 - 4.90: 117641 Nonbonded interactions: 292979 Sorted by model distance: nonbonded pdb=" O GLU I 200 " pdb=" OG SER I 204 " model vdw 2.307 3.040 nonbonded pdb=" O GLU C 200 " pdb=" OG SER C 204 " model vdw 2.307 3.040 nonbonded pdb=" O GLU D 200 " pdb=" OG SER D 204 " model vdw 2.308 3.040 nonbonded pdb=" O GLU G 200 " pdb=" OG SER G 204 " model vdw 2.308 3.040 nonbonded pdb=" O GLU B 200 " pdb=" OG SER B 204 " model vdw 2.308 3.040 ... (remaining 292974 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 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: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 31.010 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 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 : 0.007 0.056 39264 Z= 0.393 Angle : 1.044 10.125 53328 Z= 0.630 Chirality : 0.062 0.267 6168 Planarity : 0.007 0.059 6648 Dihedral : 14.970 89.373 14376 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.35 % Favored : 91.13 % Rotamer: Outliers : 0.56 % Allowed : 11.34 % Favored : 88.10 % Cbeta Deviations : 0.26 % 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: -4.57 (0.11), residues: 4668 helix: -3.35 (0.08), residues: 2400 sheet: -1.76 (0.24), residues: 348 loop : -2.63 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 266 TYR 0.018 0.002 TYR G 514 PHE 0.016 0.002 PHE F 210 TRP 0.006 0.001 TRP H 489 HIS 0.008 0.002 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00706 (39264) covalent geometry : angle 1.04371 (53328) hydrogen bonds : bond 0.29017 ( 1691) hydrogen bonds : angle 9.00899 ( 4785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 656 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TRP cc_start: 0.7564 (t60) cc_final: 0.7323 (t60) REVERT: A 553 ASP cc_start: 0.7387 (p0) cc_final: 0.6423 (t0) REVERT: B 216 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7493 (mm-30) REVERT: B 553 ASP cc_start: 0.6983 (p0) cc_final: 0.5975 (t0) REVERT: C 551 ILE cc_start: 0.8968 (mm) cc_final: 0.8698 (tp) REVERT: C 553 ASP cc_start: 0.7352 (p0) cc_final: 0.6222 (t0) REVERT: D 81 TRP cc_start: 0.7559 (t60) cc_final: 0.7284 (t60) REVERT: D 553 ASP cc_start: 0.7379 (p0) cc_final: 0.6430 (t0) REVERT: E 216 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7489 (mm-30) REVERT: E 553 ASP cc_start: 0.6984 (p0) cc_final: 0.5976 (t0) REVERT: F 551 ILE cc_start: 0.8968 (mm) cc_final: 0.8699 (tp) REVERT: F 553 ASP cc_start: 0.7353 (p0) cc_final: 0.6223 (t0) REVERT: G 81 TRP cc_start: 0.7562 (t60) cc_final: 0.7292 (t60) REVERT: G 553 ASP cc_start: 0.7375 (p0) cc_final: 0.6433 (t0) REVERT: H 216 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7494 (mm-30) REVERT: H 553 ASP cc_start: 0.6983 (p0) cc_final: 0.5976 (t0) REVERT: I 551 ILE cc_start: 0.8970 (mm) cc_final: 0.8700 (tp) REVERT: I 553 ASP cc_start: 0.7342 (p0) cc_final: 0.6217 (t0) REVERT: J 81 TRP cc_start: 0.7564 (t60) cc_final: 0.7296 (t60) REVERT: J 553 ASP cc_start: 0.7372 (p0) cc_final: 0.6430 (t0) REVERT: K 216 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7494 (mm-30) REVERT: K 553 ASP cc_start: 0.6986 (p0) cc_final: 0.5979 (t0) REVERT: L 551 ILE cc_start: 0.8966 (mm) cc_final: 0.8696 (tp) REVERT: L 553 ASP cc_start: 0.7354 (p0) cc_final: 0.6226 (t0) outliers start: 24 outliers final: 20 residues processed: 680 average time/residue: 0.2646 time to fit residues: 286.2664 Evaluate side-chains 419 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 399 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 247 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 247 THR Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 247 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.8980 chunk 401 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 163 HIS B 163 HIS C 163 HIS D 163 HIS E 163 HIS F 163 HIS G 163 HIS H 163 HIS I 163 HIS J 163 HIS K 163 HIS L 163 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.101623 restraints weight = 73167.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104291 restraints weight = 41903.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.105987 restraints weight = 29311.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107002 restraints weight = 23580.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107612 restraints weight = 20741.808| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 39264 Z= 0.148 Angle : 0.650 7.449 53328 Z= 0.334 Chirality : 0.045 0.140 6168 Planarity : 0.005 0.036 6648 Dihedral : 5.354 28.023 5336 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.64 % Allowed : 14.18 % Favored : 82.18 % 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: -2.81 (0.12), residues: 4668 helix: -1.81 (0.09), residues: 2388 sheet: 0.10 (0.30), residues: 288 loop : -2.11 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 133 TYR 0.013 0.001 TYR E 511 PHE 0.013 0.001 PHE K 84 TRP 0.013 0.002 TRP I 489 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00337 (39264) covalent geometry : angle 0.64962 (53328) hydrogen bonds : bond 0.04662 ( 1691) hydrogen bonds : angle 5.01309 ( 4785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 419 time to evaluate : 1.624 Fit side-chains REVERT: A 493 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8431 (mm) REVERT: B 81 TRP cc_start: 0.7825 (t60) cc_final: 0.6913 (t60) REVERT: B 459 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8142 (m) REVERT: C 493 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8556 (mm) REVERT: D 493 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8357 (mm) REVERT: E 81 TRP cc_start: 0.7832 (t60) cc_final: 0.6915 (t60) REVERT: E 459 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8137 (m) REVERT: F 493 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8559 (mm) REVERT: G 493 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8360 (mm) REVERT: H 81 TRP cc_start: 0.7836 (t60) cc_final: 0.6908 (t60) REVERT: H 459 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.8139 (m) REVERT: I 493 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8557 (mm) REVERT: J 493 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8524 (mm) REVERT: K 81 TRP cc_start: 0.7826 (t60) cc_final: 0.6910 (t60) REVERT: K 459 VAL cc_start: 0.8351 (OUTLIER) cc_final: 0.8139 (m) REVERT: L 493 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8561 (mm) outliers start: 155 outliers final: 55 residues processed: 522 average time/residue: 0.2103 time to fit residues: 190.6509 Evaluate side-chains 435 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 368 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 247 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 247 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 247 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 221 optimal weight: 0.5980 chunk 161 optimal weight: 20.0000 chunk 454 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 217 optimal weight: 8.9990 chunk 239 optimal weight: 9.9990 chunk 196 optimal weight: 2.9990 chunk 446 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.131263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.102137 restraints weight = 72623.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104860 restraints weight = 41317.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.106109 restraints weight = 28759.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106711 restraints weight = 22825.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106628 restraints weight = 21363.053| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 39264 Z= 0.141 Angle : 0.595 7.224 53328 Z= 0.304 Chirality : 0.044 0.137 6168 Planarity : 0.004 0.033 6648 Dihedral : 4.900 20.510 5324 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.52 % Allowed : 15.56 % Favored : 80.92 % 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: -2.09 (0.12), residues: 4668 helix: -0.96 (0.10), residues: 2388 sheet: 0.27 (0.31), residues: 288 loop : -2.12 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 234 TYR 0.016 0.001 TYR E 514 PHE 0.010 0.001 PHE K 84 TRP 0.013 0.001 TRP A 81 HIS 0.005 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00325 (39264) covalent geometry : angle 0.59469 (53328) hydrogen bonds : bond 0.03974 ( 1691) hydrogen bonds : angle 4.58868 ( 4785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 387 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 TRP cc_start: 0.7733 (t60) cc_final: 0.6807 (t60) REVERT: D 493 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8525 (mm) REVERT: E 81 TRP cc_start: 0.7732 (t60) cc_final: 0.6805 (t60) REVERT: G 493 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8530 (mm) REVERT: H 81 TRP cc_start: 0.7704 (t60) cc_final: 0.6781 (t60) REVERT: J 493 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8618 (mm) REVERT: K 81 TRP cc_start: 0.7735 (t60) cc_final: 0.6808 (t60) outliers start: 150 outliers final: 96 residues processed: 491 average time/residue: 0.1998 time to fit residues: 175.6871 Evaluate side-chains 459 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 360 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 478 SER Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 503 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 478 SER Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 503 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 296 optimal weight: 0.8980 chunk 129 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 401 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.0470 chunk 223 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 267 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 237 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 236 HIS B 125 ASN B 236 HIS C 125 ASN D 125 ASN D 236 HIS E 125 ASN F 125 ASN F 236 HIS G 125 ASN G 236 HIS H 125 ASN I 125 ASN J 125 ASN J 236 HIS K 125 ASN K 236 HIS L 125 ASN L 236 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.105261 restraints weight = 72715.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.107977 restraints weight = 41422.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.109667 restraints weight = 28850.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.110720 restraints weight = 23209.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111119 restraints weight = 20406.955| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39264 Z= 0.094 Angle : 0.528 6.198 53328 Z= 0.271 Chirality : 0.043 0.136 6168 Planarity : 0.004 0.036 6648 Dihedral : 4.447 20.884 5320 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 3.08 % Allowed : 17.35 % Favored : 79.58 % 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: -1.54 (0.12), residues: 4668 helix: -0.28 (0.10), residues: 2376 sheet: 0.14 (0.31), residues: 288 loop : -2.09 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 234 TYR 0.008 0.001 TYR D 514 PHE 0.010 0.001 PHE F 210 TRP 0.035 0.001 TRP A 81 HIS 0.006 0.001 HIS B 79 Details of bonding type rmsd covalent geometry : bond 0.00208 (39264) covalent geometry : angle 0.52815 (53328) hydrogen bonds : bond 0.03046 ( 1691) hydrogen bonds : angle 4.28721 ( 4785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 464 time to evaluate : 1.492 Fit side-chains REVERT: A 493 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8498 (mm) REVERT: C 493 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8643 (mm) REVERT: F 493 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8647 (mm) REVERT: H 81 TRP cc_start: 0.7630 (t60) cc_final: 0.6721 (t60) REVERT: I 493 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8657 (mm) REVERT: L 493 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8658 (mm) outliers start: 131 outliers final: 93 residues processed: 553 average time/residue: 0.1911 time to fit residues: 191.8133 Evaluate side-chains 468 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 370 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 478 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 282 LEU Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 503 VAL Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 282 LEU Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 478 SER Chi-restraints excluded: chain K residue 503 VAL Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 318 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 348 optimal weight: 6.9990 chunk 326 optimal weight: 8.9990 chunk 268 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 152 optimal weight: 0.7980 chunk 332 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 GLN D 35 GLN F 35 GLN G 35 GLN I 35 GLN J 35 GLN L 35 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.129567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.099428 restraints weight = 72862.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102765 restraints weight = 42895.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.103754 restraints weight = 29566.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.104720 restraints weight = 22939.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.104705 restraints weight = 21667.768| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 39264 Z= 0.206 Angle : 0.628 7.600 53328 Z= 0.319 Chirality : 0.046 0.147 6168 Planarity : 0.004 0.032 6648 Dihedral : 4.695 20.910 5320 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.98 % Allowed : 18.71 % Favored : 76.31 % 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: -1.41 (0.12), residues: 4668 helix: -0.17 (0.10), residues: 2400 sheet: 0.19 (0.29), residues: 288 loop : -2.05 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 140 TYR 0.017 0.002 TYR H 514 PHE 0.011 0.002 PHE J 497 TRP 0.030 0.002 TRP A 81 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00484 (39264) covalent geometry : angle 0.62835 (53328) hydrogen bonds : bond 0.03929 ( 1691) hydrogen bonds : angle 4.38579 ( 4785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 366 time to evaluate : 1.567 Fit side-chains REVERT: A 50 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9009 (pp) REVERT: A 493 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8695 (mm) REVERT: C 493 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8927 (mm) REVERT: D 50 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9010 (pp) REVERT: D 493 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8687 (mm) REVERT: F 493 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8928 (mm) REVERT: G 50 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9006 (pp) REVERT: G 493 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8686 (mm) REVERT: H 81 TRP cc_start: 0.7743 (t60) cc_final: 0.6676 (t60) REVERT: I 493 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8933 (mm) REVERT: J 493 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8699 (mm) REVERT: L 493 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8937 (mm) outliers start: 212 outliers final: 129 residues processed: 537 average time/residue: 0.1943 time to fit residues: 189.3263 Evaluate side-chains 484 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 344 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 520 SER Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 478 SER Chi-restraints excluded: chain E residue 503 VAL Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 520 SER Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 520 SER Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 520 SER Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 478 SER Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 520 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 84 optimal weight: 1.9990 chunk 255 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 447 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 chunk 258 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 432 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102812 restraints weight = 72532.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105470 restraints weight = 41525.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107192 restraints weight = 29075.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108220 restraints weight = 23374.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.108827 restraints weight = 20601.246| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39264 Z= 0.107 Angle : 0.565 7.840 53328 Z= 0.286 Chirality : 0.043 0.171 6168 Planarity : 0.003 0.032 6648 Dihedral : 4.430 19.315 5320 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.57 % Allowed : 20.00 % Favored : 76.43 % 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: -1.24 (0.12), residues: 4668 helix: -0.03 (0.10), residues: 2520 sheet: 0.16 (0.30), residues: 288 loop : -2.07 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 234 TYR 0.008 0.001 TYR I 217 PHE 0.011 0.001 PHE F 210 TRP 0.015 0.001 TRP A 81 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00241 (39264) covalent geometry : angle 0.56533 (53328) hydrogen bonds : bond 0.03126 ( 1691) hydrogen bonds : angle 4.21752 ( 4785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 386 time to evaluate : 1.522 Fit side-chains REVERT: A 50 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8852 (pp) REVERT: A 160 GLN cc_start: 0.7652 (tp-100) cc_final: 0.7362 (tp40) REVERT: A 493 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8634 (mm) REVERT: C 31 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (t80) REVERT: C 81 TRP cc_start: 0.7542 (t60) cc_final: 0.6900 (t60) REVERT: C 251 ASP cc_start: 0.7419 (t70) cc_final: 0.7218 (t70) REVERT: C 269 GLU cc_start: 0.7566 (tt0) cc_final: 0.7320 (tt0) REVERT: C 493 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8787 (mm) REVERT: D 50 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8872 (pp) REVERT: D 493 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8586 (mm) REVERT: F 31 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8526 (t80) REVERT: F 81 TRP cc_start: 0.7534 (t60) cc_final: 0.6896 (t60) REVERT: F 269 GLU cc_start: 0.7567 (tt0) cc_final: 0.7318 (tt0) REVERT: F 493 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8788 (mm) REVERT: G 50 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8873 (pp) REVERT: G 493 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (mm) REVERT: I 31 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8531 (t80) REVERT: I 81 TRP cc_start: 0.7550 (t60) cc_final: 0.6897 (t60) REVERT: I 269 GLU cc_start: 0.7567 (tt0) cc_final: 0.7317 (tt0) REVERT: I 493 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8794 (mm) REVERT: J 50 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8866 (pp) REVERT: J 493 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8672 (mm) REVERT: L 31 PHE cc_start: 0.8913 (OUTLIER) cc_final: 0.8530 (t80) REVERT: L 81 TRP cc_start: 0.7541 (t60) cc_final: 0.6945 (t60) REVERT: L 251 ASP cc_start: 0.7420 (t70) cc_final: 0.7217 (t70) REVERT: L 493 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8798 (mm) outliers start: 152 outliers final: 117 residues processed: 506 average time/residue: 0.1966 time to fit residues: 179.2640 Evaluate side-chains 496 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 363 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 478 SER Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 478 SER Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 388 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 371 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 7.9990 chunk 361 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 280 optimal weight: 20.0000 chunk 292 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 overall best weight: 3.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 GLN H 35 GLN K 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.128949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099126 restraints weight = 73025.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.101784 restraints weight = 42822.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102968 restraints weight = 29928.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103541 restraints weight = 23738.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103592 restraints weight = 22732.235| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 39264 Z= 0.212 Angle : 0.653 8.229 53328 Z= 0.330 Chirality : 0.047 0.204 6168 Planarity : 0.004 0.031 6648 Dihedral : 4.687 20.668 5320 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.44 % Allowed : 20.63 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.12), residues: 4668 helix: 0.04 (0.10), residues: 2472 sheet: 0.05 (0.30), residues: 288 loop : -1.98 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 140 TYR 0.016 0.002 TYR K 141 PHE 0.013 0.002 PHE D 65 TRP 0.021 0.001 TRP A 81 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00504 (39264) covalent geometry : angle 0.65283 (53328) hydrogen bonds : bond 0.03892 ( 1691) hydrogen bonds : angle 4.36422 ( 4785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 346 time to evaluate : 1.566 Fit side-chains REVERT: A 50 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9001 (pp) REVERT: A 160 GLN cc_start: 0.7619 (tp-100) cc_final: 0.7349 (tp40) REVERT: A 493 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8793 (mm) REVERT: C 31 PHE cc_start: 0.8980 (OUTLIER) cc_final: 0.8566 (t80) REVERT: C 493 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9001 (mm) REVERT: D 493 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8767 (mm) REVERT: F 31 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8555 (t80) REVERT: F 493 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8995 (mm) REVERT: G 493 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8758 (mm) REVERT: I 31 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8565 (t80) REVERT: I 493 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9003 (mm) REVERT: J 493 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8752 (mm) REVERT: L 31 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.8565 (t80) REVERT: L 493 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9003 (mm) outliers start: 189 outliers final: 149 residues processed: 506 average time/residue: 0.1898 time to fit residues: 173.9968 Evaluate side-chains 498 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 336 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 478 SER Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 520 SER Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 520 SER Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 282 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 277 LEU Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 478 SER Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 520 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 92 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 325 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 213 optimal weight: 0.0670 chunk 151 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100006 restraints weight = 72642.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102593 restraints weight = 42500.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.104231 restraints weight = 30115.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105211 restraints weight = 24464.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.105672 restraints weight = 21677.452| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 39264 Z= 0.151 Angle : 0.603 7.354 53328 Z= 0.305 Chirality : 0.045 0.207 6168 Planarity : 0.004 0.030 6648 Dihedral : 4.589 19.916 5320 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.97 % Allowed : 21.53 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.17 (0.12), residues: 4668 helix: 0.13 (0.10), residues: 2508 sheet: -0.07 (0.30), residues: 288 loop : -2.14 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 51 TYR 0.011 0.001 TYR D 141 PHE 0.012 0.001 PHE D 65 TRP 0.025 0.001 TRP J 81 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00359 (39264) covalent geometry : angle 0.60286 (53328) hydrogen bonds : bond 0.03486 ( 1691) hydrogen bonds : angle 4.29850 ( 4785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 348 time to evaluate : 1.316 Fit side-chains REVERT: A 50 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.8968 (pp) REVERT: A 160 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7486 (tp40) REVERT: A 493 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8742 (mm) REVERT: B 81 TRP cc_start: 0.7604 (t60) cc_final: 0.6711 (t60) REVERT: C 31 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8546 (t80) REVERT: C 493 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8933 (mm) REVERT: D 50 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8949 (pp) REVERT: D 493 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8712 (mm) REVERT: E 81 TRP cc_start: 0.7607 (t60) cc_final: 0.6709 (t60) REVERT: F 31 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.8541 (t80) REVERT: F 493 LEU cc_start: 0.9222 (OUTLIER) cc_final: 0.8929 (mm) REVERT: G 50 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8926 (pp) REVERT: G 493 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8713 (mm) REVERT: I 31 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8557 (t80) REVERT: I 493 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8935 (mm) REVERT: J 50 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8916 (pp) REVERT: J 493 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8718 (mm) REVERT: K 81 TRP cc_start: 0.7602 (t60) cc_final: 0.6704 (t60) REVERT: L 31 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8556 (t80) REVERT: L 81 TRP cc_start: 0.7640 (t60) cc_final: 0.6963 (t60) REVERT: L 493 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8937 (mm) outliers start: 169 outliers final: 139 residues processed: 491 average time/residue: 0.1860 time to fit residues: 165.8328 Evaluate side-chains 483 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 328 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 520 SER Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 478 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 536 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 478 SER Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain E residue 536 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 536 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain H residue 536 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain I residue 536 VAL Chi-restraints excluded: chain I residue 539 VAL Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 520 SER Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 478 SER Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain K residue 536 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 536 VAL Chi-restraints excluded: chain L residue 539 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 142 optimal weight: 0.0050 chunk 26 optimal weight: 2.9990 chunk 365 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 134 optimal weight: 0.0050 chunk 88 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 13 optimal weight: 20.0000 chunk 420 optimal weight: 0.0020 chunk 47 optimal weight: 5.9990 overall best weight: 1.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 HIS ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.132764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.102868 restraints weight = 72708.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105551 restraints weight = 41857.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107257 restraints weight = 29315.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108303 restraints weight = 23559.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108786 restraints weight = 20739.230| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 39264 Z= 0.108 Angle : 0.570 7.882 53328 Z= 0.290 Chirality : 0.044 0.198 6168 Planarity : 0.003 0.032 6648 Dihedral : 4.350 19.233 5320 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.62 % Allowed : 22.04 % Favored : 74.34 % 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: -0.88 (0.12), residues: 4668 helix: 0.43 (0.11), residues: 2496 sheet: -0.13 (0.31), residues: 288 loop : -2.07 (0.14), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 560 TYR 0.008 0.001 TYR F 217 PHE 0.011 0.001 PHE A 210 TRP 0.024 0.001 TRP A 81 HIS 0.006 0.001 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00243 (39264) covalent geometry : angle 0.56996 (53328) hydrogen bonds : bond 0.03021 ( 1691) hydrogen bonds : angle 4.15315 ( 4785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 381 time to evaluate : 1.551 Fit side-chains REVERT: A 50 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8862 (pp) REVERT: A 81 TRP cc_start: 0.7406 (t60) cc_final: 0.7046 (t60) REVERT: A 493 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8615 (mm) REVERT: B 81 TRP cc_start: 0.7416 (t60) cc_final: 0.6715 (t60) REVERT: B 113 THR cc_start: 0.8995 (p) cc_final: 0.8783 (t) REVERT: B 251 ASP cc_start: 0.7163 (t70) cc_final: 0.6934 (t70) REVERT: C 31 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8512 (t80) REVERT: C 81 TRP cc_start: 0.7580 (t60) cc_final: 0.7110 (t60) REVERT: C 251 ASP cc_start: 0.7421 (t70) cc_final: 0.7199 (t70) REVERT: C 493 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8836 (mm) REVERT: D 50 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8856 (pp) REVERT: D 493 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8618 (mm) REVERT: E 81 TRP cc_start: 0.7419 (t60) cc_final: 0.6716 (t60) REVERT: E 113 THR cc_start: 0.9004 (p) cc_final: 0.8790 (t) REVERT: E 251 ASP cc_start: 0.7174 (t70) cc_final: 0.6943 (t70) REVERT: F 31 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8520 (t80) REVERT: F 81 TRP cc_start: 0.7575 (t60) cc_final: 0.7107 (t60) REVERT: F 493 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8838 (mm) REVERT: G 50 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8851 (pp) REVERT: G 493 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8609 (mm) REVERT: H 81 TRP cc_start: 0.7474 (t60) cc_final: 0.6753 (t60) REVERT: H 113 THR cc_start: 0.8998 (p) cc_final: 0.8796 (t) REVERT: H 251 ASP cc_start: 0.7177 (t70) cc_final: 0.6946 (t70) REVERT: I 31 PHE cc_start: 0.8905 (OUTLIER) cc_final: 0.8502 (t80) REVERT: I 81 TRP cc_start: 0.7582 (t60) cc_final: 0.7114 (t60) REVERT: I 493 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (mm) REVERT: J 50 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8825 (pp) REVERT: J 493 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8703 (mm) REVERT: K 81 TRP cc_start: 0.7417 (t60) cc_final: 0.6714 (t60) REVERT: K 113 THR cc_start: 0.9004 (p) cc_final: 0.8792 (t) REVERT: K 251 ASP cc_start: 0.7185 (t70) cc_final: 0.6957 (t70) REVERT: L 31 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8520 (t80) REVERT: L 81 TRP cc_start: 0.7568 (t60) cc_final: 0.7164 (t60) REVERT: L 251 ASP cc_start: 0.7431 (t70) cc_final: 0.7205 (t70) REVERT: L 493 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8839 (mm) outliers start: 154 outliers final: 119 residues processed: 502 average time/residue: 0.1912 time to fit residues: 173.3497 Evaluate side-chains 481 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 346 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 368 optimal weight: 0.0970 chunk 28 optimal weight: 10.0000 chunk 308 optimal weight: 4.9990 chunk 373 optimal weight: 9.9990 chunk 205 optimal weight: 0.7980 chunk 127 optimal weight: 9.9990 chunk 186 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 406 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.131452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.101265 restraints weight = 72572.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.103886 restraints weight = 42200.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105537 restraints weight = 29773.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106541 restraints weight = 24111.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107145 restraints weight = 21275.407| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39264 Z= 0.139 Angle : 0.601 7.654 53328 Z= 0.307 Chirality : 0.045 0.210 6168 Planarity : 0.003 0.031 6648 Dihedral : 4.399 19.824 5320 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.36 % Allowed : 22.68 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.12), residues: 4668 helix: 0.41 (0.10), residues: 2508 sheet: -0.17 (0.30), residues: 288 loop : -1.98 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 220 TYR 0.010 0.001 TYR D 141 PHE 0.012 0.001 PHE A 210 TRP 0.022 0.001 TRP A 81 HIS 0.007 0.001 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.00327 (39264) covalent geometry : angle 0.60094 (53328) hydrogen bonds : bond 0.03248 ( 1691) hydrogen bonds : angle 4.16634 ( 4785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9336 Ramachandran restraints generated. 4668 Oldfield, 0 Emsley, 4668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 359 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8908 (pp) REVERT: A 81 TRP cc_start: 0.7439 (t60) cc_final: 0.7092 (t60) REVERT: A 493 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8695 (mm) REVERT: B 81 TRP cc_start: 0.7445 (t60) cc_final: 0.6680 (t60) REVERT: B 113 THR cc_start: 0.9034 (p) cc_final: 0.8822 (t) REVERT: B 251 ASP cc_start: 0.7186 (t70) cc_final: 0.6935 (t70) REVERT: C 31 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8493 (t80) REVERT: C 81 TRP cc_start: 0.7612 (t60) cc_final: 0.7086 (t60) REVERT: C 251 ASP cc_start: 0.7472 (t70) cc_final: 0.7235 (t70) REVERT: C 493 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8863 (mm) REVERT: D 50 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8914 (pp) REVERT: D 493 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 81 TRP cc_start: 0.7453 (t60) cc_final: 0.6681 (t60) REVERT: E 113 THR cc_start: 0.9044 (p) cc_final: 0.8832 (t) REVERT: E 251 ASP cc_start: 0.7201 (t70) cc_final: 0.6950 (t70) REVERT: F 31 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8502 (t80) REVERT: F 81 TRP cc_start: 0.7609 (t60) cc_final: 0.7083 (t60) REVERT: F 493 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8866 (mm) REVERT: G 50 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8911 (pp) REVERT: G 493 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8657 (mm) REVERT: H 81 TRP cc_start: 0.7523 (t60) cc_final: 0.6670 (t60) REVERT: H 113 THR cc_start: 0.9041 (p) cc_final: 0.8834 (t) REVERT: H 251 ASP cc_start: 0.7204 (t70) cc_final: 0.6955 (t70) REVERT: I 31 PHE cc_start: 0.8915 (OUTLIER) cc_final: 0.8511 (t80) REVERT: I 81 TRP cc_start: 0.7617 (t60) cc_final: 0.7091 (t60) REVERT: I 493 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8866 (mm) REVERT: J 50 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8902 (pp) REVERT: J 493 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8752 (mm) REVERT: K 81 TRP cc_start: 0.7454 (t60) cc_final: 0.6680 (t60) REVERT: K 113 THR cc_start: 0.9043 (p) cc_final: 0.8836 (t) REVERT: K 251 ASP cc_start: 0.7209 (t70) cc_final: 0.6965 (t70) REVERT: L 31 PHE cc_start: 0.8919 (OUTLIER) cc_final: 0.8500 (t80) REVERT: L 81 TRP cc_start: 0.7603 (t60) cc_final: 0.7190 (t60) REVERT: L 251 ASP cc_start: 0.7473 (t70) cc_final: 0.7235 (t70) REVERT: L 493 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8866 (mm) outliers start: 143 outliers final: 124 residues processed: 471 average time/residue: 0.1780 time to fit residues: 151.3849 Evaluate side-chains 489 residues out of total 4308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 349 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 536 VAL Chi-restraints excluded: chain B residue 31 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain C residue 31 PHE Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 115 LYS Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 159 THR Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain D residue 31 PHE Chi-restraints excluded: chain D residue 46 ILE Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 263 MET Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 503 VAL Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 536 VAL Chi-restraints excluded: chain E residue 31 PHE Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 159 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 491 SER Chi-restraints excluded: chain E residue 493 LEU Chi-restraints excluded: chain E residue 530 VAL Chi-restraints excluded: chain F residue 31 PHE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 143 ASP Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 263 MET Chi-restraints excluded: chain F residue 493 LEU Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain F residue 530 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain G residue 31 PHE Chi-restraints excluded: chain G residue 46 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 115 LYS Chi-restraints excluded: chain G residue 143 ASP Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 159 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 459 VAL Chi-restraints excluded: chain G residue 493 LEU Chi-restraints excluded: chain G residue 503 VAL Chi-restraints excluded: chain G residue 510 LEU Chi-restraints excluded: chain G residue 536 VAL Chi-restraints excluded: chain H residue 31 PHE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 143 ASP Chi-restraints excluded: chain H residue 145 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 459 VAL Chi-restraints excluded: chain H residue 491 SER Chi-restraints excluded: chain H residue 493 LEU Chi-restraints excluded: chain H residue 530 VAL Chi-restraints excluded: chain I residue 31 PHE Chi-restraints excluded: chain I residue 46 ILE Chi-restraints excluded: chain I residue 115 LYS Chi-restraints excluded: chain I residue 143 ASP Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 159 THR Chi-restraints excluded: chain I residue 218 LEU Chi-restraints excluded: chain I residue 493 LEU Chi-restraints excluded: chain I residue 503 VAL Chi-restraints excluded: chain I residue 530 VAL Chi-restraints excluded: chain J residue 31 PHE Chi-restraints excluded: chain J residue 46 ILE Chi-restraints excluded: chain J residue 50 LEU Chi-restraints excluded: chain J residue 115 LYS Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 145 ILE Chi-restraints excluded: chain J residue 159 THR Chi-restraints excluded: chain J residue 225 VAL Chi-restraints excluded: chain J residue 263 MET Chi-restraints excluded: chain J residue 277 LEU Chi-restraints excluded: chain J residue 459 VAL Chi-restraints excluded: chain J residue 493 LEU Chi-restraints excluded: chain J residue 503 VAL Chi-restraints excluded: chain J residue 510 LEU Chi-restraints excluded: chain J residue 536 VAL Chi-restraints excluded: chain K residue 31 PHE Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain K residue 143 ASP Chi-restraints excluded: chain K residue 145 ILE Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain K residue 459 VAL Chi-restraints excluded: chain K residue 491 SER Chi-restraints excluded: chain K residue 493 LEU Chi-restraints excluded: chain K residue 530 VAL Chi-restraints excluded: chain L residue 31 PHE Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 115 LYS Chi-restraints excluded: chain L residue 143 ASP Chi-restraints excluded: chain L residue 145 ILE Chi-restraints excluded: chain L residue 159 THR Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 493 LEU Chi-restraints excluded: chain L residue 503 VAL Chi-restraints excluded: chain L residue 530 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 121 optimal weight: 1.9990 chunk 389 optimal weight: 6.9990 chunk 151 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 393 optimal weight: 0.4980 chunk 52 optimal weight: 10.0000 chunk 285 optimal weight: 1.9990 chunk 378 optimal weight: 0.5980 chunk 317 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.133141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103168 restraints weight = 72475.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105836 restraints weight = 41801.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107513 restraints weight = 29426.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108540 restraints weight = 23756.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109039 restraints weight = 20971.623| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39264 Z= 0.106 Angle : 0.575 7.882 53328 Z= 0.293 Chirality : 0.044 0.215 6168 Planarity : 0.003 0.032 6648 Dihedral : 4.309 18.998 5320 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.43 % Allowed : 22.56 % Favored : 74.01 % 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: -0.66 (0.13), residues: 4668 helix: 0.56 (0.11), residues: 2484 sheet: -0.15 (0.30), residues: 288 loop : -1.85 (0.15), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 220 TYR 0.007 0.001 TYR D 141 PHE 0.012 0.001 PHE A 210 TRP 0.020 0.001 TRP A 81 HIS 0.007 0.001 HIS K 79 Details of bonding type rmsd covalent geometry : bond 0.00240 (39264) covalent geometry : angle 0.57510 (53328) hydrogen bonds : bond 0.02975 ( 1691) hydrogen bonds : angle 4.10033 ( 4785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6560.78 seconds wall clock time: 114 minutes 36.60 seconds (6876.60 seconds total)