Starting phenix.real_space_refine on Mon Jan 20 19:19:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.cif Found real_map, /net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.map" model { file = "/net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9axe_43965/01_2025/9axe_43965.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 308 5.16 5 C 41874 2.51 5 N 10808 2.21 5 O 12642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65632 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "B" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "C" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "E" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "F" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "G" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "H" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "I" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "J" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "K" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "L" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "M" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Chain: "N" Number of atoms: 4688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4688 Classifications: {'peptide': 579} Link IDs: {'CIS': 1, 'PTRANS': 22, 'TRANS': 555} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 56 residue: pdb=" N ARG A 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG A 78 " occ=0.86 residue: pdb=" N GLY A 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY A 79 " occ=0.82 residue: pdb=" N GLY A 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY A 80 " occ=0.83 residue: pdb=" N ARG A 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG A 81 " occ=0.62 residue: pdb=" N ARG B 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG B 78 " occ=0.86 residue: pdb=" N GLY B 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY B 79 " occ=0.82 residue: pdb=" N GLY B 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY B 80 " occ=0.83 residue: pdb=" N ARG B 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG B 81 " occ=0.62 residue: pdb=" N ARG C 78 " occ=0.86 ... (9 atoms not shown) pdb=" NH2 ARG C 78 " occ=0.86 residue: pdb=" N GLY C 79 " occ=0.82 ... (2 atoms not shown) pdb=" O GLY C 79 " occ=0.82 residue: pdb=" N GLY C 80 " occ=0.83 ... (2 atoms not shown) pdb=" O GLY C 80 " occ=0.83 residue: pdb=" N ARG C 81 " occ=0.62 ... (9 atoms not shown) pdb=" NH2 ARG C 81 " occ=0.62 ... (remaining 44 not shown) Time building chain proxies: 25.90, per 1000 atoms: 0.39 Number of scatterers: 65632 At special positions: 0 Unit cell: (131.544, 249.516, 312.156, 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 308 16.00 O 12642 8.00 N 10808 7.00 C 41874 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: 11.46 Conformation dependent library (CDL) restraints added in 6.1 seconds 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15428 Finding SS restraints... Secondary structure from input PDB file: 377 helices and 56 sheets defined 42.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.05 Creating SS restraints... Processing helix chain 'A' and resid 6 through 12 removed outlier: 3.545A pdb=" N ALA A 10 " --> pdb=" O GLY A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN A 22 " --> pdb=" O ASN A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 106 through 118 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 158 through 162 removed outlier: 3.988A pdb=" N ASP A 162 " --> pdb=" O GLU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 removed outlier: 3.601A pdb=" N PHE A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE A 209 " --> pdb=" O VAL A 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 206 through 209' Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 240 removed outlier: 3.529A pdb=" N HIS A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 324 Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.644A pdb=" N GLY A 330 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN A 331 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 354 through 366 Processing helix chain 'A' and resid 426 through 430 Processing helix chain 'A' and resid 431 through 443 Processing helix chain 'A' and resid 449 through 456 removed outlier: 3.647A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 454 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.587A pdb=" N SER A 511 " --> pdb=" O THR A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 Processing helix chain 'A' and resid 538 through 550 removed outlier: 3.679A pdb=" N ASN A 550 " --> pdb=" O ILE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 559 Processing helix chain 'A' and resid 562 through 576 Processing helix chain 'A' and resid 579 through 588 Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.546A pdb=" N ALA B 10 " --> pdb=" O GLY B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN B 22 " --> pdb=" O ASN B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 44 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 87 through 94 Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 158 through 162 removed outlier: 3.987A pdb=" N ASP B 162 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.599A pdb=" N PHE B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.580A pdb=" N ILE B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 185 " --> pdb=" O ILE B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE B 209 " --> pdb=" O VAL B 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 206 through 209' Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 229 through 240 removed outlier: 3.528A pdb=" N HIS B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.650A pdb=" N GLY B 330 " --> pdb=" O PRO B 327 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN B 331 " --> pdb=" O GLU B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 354 through 366 Processing helix chain 'B' and resid 426 through 430 Processing helix chain 'B' and resid 431 through 443 Processing helix chain 'B' and resid 449 through 456 removed outlier: 3.649A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 523 removed outlier: 3.588A pdb=" N SER B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 537 Processing helix chain 'B' and resid 538 through 550 removed outlier: 3.679A pdb=" N ASN B 550 " --> pdb=" O ILE B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 559 Processing helix chain 'B' and resid 562 through 576 Processing helix chain 'B' and resid 579 through 588 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.545A pdb=" N ALA C 10 " --> pdb=" O GLY C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 23 removed outlier: 3.512A pdb=" N ASN C 22 " --> pdb=" O ASN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 44 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 87 through 94 Processing helix chain 'C' and resid 106 through 118 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 158 through 162 removed outlier: 3.990A pdb=" N ASP C 162 " --> pdb=" O GLU C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 176 removed outlier: 3.601A pdb=" N PHE C 175 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE C 209 " --> pdb=" O VAL C 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 209' Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 324 Processing helix chain 'C' and resid 326 through 331 removed outlier: 3.641A pdb=" N GLY C 330 " --> pdb=" O PRO C 327 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN C 331 " --> pdb=" O GLU C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 354 through 366 Processing helix chain 'C' and resid 426 through 430 Processing helix chain 'C' and resid 431 through 443 Processing helix chain 'C' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU C 453 " --> pdb=" O LYS C 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA C 454 " --> pdb=" O ILE C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 523 removed outlier: 3.589A pdb=" N SER C 511 " --> pdb=" O THR C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 537 Processing helix chain 'C' and resid 538 through 550 removed outlier: 3.680A pdb=" N ASN C 550 " --> pdb=" O ILE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 559 Processing helix chain 'C' and resid 562 through 576 Processing helix chain 'C' and resid 579 through 588 Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.546A pdb=" N ALA D 10 " --> pdb=" O GLY D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN D 22 " --> pdb=" O ASN D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 44 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 87 through 94 Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 143 through 155 Processing helix chain 'D' and resid 158 through 162 removed outlier: 3.989A pdb=" N ASP D 162 " --> pdb=" O GLU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 176 removed outlier: 3.600A pdb=" N PHE D 175 " --> pdb=" O SER D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR D 185 " --> pdb=" O ILE D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 205 Processing helix chain 'D' and resid 206 through 209 removed outlier: 3.768A pdb=" N ILE D 209 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 209' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 229 through 240 removed outlier: 3.527A pdb=" N HIS D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 324 Processing helix chain 'D' and resid 326 through 331 removed outlier: 3.645A pdb=" N GLY D 330 " --> pdb=" O PRO D 327 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN D 331 " --> pdb=" O GLU D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 354 through 366 Processing helix chain 'D' and resid 426 through 430 Processing helix chain 'D' and resid 431 through 443 Processing helix chain 'D' and resid 449 through 456 removed outlier: 3.650A pdb=" N LEU D 453 " --> pdb=" O LYS D 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 454 " --> pdb=" O ILE D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 523 removed outlier: 3.588A pdb=" N SER D 511 " --> pdb=" O THR D 507 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 537 Processing helix chain 'D' and resid 538 through 550 removed outlier: 3.678A pdb=" N ASN D 550 " --> pdb=" O ILE D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 559 Processing helix chain 'D' and resid 562 through 576 Processing helix chain 'D' and resid 579 through 588 Processing helix chain 'E' and resid 6 through 12 removed outlier: 3.545A pdb=" N ALA E 10 " --> pdb=" O GLY E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 23 removed outlier: 3.512A pdb=" N ASN E 22 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 44 Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 87 through 94 Processing helix chain 'E' and resid 106 through 118 Processing helix chain 'E' and resid 143 through 155 Processing helix chain 'E' and resid 158 through 162 removed outlier: 3.987A pdb=" N ASP E 162 " --> pdb=" O GLU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 176 removed outlier: 3.598A pdb=" N PHE E 175 " --> pdb=" O SER E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 205 Processing helix chain 'E' and resid 206 through 209 removed outlier: 3.769A pdb=" N ILE E 209 " --> pdb=" O VAL E 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 206 through 209' Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 229 through 240 removed outlier: 3.531A pdb=" N HIS E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 324 Processing helix chain 'E' and resid 326 through 331 removed outlier: 3.637A pdb=" N GLY E 330 " --> pdb=" O PRO E 327 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN E 331 " --> pdb=" O GLU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 354 through 366 Processing helix chain 'E' and resid 426 through 430 Processing helix chain 'E' and resid 431 through 443 Processing helix chain 'E' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU E 453 " --> pdb=" O LYS E 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA E 454 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 523 removed outlier: 3.589A pdb=" N SER E 511 " --> pdb=" O THR E 507 " (cutoff:3.500A) Processing helix chain 'E' and resid 534 through 537 Processing helix chain 'E' and resid 538 through 550 removed outlier: 3.678A pdb=" N ASN E 550 " --> pdb=" O ILE E 546 " (cutoff:3.500A) Processing helix chain 'E' and resid 554 through 559 Processing helix chain 'E' and resid 562 through 576 Processing helix chain 'E' and resid 579 through 588 Processing helix chain 'F' and resid 6 through 12 removed outlier: 3.549A pdb=" N ALA F 10 " --> pdb=" O GLY F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 23 removed outlier: 3.512A pdb=" N ASN F 22 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 44 Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 87 through 94 Processing helix chain 'F' and resid 106 through 118 Processing helix chain 'F' and resid 143 through 155 Processing helix chain 'F' and resid 158 through 162 removed outlier: 3.986A pdb=" N ASP F 162 " --> pdb=" O GLU F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.601A pdb=" N PHE F 175 " --> pdb=" O SER F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.584A pdb=" N ILE F 181 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 185 " --> pdb=" O ILE F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 205 Processing helix chain 'F' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE F 209 " --> pdb=" O VAL F 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 206 through 209' Processing helix chain 'F' and resid 224 through 229 Processing helix chain 'F' and resid 229 through 240 removed outlier: 3.528A pdb=" N HIS F 240 " --> pdb=" O TYR F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 324 Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.640A pdb=" N GLY F 330 " --> pdb=" O PRO F 327 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ASN F 331 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 354 through 366 Processing helix chain 'F' and resid 426 through 430 Processing helix chain 'F' and resid 431 through 443 Processing helix chain 'F' and resid 449 through 456 removed outlier: 3.649A pdb=" N LEU F 453 " --> pdb=" O LYS F 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA F 454 " --> pdb=" O ILE F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 523 removed outlier: 3.590A pdb=" N SER F 511 " --> pdb=" O THR F 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 537 Processing helix chain 'F' and resid 538 through 550 removed outlier: 3.676A pdb=" N ASN F 550 " --> pdb=" O ILE F 546 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 559 Processing helix chain 'F' and resid 562 through 576 Processing helix chain 'F' and resid 579 through 588 Processing helix chain 'G' and resid 6 through 12 removed outlier: 3.546A pdb=" N ALA G 10 " --> pdb=" O GLY G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN G 22 " --> pdb=" O ASN G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 44 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 106 through 118 Processing helix chain 'G' and resid 143 through 155 Processing helix chain 'G' and resid 158 through 162 removed outlier: 3.993A pdb=" N ASP G 162 " --> pdb=" O GLU G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.598A pdb=" N PHE G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 187 removed outlier: 3.582A pdb=" N ILE G 181 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR G 185 " --> pdb=" O ILE G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 205 Processing helix chain 'G' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE G 209 " --> pdb=" O VAL G 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 206 through 209' Processing helix chain 'G' and resid 224 through 229 Processing helix chain 'G' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS G 240 " --> pdb=" O TYR G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 324 Processing helix chain 'G' and resid 326 through 331 removed outlier: 3.636A pdb=" N GLY G 330 " --> pdb=" O PRO G 327 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ASN G 331 " --> pdb=" O GLU G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 354 through 366 Processing helix chain 'G' and resid 426 through 430 Processing helix chain 'G' and resid 431 through 443 Processing helix chain 'G' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU G 453 " --> pdb=" O LYS G 449 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 454 " --> pdb=" O ILE G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 523 removed outlier: 3.590A pdb=" N SER G 511 " --> pdb=" O THR G 507 " (cutoff:3.500A) Processing helix chain 'G' and resid 534 through 537 Processing helix chain 'G' and resid 538 through 550 removed outlier: 3.677A pdb=" N ASN G 550 " --> pdb=" O ILE G 546 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 559 Processing helix chain 'G' and resid 562 through 576 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'H' and resid 6 through 12 removed outlier: 3.549A pdb=" N ALA H 10 " --> pdb=" O GLY H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN H 22 " --> pdb=" O ASN H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 44 Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 87 through 94 Processing helix chain 'H' and resid 106 through 118 Processing helix chain 'H' and resid 143 through 155 Processing helix chain 'H' and resid 158 through 162 removed outlier: 3.986A pdb=" N ASP H 162 " --> pdb=" O GLU H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 3.600A pdb=" N PHE H 175 " --> pdb=" O SER H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 187 removed outlier: 3.582A pdb=" N ILE H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR H 185 " --> pdb=" O ILE H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 205 Processing helix chain 'H' and resid 206 through 209 removed outlier: 3.769A pdb=" N ILE H 209 " --> pdb=" O VAL H 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 206 through 209' Processing helix chain 'H' and resid 224 through 229 Processing helix chain 'H' and resid 229 through 240 removed outlier: 3.528A pdb=" N HIS H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 324 Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.640A pdb=" N GLY H 330 " --> pdb=" O PRO H 327 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASN H 331 " --> pdb=" O GLU H 328 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 354 through 366 Processing helix chain 'H' and resid 426 through 430 Processing helix chain 'H' and resid 431 through 443 Processing helix chain 'H' and resid 449 through 456 removed outlier: 3.650A pdb=" N LEU H 453 " --> pdb=" O LYS H 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA H 454 " --> pdb=" O ILE H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 523 removed outlier: 3.588A pdb=" N SER H 511 " --> pdb=" O THR H 507 " (cutoff:3.500A) Processing helix chain 'H' and resid 534 through 537 Processing helix chain 'H' and resid 538 through 550 removed outlier: 3.676A pdb=" N ASN H 550 " --> pdb=" O ILE H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 559 Processing helix chain 'H' and resid 562 through 576 Processing helix chain 'H' and resid 579 through 588 Processing helix chain 'I' and resid 6 through 12 removed outlier: 3.544A pdb=" N ALA I 10 " --> pdb=" O GLY I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 23 removed outlier: 3.513A pdb=" N ASN I 22 " --> pdb=" O ASN I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 31 through 44 Processing helix chain 'I' and resid 48 through 50 No H-bonds generated for 'chain 'I' and resid 48 through 50' Processing helix chain 'I' and resid 87 through 94 Processing helix chain 'I' and resid 106 through 118 Processing helix chain 'I' and resid 143 through 155 Processing helix chain 'I' and resid 158 through 162 removed outlier: 3.989A pdb=" N ASP I 162 " --> pdb=" O GLU I 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.600A pdb=" N PHE I 175 " --> pdb=" O SER I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE I 181 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 185 " --> pdb=" O ILE I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 194 through 205 Processing helix chain 'I' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE I 209 " --> pdb=" O VAL I 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 206 through 209' Processing helix chain 'I' and resid 224 through 229 Processing helix chain 'I' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS I 240 " --> pdb=" O TYR I 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 324 Processing helix chain 'I' and resid 326 through 331 removed outlier: 3.640A pdb=" N GLY I 330 " --> pdb=" O PRO I 327 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ASN I 331 " --> pdb=" O GLU I 328 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 337 Processing helix chain 'I' and resid 354 through 366 Processing helix chain 'I' and resid 426 through 430 Processing helix chain 'I' and resid 431 through 443 Processing helix chain 'I' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU I 453 " --> pdb=" O LYS I 449 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA I 454 " --> pdb=" O ILE I 450 " (cutoff:3.500A) Processing helix chain 'I' and resid 507 through 523 removed outlier: 3.589A pdb=" N SER I 511 " --> pdb=" O THR I 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 534 through 537 Processing helix chain 'I' and resid 538 through 550 removed outlier: 3.675A pdb=" N ASN I 550 " --> pdb=" O ILE I 546 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 559 Processing helix chain 'I' and resid 562 through 576 Processing helix chain 'I' and resid 579 through 588 Processing helix chain 'J' and resid 6 through 12 removed outlier: 3.545A pdb=" N ALA J 10 " --> pdb=" O GLY J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN J 22 " --> pdb=" O ASN J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 44 Processing helix chain 'J' and resid 48 through 50 No H-bonds generated for 'chain 'J' and resid 48 through 50' Processing helix chain 'J' and resid 87 through 94 Processing helix chain 'J' and resid 106 through 118 Processing helix chain 'J' and resid 143 through 155 Processing helix chain 'J' and resid 158 through 162 removed outlier: 3.987A pdb=" N ASP J 162 " --> pdb=" O GLU J 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 176 removed outlier: 3.596A pdb=" N PHE J 175 " --> pdb=" O SER J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE J 181 " --> pdb=" O SER J 177 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR J 185 " --> pdb=" O ILE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 205 Processing helix chain 'J' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE J 209 " --> pdb=" O VAL J 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 206 through 209' Processing helix chain 'J' and resid 224 through 229 Processing helix chain 'J' and resid 229 through 240 removed outlier: 3.529A pdb=" N HIS J 240 " --> pdb=" O TYR J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 324 Processing helix chain 'J' and resid 326 through 331 removed outlier: 3.637A pdb=" N GLY J 330 " --> pdb=" O PRO J 327 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASN J 331 " --> pdb=" O GLU J 328 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 337 Processing helix chain 'J' and resid 354 through 366 Processing helix chain 'J' and resid 431 through 443 Processing helix chain 'J' and resid 449 through 456 removed outlier: 3.649A pdb=" N LEU J 453 " --> pdb=" O LYS J 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA J 454 " --> pdb=" O ILE J 450 " (cutoff:3.500A) Processing helix chain 'J' and resid 507 through 523 removed outlier: 3.591A pdb=" N SER J 511 " --> pdb=" O THR J 507 " (cutoff:3.500A) Processing helix chain 'J' and resid 534 through 537 Processing helix chain 'J' and resid 538 through 550 removed outlier: 3.675A pdb=" N ASN J 550 " --> pdb=" O ILE J 546 " (cutoff:3.500A) Processing helix chain 'J' and resid 554 through 559 Processing helix chain 'J' and resid 562 through 576 Processing helix chain 'J' and resid 579 through 588 Processing helix chain 'K' and resid 6 through 12 removed outlier: 3.546A pdb=" N ALA K 10 " --> pdb=" O GLY K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN K 22 " --> pdb=" O ASN K 19 " (cutoff:3.500A) Processing helix chain 'K' and resid 31 through 44 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 87 through 94 Processing helix chain 'K' and resid 106 through 118 Processing helix chain 'K' and resid 143 through 155 Processing helix chain 'K' and resid 158 through 162 removed outlier: 3.990A pdb=" N ASP K 162 " --> pdb=" O GLU K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 176 removed outlier: 3.598A pdb=" N PHE K 175 " --> pdb=" O SER K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 177 through 187 removed outlier: 3.583A pdb=" N ILE K 181 " --> pdb=" O SER K 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR K 185 " --> pdb=" O ILE K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 194 through 205 Processing helix chain 'K' and resid 206 through 209 removed outlier: 3.769A pdb=" N ILE K 209 " --> pdb=" O VAL K 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 206 through 209' Processing helix chain 'K' and resid 224 through 229 Processing helix chain 'K' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS K 240 " --> pdb=" O TYR K 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 324 Processing helix chain 'K' and resid 326 through 331 removed outlier: 3.646A pdb=" N GLY K 330 " --> pdb=" O PRO K 327 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASN K 331 " --> pdb=" O GLU K 328 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 337 Processing helix chain 'K' and resid 354 through 366 Processing helix chain 'K' and resid 426 through 430 Processing helix chain 'K' and resid 431 through 443 Processing helix chain 'K' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU K 453 " --> pdb=" O LYS K 449 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA K 454 " --> pdb=" O ILE K 450 " (cutoff:3.500A) Processing helix chain 'K' and resid 507 through 523 removed outlier: 3.587A pdb=" N SER K 511 " --> pdb=" O THR K 507 " (cutoff:3.500A) Processing helix chain 'K' and resid 534 through 537 Processing helix chain 'K' and resid 538 through 550 removed outlier: 3.677A pdb=" N ASN K 550 " --> pdb=" O ILE K 546 " (cutoff:3.500A) Processing helix chain 'K' and resid 554 through 559 Processing helix chain 'K' and resid 562 through 576 Processing helix chain 'K' and resid 579 through 588 Processing helix chain 'L' and resid 6 through 12 removed outlier: 3.548A pdb=" N ALA L 10 " --> pdb=" O GLY L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 23 removed outlier: 3.509A pdb=" N ASN L 22 " --> pdb=" O ASN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 31 through 44 Processing helix chain 'L' and resid 48 through 50 No H-bonds generated for 'chain 'L' and resid 48 through 50' Processing helix chain 'L' and resid 87 through 94 Processing helix chain 'L' and resid 106 through 118 Processing helix chain 'L' and resid 143 through 155 Processing helix chain 'L' and resid 158 through 162 removed outlier: 3.986A pdb=" N ASP L 162 " --> pdb=" O GLU L 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 176 removed outlier: 3.599A pdb=" N PHE L 175 " --> pdb=" O SER L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 187 removed outlier: 3.582A pdb=" N ILE L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR L 185 " --> pdb=" O ILE L 181 " (cutoff:3.500A) Processing helix chain 'L' and resid 194 through 205 Processing helix chain 'L' and resid 206 through 209 removed outlier: 3.770A pdb=" N ILE L 209 " --> pdb=" O VAL L 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 206 through 209' Processing helix chain 'L' and resid 224 through 229 Processing helix chain 'L' and resid 229 through 240 removed outlier: 3.529A pdb=" N HIS L 240 " --> pdb=" O TYR L 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 324 Processing helix chain 'L' and resid 326 through 331 removed outlier: 3.640A pdb=" N GLY L 330 " --> pdb=" O PRO L 327 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN L 331 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 337 Processing helix chain 'L' and resid 354 through 366 Processing helix chain 'L' and resid 426 through 430 Processing helix chain 'L' and resid 431 through 443 Processing helix chain 'L' and resid 449 through 456 removed outlier: 3.648A pdb=" N LEU L 453 " --> pdb=" O LYS L 449 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA L 454 " --> pdb=" O ILE L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 507 through 523 removed outlier: 3.591A pdb=" N SER L 511 " --> pdb=" O THR L 507 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 537 Processing helix chain 'L' and resid 538 through 550 removed outlier: 3.677A pdb=" N ASN L 550 " --> pdb=" O ILE L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 554 through 559 Processing helix chain 'L' and resid 562 through 576 Processing helix chain 'L' and resid 579 through 588 Processing helix chain 'M' and resid 6 through 12 removed outlier: 3.547A pdb=" N ALA M 10 " --> pdb=" O GLY M 6 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 23 removed outlier: 3.513A pdb=" N ASN M 22 " --> pdb=" O ASN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 44 Processing helix chain 'M' and resid 48 through 50 No H-bonds generated for 'chain 'M' and resid 48 through 50' Processing helix chain 'M' and resid 87 through 94 Processing helix chain 'M' and resid 106 through 118 Processing helix chain 'M' and resid 143 through 155 Processing helix chain 'M' and resid 158 through 162 removed outlier: 3.989A pdb=" N ASP M 162 " --> pdb=" O GLU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 removed outlier: 3.600A pdb=" N PHE M 175 " --> pdb=" O SER M 171 " (cutoff:3.500A) Processing helix chain 'M' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE M 181 " --> pdb=" O SER M 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR M 185 " --> pdb=" O ILE M 181 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 Processing helix chain 'M' and resid 206 through 209 removed outlier: 3.772A pdb=" N ILE M 209 " --> pdb=" O VAL M 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 206 through 209' Processing helix chain 'M' and resid 224 through 229 Processing helix chain 'M' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS M 240 " --> pdb=" O TYR M 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 324 Processing helix chain 'M' and resid 326 through 331 removed outlier: 3.650A pdb=" N GLY M 330 " --> pdb=" O PRO M 327 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN M 331 " --> pdb=" O GLU M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 332 through 337 Processing helix chain 'M' and resid 354 through 366 Processing helix chain 'M' and resid 426 through 430 Processing helix chain 'M' and resid 431 through 443 Processing helix chain 'M' and resid 449 through 456 removed outlier: 3.649A pdb=" N LEU M 453 " --> pdb=" O LYS M 449 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA M 454 " --> pdb=" O ILE M 450 " (cutoff:3.500A) Processing helix chain 'M' and resid 507 through 523 removed outlier: 3.587A pdb=" N SER M 511 " --> pdb=" O THR M 507 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 537 Processing helix chain 'M' and resid 538 through 550 removed outlier: 3.679A pdb=" N ASN M 550 " --> pdb=" O ILE M 546 " (cutoff:3.500A) Processing helix chain 'M' and resid 554 through 559 Processing helix chain 'M' and resid 562 through 576 Processing helix chain 'M' and resid 579 through 588 Processing helix chain 'N' and resid 6 through 12 removed outlier: 3.546A pdb=" N ALA N 10 " --> pdb=" O GLY N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 23 removed outlier: 3.511A pdb=" N ASN N 22 " --> pdb=" O ASN N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 48 through 50 No H-bonds generated for 'chain 'N' and resid 48 through 50' Processing helix chain 'N' and resid 87 through 94 Processing helix chain 'N' and resid 106 through 118 Processing helix chain 'N' and resid 143 through 155 Processing helix chain 'N' and resid 158 through 162 removed outlier: 3.988A pdb=" N ASP N 162 " --> pdb=" O GLU N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 176 removed outlier: 3.599A pdb=" N PHE N 175 " --> pdb=" O SER N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 187 removed outlier: 3.581A pdb=" N ILE N 181 " --> pdb=" O SER N 177 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR N 185 " --> pdb=" O ILE N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 194 through 205 Processing helix chain 'N' and resid 206 through 209 removed outlier: 3.771A pdb=" N ILE N 209 " --> pdb=" O VAL N 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 206 through 209' Processing helix chain 'N' and resid 224 through 229 Processing helix chain 'N' and resid 229 through 240 removed outlier: 3.530A pdb=" N HIS N 240 " --> pdb=" O TYR N 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 324 Processing helix chain 'N' and resid 326 through 331 removed outlier: 3.646A pdb=" N GLY N 330 " --> pdb=" O PRO N 327 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ASN N 331 " --> pdb=" O GLU N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 332 through 337 Processing helix chain 'N' and resid 354 through 366 Processing helix chain 'N' and resid 426 through 430 Processing helix chain 'N' and resid 431 through 443 Processing helix chain 'N' and resid 449 through 456 removed outlier: 3.647A pdb=" N LEU N 453 " --> pdb=" O LYS N 449 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA N 454 " --> pdb=" O ILE N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 507 through 523 removed outlier: 3.588A pdb=" N SER N 511 " --> pdb=" O THR N 507 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 537 Processing helix chain 'N' and resid 538 through 550 removed outlier: 3.678A pdb=" N ASN N 550 " --> pdb=" O ILE N 546 " (cutoff:3.500A) Processing helix chain 'N' and resid 554 through 559 Processing helix chain 'N' and resid 562 through 576 Processing helix chain 'N' and resid 579 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE A 52 " --> pdb=" O GLN A 243 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU A 245 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILE A 54 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA A 25 " --> pdb=" O HIS A 53 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU A 55 " --> pdb=" O ALA A 25 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 27 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 289 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 286 " --> pdb=" O ALA A 492 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE A 494 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL A 288 " --> pdb=" O ILE A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET A 389 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 413 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL A 346 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 248 through 257 removed outlier: 6.034A pdb=" N VAL A 250 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP A 270 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP A 252 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 266 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ASP A 256 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ALA A 264 " --> pdb=" O ASP A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 4 Processing sheet with id=AA6, first strand: chain 'B' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE B 52 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU B 245 " --> pdb=" O ILE B 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE B 54 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 25 " --> pdb=" O HIS B 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU B 55 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 27 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR B 289 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 286 " --> pdb=" O ALA B 492 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE B 494 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 288 " --> pdb=" O ILE B 494 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET B 389 " --> pdb=" O ILE B 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 413 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL B 346 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 248 through 257 removed outlier: 6.038A pdb=" N VAL B 250 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP B 270 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP B 252 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 266 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP B 256 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA B 264 " --> pdb=" O ASP B 256 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 243 through 245 removed outlier: 6.272A pdb=" N ILE C 52 " --> pdb=" O GLN C 243 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLU C 245 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE C 54 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA C 25 " --> pdb=" O HIS C 53 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU C 55 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU C 27 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR C 289 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL C 286 " --> pdb=" O ALA C 492 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE C 494 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL C 288 " --> pdb=" O ILE C 494 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET C 389 " --> pdb=" O ILE C 382 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 413 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL C 346 " --> pdb=" O ALA C 413 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 248 through 257 removed outlier: 6.033A pdb=" N VAL C 250 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP C 270 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 252 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 266 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP C 256 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA C 264 " --> pdb=" O ASP C 256 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 4 Processing sheet with id=AB5, first strand: chain 'D' and resid 243 through 245 removed outlier: 6.276A pdb=" N ILE D 52 " --> pdb=" O GLN D 243 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLU D 245 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ILE D 54 " --> pdb=" O GLU D 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA D 25 " --> pdb=" O HIS D 53 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU D 55 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU D 27 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR D 289 " --> pdb=" O ILE D 28 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL D 286 " --> pdb=" O ALA D 492 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE D 494 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL D 288 " --> pdb=" O ILE D 494 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.378A pdb=" N MET D 389 " --> pdb=" O ILE D 382 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA D 413 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL D 346 " --> pdb=" O ALA D 413 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 248 through 257 removed outlier: 6.035A pdb=" N VAL D 250 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASP D 270 " --> pdb=" O VAL D 250 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP D 252 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU D 266 " --> pdb=" O LYS D 254 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ASP D 256 " --> pdb=" O ALA D 264 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA D 264 " --> pdb=" O ASP D 256 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB9, first strand: chain 'E' and resid 243 through 245 removed outlier: 6.269A pdb=" N ILE E 52 " --> pdb=" O GLN E 243 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLU E 245 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE E 54 " --> pdb=" O GLU E 245 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA E 25 " --> pdb=" O HIS E 53 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N LEU E 55 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU E 27 " --> pdb=" O LEU E 55 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR E 289 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL E 286 " --> pdb=" O ALA E 492 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE E 494 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL E 288 " --> pdb=" O ILE E 494 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 132 through 133 removed outlier: 4.378A pdb=" N MET E 389 " --> pdb=" O ILE E 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA E 413 " --> pdb=" O VAL E 346 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL E 346 " --> pdb=" O ALA E 413 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 248 through 257 removed outlier: 6.032A pdb=" N VAL E 250 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP E 270 " --> pdb=" O VAL E 250 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP E 252 " --> pdb=" O LEU E 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU E 266 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ASP E 256 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ALA E 264 " --> pdb=" O ASP E 256 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AC4, first strand: chain 'F' and resid 243 through 245 removed outlier: 6.277A pdb=" N ILE F 52 " --> pdb=" O GLN F 243 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU F 245 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ILE F 54 " --> pdb=" O GLU F 245 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA F 25 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU F 55 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 27 " --> pdb=" O LEU F 55 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR F 289 " --> pdb=" O ILE F 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 286 " --> pdb=" O ALA F 492 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE F 494 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N VAL F 288 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 132 through 133 removed outlier: 4.379A pdb=" N MET F 389 " --> pdb=" O ILE F 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA F 413 " --> pdb=" O VAL F 346 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N VAL F 346 " --> pdb=" O ALA F 413 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 248 through 257 removed outlier: 6.032A pdb=" N VAL F 250 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP F 270 " --> pdb=" O VAL F 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 252 " --> pdb=" O LEU F 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU F 266 " --> pdb=" O LYS F 254 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP F 256 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA F 264 " --> pdb=" O ASP F 256 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 4 Processing sheet with id=AC8, first strand: chain 'G' and resid 243 through 245 removed outlier: 6.271A pdb=" N ILE G 52 " --> pdb=" O GLN G 243 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU G 245 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE G 54 " --> pdb=" O GLU G 245 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA G 25 " --> pdb=" O HIS G 53 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU G 55 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU G 27 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR G 289 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N VAL G 286 " --> pdb=" O ALA G 492 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE G 494 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL G 288 " --> pdb=" O ILE G 494 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 132 through 133 removed outlier: 4.374A pdb=" N MET G 389 " --> pdb=" O ILE G 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA G 413 " --> pdb=" O VAL G 346 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL G 346 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 248 through 257 removed outlier: 6.032A pdb=" N VAL G 250 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP G 270 " --> pdb=" O VAL G 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP G 252 " --> pdb=" O LEU G 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU G 266 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP G 256 " --> pdb=" O ALA G 264 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA G 264 " --> pdb=" O ASP G 256 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 4 Processing sheet with id=AD3, first strand: chain 'H' and resid 243 through 245 removed outlier: 6.277A pdb=" N ILE H 52 " --> pdb=" O GLN H 243 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N GLU H 245 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE H 54 " --> pdb=" O GLU H 245 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA H 25 " --> pdb=" O HIS H 53 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU H 55 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU H 27 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR H 289 " --> pdb=" O ILE H 28 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL H 286 " --> pdb=" O ALA H 492 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE H 494 " --> pdb=" O VAL H 286 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL H 288 " --> pdb=" O ILE H 494 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 132 through 133 removed outlier: 4.384A pdb=" N MET H 389 " --> pdb=" O ILE H 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA H 413 " --> pdb=" O VAL H 346 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL H 346 " --> pdb=" O ALA H 413 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 248 through 257 removed outlier: 6.031A pdb=" N VAL H 250 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP H 270 " --> pdb=" O VAL H 250 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP H 252 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU H 266 " --> pdb=" O LYS H 254 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASP H 256 " --> pdb=" O ALA H 264 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ALA H 264 " --> pdb=" O ASP H 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AD7, first strand: chain 'I' and resid 243 through 245 removed outlier: 6.271A pdb=" N ILE I 52 " --> pdb=" O GLN I 243 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU I 245 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE I 54 " --> pdb=" O GLU I 245 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA I 25 " --> pdb=" O HIS I 53 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU I 55 " --> pdb=" O ALA I 25 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU I 27 " --> pdb=" O LEU I 55 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR I 289 " --> pdb=" O ILE I 28 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL I 286 " --> pdb=" O ALA I 492 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE I 494 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL I 288 " --> pdb=" O ILE I 494 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 132 through 133 removed outlier: 4.376A pdb=" N MET I 389 " --> pdb=" O ILE I 382 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA I 413 " --> pdb=" O VAL I 346 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL I 346 " --> pdb=" O ALA I 413 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 248 through 257 removed outlier: 6.034A pdb=" N VAL I 250 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ASP I 270 " --> pdb=" O VAL I 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP I 252 " --> pdb=" O LEU I 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU I 266 " --> pdb=" O LYS I 254 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ASP I 256 " --> pdb=" O ALA I 264 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ALA I 264 " --> pdb=" O ASP I 256 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AE2, first strand: chain 'J' and resid 243 through 245 removed outlier: 6.277A pdb=" N ILE J 52 " --> pdb=" O GLN J 243 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N GLU J 245 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE J 54 " --> pdb=" O GLU J 245 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA J 25 " --> pdb=" O HIS J 53 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU J 55 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU J 27 " --> pdb=" O LEU J 55 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR J 289 " --> pdb=" O ILE J 28 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 286 " --> pdb=" O ALA J 492 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE J 494 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N VAL J 288 " --> pdb=" O ILE J 494 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 132 through 133 removed outlier: 4.381A pdb=" N MET J 389 " --> pdb=" O ILE J 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA J 413 " --> pdb=" O VAL J 346 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N VAL J 346 " --> pdb=" O ALA J 413 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 248 through 257 removed outlier: 6.029A pdb=" N VAL J 250 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP J 270 " --> pdb=" O VAL J 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP J 252 " --> pdb=" O LEU J 268 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU J 266 " --> pdb=" O LYS J 254 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP J 256 " --> pdb=" O ALA J 264 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA J 264 " --> pdb=" O ASP J 256 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 4 Processing sheet with id=AE6, first strand: chain 'K' and resid 243 through 245 removed outlier: 6.271A pdb=" N ILE K 52 " --> pdb=" O GLN K 243 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU K 245 " --> pdb=" O ILE K 52 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE K 54 " --> pdb=" O GLU K 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA K 25 " --> pdb=" O HIS K 53 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU K 55 " --> pdb=" O ALA K 25 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU K 27 " --> pdb=" O LEU K 55 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR K 289 " --> pdb=" O ILE K 28 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL K 286 " --> pdb=" O ALA K 492 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N ILE K 494 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N VAL K 288 " --> pdb=" O ILE K 494 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 132 through 133 removed outlier: 4.379A pdb=" N MET K 389 " --> pdb=" O ILE K 382 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA K 413 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N VAL K 346 " --> pdb=" O ALA K 413 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 248 through 257 removed outlier: 6.034A pdb=" N VAL K 250 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASP K 270 " --> pdb=" O VAL K 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP K 252 " --> pdb=" O LEU K 268 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU K 266 " --> pdb=" O LYS K 254 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASP K 256 " --> pdb=" O ALA K 264 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA K 264 " --> pdb=" O ASP K 256 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 3 through 4 Processing sheet with id=AF1, first strand: chain 'L' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE L 52 " --> pdb=" O GLN L 243 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU L 245 " --> pdb=" O ILE L 52 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N ILE L 54 " --> pdb=" O GLU L 245 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA L 25 " --> pdb=" O HIS L 53 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU L 55 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU L 27 " --> pdb=" O LEU L 55 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR L 289 " --> pdb=" O ILE L 28 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL L 286 " --> pdb=" O ALA L 492 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE L 494 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N VAL L 288 " --> pdb=" O ILE L 494 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET L 389 " --> pdb=" O ILE L 382 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA L 413 " --> pdb=" O VAL L 346 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL L 346 " --> pdb=" O ALA L 413 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 248 through 257 removed outlier: 6.035A pdb=" N VAL L 250 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP L 270 " --> pdb=" O VAL L 250 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASP L 252 " --> pdb=" O LEU L 268 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU L 266 " --> pdb=" O LYS L 254 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ASP L 256 " --> pdb=" O ALA L 264 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA L 264 " --> pdb=" O ASP L 256 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 4 Processing sheet with id=AF5, first strand: chain 'M' and resid 243 through 245 removed outlier: 6.273A pdb=" N ILE M 52 " --> pdb=" O GLN M 243 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU M 245 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE M 54 " --> pdb=" O GLU M 245 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA M 25 " --> pdb=" O HIS M 53 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LEU M 55 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU M 27 " --> pdb=" O LEU M 55 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR M 289 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL M 286 " --> pdb=" O ALA M 492 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE M 494 " --> pdb=" O VAL M 286 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL M 288 " --> pdb=" O ILE M 494 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 132 through 133 removed outlier: 4.380A pdb=" N MET M 389 " --> pdb=" O ILE M 382 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA M 413 " --> pdb=" O VAL M 346 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N VAL M 346 " --> pdb=" O ALA M 413 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 248 through 257 removed outlier: 6.038A pdb=" N VAL M 250 " --> pdb=" O ASP M 270 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASP M 270 " --> pdb=" O VAL M 250 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASP M 252 " --> pdb=" O LEU M 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU M 266 " --> pdb=" O LYS M 254 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ASP M 256 " --> pdb=" O ALA M 264 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ALA M 264 " --> pdb=" O ASP M 256 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 3 through 4 Processing sheet with id=AF9, first strand: chain 'N' and resid 243 through 245 removed outlier: 6.271A pdb=" N ILE N 52 " --> pdb=" O GLN N 243 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU N 245 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N ILE N 54 " --> pdb=" O GLU N 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA N 25 " --> pdb=" O HIS N 53 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU N 55 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU N 27 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR N 289 " --> pdb=" O ILE N 28 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL N 286 " --> pdb=" O ALA N 492 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N ILE N 494 " --> pdb=" O VAL N 286 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL N 288 " --> pdb=" O ILE N 494 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 132 through 133 removed outlier: 4.381A pdb=" N MET N 389 " --> pdb=" O ILE N 382 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA N 413 " --> pdb=" O VAL N 346 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N VAL N 346 " --> pdb=" O ALA N 413 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 248 through 257 removed outlier: 6.037A pdb=" N VAL N 250 " --> pdb=" O ASP N 270 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASP N 270 " --> pdb=" O VAL N 250 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP N 252 " --> pdb=" O LEU N 268 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU N 266 " --> pdb=" O LYS N 254 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP N 256 " --> pdb=" O ALA N 264 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA N 264 " --> pdb=" O ASP N 256 " (cutoff:3.500A) 2350 hydrogen bonds defined for protein. 6636 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: 29.49 Time building geometry restraints manager: 13.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13039 1.33 - 1.45: 17058 1.45 - 1.57: 36543 1.57 - 1.69: 0 1.69 - 1.82: 504 Bond restraints: 67144 Sorted by residual: bond pdb=" CA SER H 326 " pdb=" CB SER H 326 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.69e-02 3.50e+03 5.97e+00 bond pdb=" CG HIS E 86 " pdb=" CD2 HIS E 86 " ideal model delta sigma weight residual 1.354 1.328 0.026 1.10e-02 8.26e+03 5.71e+00 bond pdb=" CA SER J 326 " pdb=" CB SER J 326 " ideal model delta sigma weight residual 1.532 1.492 0.040 1.69e-02 3.50e+03 5.62e+00 bond pdb=" C PHE G 94 " pdb=" O PHE G 94 " ideal model delta sigma weight residual 1.235 1.206 0.030 1.26e-02 6.30e+03 5.56e+00 bond pdb=" CG HIS G 193 " pdb=" CD2 HIS G 193 " ideal model delta sigma weight residual 1.354 1.329 0.025 1.10e-02 8.26e+03 5.34e+00 ... (remaining 67139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 77469 0.98 - 1.96: 12007 1.96 - 2.94: 1265 2.94 - 3.92: 214 3.92 - 4.90: 31 Bond angle restraints: 90986 Sorted by residual: angle pdb=" N VAL H 169 " pdb=" CA VAL H 169 " pdb=" C VAL H 169 " ideal model delta sigma weight residual 113.47 110.78 2.69 1.01e+00 9.80e-01 7.09e+00 angle pdb=" N VAL C 169 " pdb=" CA VAL C 169 " pdb=" C VAL C 169 " ideal model delta sigma weight residual 113.47 110.79 2.68 1.01e+00 9.80e-01 7.04e+00 angle pdb=" N VAL K 169 " pdb=" CA VAL K 169 " pdb=" C VAL K 169 " ideal model delta sigma weight residual 113.47 110.81 2.66 1.01e+00 9.80e-01 6.95e+00 angle pdb=" N VAL G 169 " pdb=" CA VAL G 169 " pdb=" C VAL G 169 " ideal model delta sigma weight residual 113.47 110.81 2.66 1.01e+00 9.80e-01 6.94e+00 angle pdb=" N VAL F 169 " pdb=" CA VAL F 169 " pdb=" C VAL F 169 " ideal model delta sigma weight residual 113.47 110.81 2.66 1.01e+00 9.80e-01 6.94e+00 ... (remaining 90981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 35623 14.84 - 29.67: 3569 29.67 - 44.51: 764 44.51 - 59.34: 154 59.34 - 74.18: 112 Dihedral angle restraints: 40222 sinusoidal: 16352 harmonic: 23870 Sorted by residual: dihedral pdb=" CA VAL I 483 " pdb=" C VAL I 483 " pdb=" N VAL I 484 " pdb=" CA VAL I 484 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL C 483 " pdb=" C VAL C 483 " pdb=" N VAL C 484 " pdb=" CA VAL C 484 " ideal model delta harmonic sigma weight residual 180.00 162.72 17.28 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA VAL G 483 " pdb=" C VAL G 483 " pdb=" N VAL G 484 " pdb=" CA VAL G 484 " ideal model delta harmonic sigma weight residual 180.00 162.74 17.26 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 40219 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 5170 0.046 - 0.092: 3425 0.092 - 0.138: 1131 0.138 - 0.184: 221 0.184 - 0.230: 35 Chirality restraints: 9982 Sorted by residual: chirality pdb=" CG LEU F 585 " pdb=" CB LEU F 585 " pdb=" CD1 LEU F 585 " pdb=" CD2 LEU F 585 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LYS J 589 " pdb=" N LYS J 589 " pdb=" C LYS J 589 " pdb=" CB LYS J 589 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA LYS F 589 " pdb=" N LYS F 589 " pdb=" C LYS F 589 " pdb=" CB LYS F 589 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 9979 not shown) Planarity restraints: 11676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 112 " 0.025 2.00e-02 2.50e+03 3.08e-02 1.90e+01 pdb=" CG TYR D 112 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 112 " -0.058 2.00e-02 2.50e+03 pdb=" CD2 TYR D 112 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 112 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR D 112 " -0.030 2.00e-02 2.50e+03 pdb=" CZ TYR D 112 " 0.031 2.00e-02 2.50e+03 pdb=" OH TYR D 112 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 112 " -0.012 2.00e-02 2.50e+03 2.56e-02 1.31e+01 pdb=" CG TYR J 112 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR J 112 " 0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR J 112 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR J 112 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR J 112 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR J 112 " -0.026 2.00e-02 2.50e+03 pdb=" OH TYR J 112 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 112 " 0.011 2.00e-02 2.50e+03 2.44e-02 1.19e+01 pdb=" CG TYR F 112 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TYR F 112 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR F 112 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR F 112 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR F 112 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR F 112 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR F 112 " -0.015 2.00e-02 2.50e+03 ... (remaining 11673 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.23: 26 2.23 - 2.90: 25877 2.90 - 3.56: 96559 3.56 - 4.23: 170665 4.23 - 4.90: 284045 Nonbonded interactions: 577172 Sorted by model distance: nonbonded pdb=" NH1 ARG A 324 " pdb=" OE2 GLU C 362 " model vdw 1.561 3.120 nonbonded pdb=" OE2 GLU H 362 " pdb=" NH1 ARG J 324 " model vdw 1.704 3.120 nonbonded pdb=" OE2 GLU F 362 " pdb=" NH1 ARG H 324 " model vdw 1.706 3.120 nonbonded pdb=" NH1 ARG K 324 " pdb=" OE2 GLU M 362 " model vdw 1.712 3.120 nonbonded pdb=" NH1 ARG C 324 " pdb=" OE2 GLU E 362 " model vdw 1.752 3.120 ... (remaining 577167 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: 0.43 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'N' } 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 28.080 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: 0.000 Extract box with map and model: 1.460 Check model and map are aligned: 0.360 Set scattering table: 0.460 Process input model: 116.590 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.048 67144 Z= 0.475 Angle : 0.718 4.905 90986 Z= 0.452 Chirality : 0.063 0.230 9982 Planarity : 0.004 0.051 11676 Dihedral : 13.287 74.176 24794 Min Nonbonded Distance : 1.561 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.09), residues: 8050 helix: -0.58 (0.09), residues: 2716 sheet: 0.17 (0.18), residues: 994 loop : -0.34 (0.09), residues: 4340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 439 HIS 0.009 0.002 HIS L 0 PHE 0.016 0.002 PHE F 11 TYR 0.058 0.004 TYR D 112 ARG 0.043 0.002 ARG J 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1335 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 TRP cc_start: 0.8641 (t60) cc_final: 0.8428 (t60) REVERT: A 435 ILE cc_start: 0.9032 (mt) cc_final: 0.8754 (tp) REVERT: A 506 PHE cc_start: 0.8663 (t80) cc_final: 0.8398 (t80) REVERT: A 560 LYS cc_start: 0.9423 (pttm) cc_final: 0.9106 (tptt) REVERT: B 293 ILE cc_start: 0.7894 (pt) cc_final: 0.7596 (tt) REVERT: B 294 THR cc_start: 0.8371 (p) cc_final: 0.7948 (p) REVERT: B 356 GLU cc_start: 0.8113 (pt0) cc_final: 0.7899 (mp0) REVERT: B 422 TYR cc_start: 0.7133 (t80) cc_final: 0.6798 (t80) REVERT: B 473 MET cc_start: 0.8661 (mmm) cc_final: 0.8278 (mtp) REVERT: D 57 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7425 (mt-10) REVERT: E 564 MET cc_start: 0.8169 (mmp) cc_final: 0.7909 (ptm) REVERT: F 97 ILE cc_start: 0.7796 (mm) cc_final: 0.7572 (mm) REVERT: F 471 TYR cc_start: 0.6948 (p90) cc_final: 0.6740 (p90) REVERT: H 564 MET cc_start: 0.8288 (mmp) cc_final: 0.7852 (mpp) REVERT: I 564 MET cc_start: 0.8904 (mmp) cc_final: 0.7939 (ptp) REVERT: J 564 MET cc_start: 0.8836 (mmp) cc_final: 0.8488 (ptp) REVERT: K 471 TYR cc_start: 0.7245 (p90) cc_final: 0.6755 (p90) REVERT: K 557 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8705 (mp0) REVERT: K 565 GLN cc_start: 0.8201 (mm-40) cc_final: 0.7981 (mp10) REVERT: L 574 LYS cc_start: 0.8561 (mtmt) cc_final: 0.8142 (tmtt) REVERT: M 128 GLU cc_start: 0.8766 (pt0) cc_final: 0.8542 (pm20) REVERT: M 501 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7038 (pt0) outliers start: 0 outliers final: 0 residues processed: 1335 average time/residue: 0.6424 time to fit residues: 1457.1564 Evaluate side-chains 622 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 673 optimal weight: 2.9990 chunk 604 optimal weight: 0.7980 chunk 335 optimal weight: 0.9990 chunk 206 optimal weight: 0.4980 chunk 407 optimal weight: 1.9990 chunk 323 optimal weight: 0.8980 chunk 625 optimal weight: 6.9990 chunk 242 optimal weight: 0.8980 chunk 380 optimal weight: 0.9990 chunk 465 optimal weight: 3.9990 chunk 724 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS B 7 ASN B 240 HIS C 442 HIS D 178 ASN ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 442 HIS G 442 HIS H 402 GLN H 442 HIS H 486 HIS H 565 GLN I 240 HIS J 402 GLN J 442 HIS K 565 GLN L 331 ASN ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 240 HIS M 338 ASN M 442 HIS N 240 HIS N 442 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.088655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.061501 restraints weight = 205191.253| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 3.12 r_work: 0.3025 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67144 Z= 0.203 Angle : 0.541 11.102 90986 Z= 0.282 Chirality : 0.045 0.214 9982 Planarity : 0.003 0.078 11676 Dihedral : 4.105 16.755 8764 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.02 % Allowed : 7.73 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.09), residues: 8050 helix: 0.38 (0.10), residues: 2800 sheet: -0.30 (0.17), residues: 980 loop : 0.00 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 192 HIS 0.004 0.001 HIS J 588 PHE 0.022 0.001 PHE B 472 TYR 0.019 0.001 TYR L 422 ARG 0.006 0.000 ARG G 556 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 682 time to evaluate : 5.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TRP cc_start: 0.8919 (m100) cc_final: 0.8161 (m100) REVERT: A 96 SER cc_start: 0.8647 (m) cc_final: 0.8404 (p) REVERT: A 142 LEU cc_start: 0.8808 (mt) cc_final: 0.8331 (mt) REVERT: A 198 MET cc_start: 0.9169 (ttm) cc_final: 0.8467 (tpp) REVERT: A 326 SER cc_start: 0.8881 (t) cc_final: 0.8577 (t) REVERT: A 344 TRP cc_start: 0.8707 (t60) cc_final: 0.8429 (t60) REVERT: A 439 TRP cc_start: 0.7925 (t60) cc_final: 0.7716 (t60) REVERT: A 465 MET cc_start: 0.8649 (mmm) cc_final: 0.8330 (mmm) REVERT: A 473 MET cc_start: 0.8851 (tpp) cc_final: 0.8366 (tpp) REVERT: A 560 LYS cc_start: 0.9411 (pttm) cc_final: 0.9178 (tptt) REVERT: B 238 LYS cc_start: 0.8978 (mttt) cc_final: 0.8703 (mmmt) REVERT: B 329 PHE cc_start: 0.8737 (m-10) cc_final: 0.8438 (m-10) REVERT: B 471 TYR cc_start: 0.6452 (p90) cc_final: 0.5857 (p90) REVERT: B 472 PHE cc_start: 0.8833 (m-10) cc_final: 0.8145 (m-10) REVERT: B 473 MET cc_start: 0.8518 (mmm) cc_final: 0.7632 (mtp) REVERT: B 506 PHE cc_start: 0.7706 (t80) cc_final: 0.7429 (t80) REVERT: C 326 SER cc_start: 0.9236 (t) cc_final: 0.9017 (t) REVERT: C 465 MET cc_start: 0.9541 (mtm) cc_final: 0.9289 (mtm) REVERT: D 82 GLU cc_start: 0.8207 (pp20) cc_final: 0.7924 (pp20) REVERT: D 116 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8561 (mttm) REVERT: D 173 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8832 (t0) REVERT: D 557 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8718 (mp0) REVERT: E 112 TYR cc_start: 0.8827 (t80) cc_final: 0.8549 (t80) REVERT: E 557 GLU cc_start: 0.8709 (mp0) cc_final: 0.8264 (mp0) REVERT: E 564 MET cc_start: 0.8479 (mmp) cc_final: 0.7848 (ptm) REVERT: E 582 GLU cc_start: 0.9246 (tt0) cc_final: 0.9004 (tt0) REVERT: F 173 ASP cc_start: 0.9055 (t0) cc_final: 0.8751 (t0) REVERT: F 198 MET cc_start: 0.9327 (tpp) cc_final: 0.8990 (tpt) REVERT: F 380 ILE cc_start: 0.8904 (mm) cc_final: 0.8502 (mt) REVERT: F 564 MET cc_start: 0.7084 (pmm) cc_final: 0.6597 (ptt) REVERT: F 575 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7991 (tptt) REVERT: F 577 LYS cc_start: 0.9336 (mttt) cc_final: 0.8917 (mmtt) REVERT: F 582 GLU cc_start: 0.8950 (tt0) cc_final: 0.8662 (tt0) REVERT: G 82 GLU cc_start: 0.8253 (pm20) cc_final: 0.7674 (mp0) REVERT: G 342 LYS cc_start: 0.8885 (tttt) cc_final: 0.8639 (ttmm) REVERT: G 557 GLU cc_start: 0.8687 (mp0) cc_final: 0.8454 (mp0) REVERT: H 564 MET cc_start: 0.8418 (mmp) cc_final: 0.8042 (tmm) REVERT: H 585 LEU cc_start: 0.9302 (mm) cc_final: 0.9082 (mm) REVERT: I 471 TYR cc_start: 0.8615 (p90) cc_final: 0.8376 (p90) REVERT: I 582 GLU cc_start: 0.9090 (tt0) cc_final: 0.8808 (tt0) REVERT: I 585 LEU cc_start: 0.9238 (mm) cc_final: 0.8976 (mm) REVERT: J 82 GLU cc_start: 0.7577 (mp0) cc_final: 0.7377 (mp0) REVERT: J 83 MET cc_start: 0.7922 (mtm) cc_final: 0.7579 (mtm) REVERT: J 144 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.7846 (tmtt) REVERT: J 152 ASP cc_start: 0.8880 (m-30) cc_final: 0.8620 (m-30) REVERT: J 419 ASN cc_start: 0.8470 (m-40) cc_final: 0.7832 (t0) REVERT: J 564 MET cc_start: 0.9060 (mmp) cc_final: 0.8622 (ttt) REVERT: J 577 LYS cc_start: 0.9373 (tptm) cc_final: 0.9024 (tppt) REVERT: K 161 LEU cc_start: 0.9178 (mp) cc_final: 0.8937 (mp) REVERT: K 196 MET cc_start: 0.8737 (ttp) cc_final: 0.8516 (ttp) REVERT: K 334 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8478 (tttt) REVERT: K 473 MET cc_start: 0.8868 (mmm) cc_final: 0.8393 (mtp) REVERT: K 557 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8488 (mp0) REVERT: K 565 GLN cc_start: 0.7612 (mm110) cc_final: 0.7346 (mp10) REVERT: M 1 MET cc_start: 0.5791 (ppp) cc_final: 0.5517 (ppp) REVERT: M 465 MET cc_start: 0.8857 (mmt) cc_final: 0.8656 (tpp) REVERT: M 501 GLU cc_start: 0.7164 (tm-30) cc_final: 0.6760 (pt0) REVERT: M 543 MET cc_start: 0.9083 (mmt) cc_final: 0.8826 (mpp) REVERT: M 564 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7693 (pmm) REVERT: N 233 MET cc_start: 0.9528 (mmm) cc_final: 0.9265 (mmm) REVERT: N 338 ASN cc_start: 0.8888 (m-40) cc_final: 0.8547 (p0) REVERT: N 389 MET cc_start: 0.6913 (tmm) cc_final: 0.6588 (tmm) REVERT: N 516 MET cc_start: 0.9010 (ttt) cc_final: 0.8719 (ttt) REVERT: N 564 MET cc_start: 0.6794 (pmm) cc_final: 0.6566 (pmm) REVERT: N 577 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8528 (mttp) outliers start: 74 outliers final: 37 residues processed: 729 average time/residue: 0.6075 time to fit residues: 770.7672 Evaluate side-chains 567 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 525 time to evaluate : 6.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 363 SER Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 508 THR Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 407 ILE Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain H residue 409 THR Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 522 LEU Chi-restraints excluded: chain H residue 529 ILE Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 508 THR Chi-restraints excluded: chain I residue 524 ASN Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain J residue 585 LEU Chi-restraints excluded: chain K residue 508 THR Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 505 VAL Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 564 MET Chi-restraints excluded: chain N residue 577 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 377 optimal weight: 1.9990 chunk 637 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 423 optimal weight: 0.9990 chunk 614 optimal weight: 4.9990 chunk 665 optimal weight: 3.9990 chunk 417 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 465 optimal weight: 0.0670 chunk 51 optimal weight: 7.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN B 388 GLN D 405 ASN E 402 GLN F 496 ASN G 402 GLN ** G 486 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 ASN J 178 ASN ** J 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 496 ASN L 402 GLN ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.084121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.056861 restraints weight = 203424.248| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.00 r_work: 0.2913 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 67144 Z= 0.201 Angle : 0.507 10.625 90986 Z= 0.265 Chirality : 0.044 0.184 9982 Planarity : 0.003 0.050 11676 Dihedral : 3.925 17.847 8764 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.41 % Allowed : 9.40 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.10), residues: 8050 helix: 1.04 (0.10), residues: 2744 sheet: -0.34 (0.17), residues: 994 loop : 0.13 (0.10), residues: 4312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 410 HIS 0.006 0.001 HIS G 486 PHE 0.047 0.001 PHE A 506 TYR 0.021 0.001 TYR A 422 ARG 0.007 0.000 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 541 time to evaluate : 5.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8173 (ppp) cc_final: 0.7867 (ppp) REVERT: A 96 SER cc_start: 0.8590 (m) cc_final: 0.8377 (p) REVERT: A 198 MET cc_start: 0.9247 (ttm) cc_final: 0.8598 (mmm) REVERT: A 326 SER cc_start: 0.8930 (t) cc_final: 0.8636 (t) REVERT: A 439 TRP cc_start: 0.7947 (t60) cc_final: 0.7720 (t60) REVERT: A 465 MET cc_start: 0.8589 (mmm) cc_final: 0.8212 (mmm) REVERT: A 473 MET cc_start: 0.8940 (tpp) cc_final: 0.8023 (mmm) REVERT: A 501 GLU cc_start: 0.8642 (tp30) cc_final: 0.8395 (tp30) REVERT: A 560 LYS cc_start: 0.9349 (pttm) cc_final: 0.9100 (tptt) REVERT: B 83 MET cc_start: 0.7032 (mpp) cc_final: 0.6470 (mpp) REVERT: B 315 SER cc_start: 0.8726 (m) cc_final: 0.8395 (p) REVERT: B 329 PHE cc_start: 0.8683 (m-10) cc_final: 0.8304 (m-10) REVERT: B 391 PHE cc_start: 0.8554 (p90) cc_final: 0.8323 (p90) REVERT: B 472 PHE cc_start: 0.8873 (m-10) cc_final: 0.8529 (m-10) REVERT: B 473 MET cc_start: 0.8595 (mmm) cc_final: 0.7749 (mtp) REVERT: B 506 PHE cc_start: 0.7744 (t80) cc_final: 0.7464 (t80) REVERT: B 516 MET cc_start: 0.8487 (tmm) cc_final: 0.8279 (tmm) REVERT: C 82 GLU cc_start: 0.7741 (pm20) cc_final: 0.7399 (mp0) REVERT: C 465 MET cc_start: 0.9587 (mtm) cc_final: 0.9359 (mtm) REVERT: C 564 MET cc_start: 0.8127 (mpp) cc_final: 0.7458 (ttt) REVERT: C 577 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8809 (mmtm) REVERT: D 82 GLU cc_start: 0.8313 (pp20) cc_final: 0.8012 (pp20) REVERT: D 557 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8785 (mp0) REVERT: E 359 ASP cc_start: 0.9085 (m-30) cc_final: 0.8711 (m-30) REVERT: E 564 MET cc_start: 0.8811 (mmp) cc_final: 0.8159 (ptm) REVERT: E 582 GLU cc_start: 0.9204 (tt0) cc_final: 0.8979 (tt0) REVERT: F 1 MET cc_start: 0.8480 (ppp) cc_final: 0.7986 (ptt) REVERT: F 39 CYS cc_start: 0.9259 (t) cc_final: 0.8877 (m) REVERT: F 173 ASP cc_start: 0.9036 (t0) cc_final: 0.8693 (t0) REVERT: F 198 MET cc_start: 0.9401 (tpp) cc_final: 0.9013 (tpt) REVERT: F 293 ILE cc_start: 0.9179 (OUTLIER) cc_final: 0.8928 (mt) REVERT: F 449 LYS cc_start: 0.9066 (ptpt) cc_final: 0.8843 (pttp) REVERT: F 471 TYR cc_start: 0.8229 (p90) cc_final: 0.7802 (p90) REVERT: F 506 PHE cc_start: 0.9259 (t80) cc_final: 0.8935 (t80) REVERT: F 577 LYS cc_start: 0.9378 (mttt) cc_final: 0.8968 (mmtt) REVERT: F 582 GLU cc_start: 0.9014 (tt0) cc_final: 0.8617 (tt0) REVERT: F 586 LYS cc_start: 0.9272 (mttp) cc_final: 0.8815 (mttp) REVERT: G 82 GLU cc_start: 0.8254 (pm20) cc_final: 0.7789 (pm20) REVERT: G 198 MET cc_start: 0.9112 (ttt) cc_final: 0.8843 (ttt) REVERT: G 508 THR cc_start: 0.8566 (m) cc_final: 0.8327 (m) REVERT: G 557 GLU cc_start: 0.8742 (mp0) cc_final: 0.8484 (mp0) REVERT: G 564 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6735 (tpp) REVERT: H 293 ILE cc_start: 0.9041 (pt) cc_final: 0.8813 (mt) REVERT: H 380 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8786 (mt) REVERT: H 471 TYR cc_start: 0.8225 (p90) cc_final: 0.8004 (p90) REVERT: H 564 MET cc_start: 0.8655 (mmp) cc_final: 0.8400 (tmm) REVERT: I 471 TYR cc_start: 0.8608 (p90) cc_final: 0.8259 (p90) REVERT: I 506 PHE cc_start: 0.9177 (t80) cc_final: 0.8920 (t80) REVERT: I 577 LYS cc_start: 0.9180 (tppt) cc_final: 0.8619 (mmtm) REVERT: I 582 GLU cc_start: 0.9105 (tt0) cc_final: 0.8814 (tt0) REVERT: J 144 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8784 (tppp) REVERT: J 152 ASP cc_start: 0.8956 (m-30) cc_final: 0.8430 (m-30) REVERT: J 349 THR cc_start: 0.8909 (OUTLIER) cc_final: 0.8535 (p) REVERT: J 564 MET cc_start: 0.9104 (mmp) cc_final: 0.8700 (pmm) REVERT: J 577 LYS cc_start: 0.9393 (tptm) cc_final: 0.9062 (tppt) REVERT: K 152 ASP cc_start: 0.9192 (m-30) cc_final: 0.8825 (m-30) REVERT: K 161 LEU cc_start: 0.9149 (mp) cc_final: 0.8842 (mp) REVERT: K 172 ASP cc_start: 0.8920 (p0) cc_final: 0.8688 (p0) REVERT: K 196 MET cc_start: 0.8824 (ttp) cc_final: 0.8587 (ttp) REVERT: K 198 MET cc_start: 0.8803 (tpp) cc_final: 0.8461 (tpp) REVERT: K 334 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8511 (tttt) REVERT: K 473 MET cc_start: 0.9078 (mmm) cc_final: 0.8645 (mtp) REVERT: K 501 GLU cc_start: 0.9046 (pt0) cc_final: 0.8700 (pm20) REVERT: L 144 LYS cc_start: 0.7383 (tptt) cc_final: 0.7164 (tptt) REVERT: L 359 ASP cc_start: 0.8851 (m-30) cc_final: 0.8565 (t0) REVERT: M 159 GLU cc_start: 0.8898 (mp0) cc_final: 0.8618 (pm20) REVERT: M 198 MET cc_start: 0.7360 (mmm) cc_final: 0.7155 (mmm) REVERT: M 356 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: M 471 TYR cc_start: 0.6679 (p90) cc_final: 0.6415 (p90) REVERT: N 161 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8879 (tt) REVERT: N 196 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8429 (mmm) REVERT: N 203 MET cc_start: 0.7861 (mmp) cc_final: 0.7490 (mmp) REVERT: N 233 MET cc_start: 0.9534 (mmm) cc_final: 0.9282 (mmm) REVERT: N 338 ASN cc_start: 0.8816 (m-40) cc_final: 0.8479 (p0) REVERT: N 389 MET cc_start: 0.7009 (tmm) cc_final: 0.6714 (tmm) REVERT: N 516 MET cc_start: 0.9076 (ttt) cc_final: 0.8744 (ttt) outliers start: 103 outliers final: 42 residues processed: 612 average time/residue: 0.5967 time to fit residues: 640.6973 Evaluate side-chains 516 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 465 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 581 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 293 ILE Chi-restraints excluded: chain F residue 346 VAL Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 352 THR Chi-restraints excluded: chain F residue 447 THR Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 380 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 505 VAL Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 551 ASP Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 196 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 0.0970 chunk 583 optimal weight: 2.9990 chunk 315 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 437 optimal weight: 0.5980 chunk 718 optimal weight: 0.5980 chunk 154 optimal weight: 5.9990 chunk 141 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 ASN ** K 178 ASN ** 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 = 0.3662 r_free = 0.3662 target = 0.083726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.056695 restraints weight = 200828.600| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.99 r_work: 0.2884 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 67144 Z= 0.184 Angle : 0.477 11.008 90986 Z= 0.249 Chirality : 0.043 0.156 9982 Planarity : 0.003 0.043 11676 Dihedral : 3.793 18.177 8764 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.33 % Allowed : 10.26 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.10), residues: 8050 helix: 1.22 (0.10), residues: 2772 sheet: -0.24 (0.17), residues: 966 loop : 0.18 (0.10), residues: 4312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 192 HIS 0.004 0.001 HIS G 486 PHE 0.023 0.001 PHE H 506 TYR 0.013 0.001 TYR G 112 ARG 0.009 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 480 time to evaluate : 5.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8094 (ppp) cc_final: 0.7875 (ppp) REVERT: A 198 MET cc_start: 0.9254 (ttm) cc_final: 0.8647 (mmm) REVERT: A 465 MET cc_start: 0.8623 (mmm) cc_final: 0.8231 (mmm) REVERT: A 473 MET cc_start: 0.8981 (tpp) cc_final: 0.8005 (mmm) REVERT: A 501 GLU cc_start: 0.8600 (tp30) cc_final: 0.8336 (tp30) REVERT: A 506 PHE cc_start: 0.8833 (t80) cc_final: 0.8603 (t80) REVERT: A 560 LYS cc_start: 0.9374 (pttm) cc_final: 0.9087 (tptt) REVERT: B 1 MET cc_start: 0.6441 (ppp) cc_final: 0.5378 (ppp) REVERT: B 315 SER cc_start: 0.8798 (m) cc_final: 0.8569 (p) REVERT: B 329 PHE cc_start: 0.8717 (m-10) cc_final: 0.8423 (m-10) REVERT: B 472 PHE cc_start: 0.8907 (m-10) cc_final: 0.8603 (m-10) REVERT: B 473 MET cc_start: 0.8553 (mmm) cc_final: 0.7664 (mtp) REVERT: B 506 PHE cc_start: 0.7998 (t80) cc_final: 0.7682 (t80) REVERT: B 516 MET cc_start: 0.8508 (tmm) cc_final: 0.8277 (tmm) REVERT: C 82 GLU cc_start: 0.7522 (pm20) cc_final: 0.7270 (mp0) REVERT: C 328 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8739 (pt0) REVERT: C 465 MET cc_start: 0.9587 (mtm) cc_final: 0.9323 (mtm) REVERT: C 564 MET cc_start: 0.8244 (mpp) cc_final: 0.7611 (ttt) REVERT: C 577 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8920 (mmtp) REVERT: D 82 GLU cc_start: 0.8310 (pp20) cc_final: 0.7972 (pp20) REVERT: D 173 ASP cc_start: 0.9146 (OUTLIER) cc_final: 0.8884 (t70) REVERT: D 557 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8713 (mp0) REVERT: E 359 ASP cc_start: 0.9083 (m-30) cc_final: 0.8678 (m-30) REVERT: E 564 MET cc_start: 0.8855 (mmp) cc_final: 0.8151 (ptm) REVERT: F 1 MET cc_start: 0.8505 (ppp) cc_final: 0.8173 (ptt) REVERT: F 128 GLU cc_start: 0.8911 (pm20) cc_final: 0.8254 (pm20) REVERT: F 173 ASP cc_start: 0.9044 (t0) cc_final: 0.8690 (t0) REVERT: F 198 MET cc_start: 0.9409 (tpp) cc_final: 0.9039 (tpt) REVERT: F 471 TYR cc_start: 0.8303 (p90) cc_final: 0.7772 (p90) REVERT: F 506 PHE cc_start: 0.9290 (t80) cc_final: 0.8974 (t80) REVERT: F 582 GLU cc_start: 0.8996 (tt0) cc_final: 0.8665 (tt0) REVERT: G 198 MET cc_start: 0.9102 (ttt) cc_final: 0.8899 (ttt) REVERT: G 557 GLU cc_start: 0.8733 (mp0) cc_final: 0.8395 (mp0) REVERT: G 564 MET cc_start: 0.7140 (OUTLIER) cc_final: 0.6853 (tpp) REVERT: H 83 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7824 (mtm) REVERT: H 380 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8798 (mt) REVERT: H 564 MET cc_start: 0.8772 (mmp) cc_final: 0.8549 (tmm) REVERT: I 471 TYR cc_start: 0.8585 (p90) cc_final: 0.8141 (p90) REVERT: I 506 PHE cc_start: 0.9231 (t80) cc_final: 0.8769 (t80) REVERT: I 577 LYS cc_start: 0.9206 (tppt) cc_final: 0.8646 (mmtm) REVERT: I 582 GLU cc_start: 0.9111 (tt0) cc_final: 0.8816 (tt0) REVERT: J 144 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8762 (tppp) REVERT: J 152 ASP cc_start: 0.8983 (m-30) cc_final: 0.8394 (m-30) REVERT: J 349 THR cc_start: 0.9151 (OUTLIER) cc_final: 0.8896 (p) REVERT: J 564 MET cc_start: 0.9074 (mmp) cc_final: 0.8760 (pmm) REVERT: J 577 LYS cc_start: 0.9415 (tptm) cc_final: 0.9149 (tppt) REVERT: K 152 ASP cc_start: 0.9241 (m-30) cc_final: 0.8856 (m-30) REVERT: K 172 ASP cc_start: 0.8905 (p0) cc_final: 0.8626 (p0) REVERT: K 334 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8748 (tttt) REVERT: K 473 MET cc_start: 0.9125 (mmm) cc_final: 0.8678 (mtp) REVERT: K 501 GLU cc_start: 0.9015 (pt0) cc_final: 0.8693 (pm20) REVERT: K 557 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8814 (mt-10) REVERT: K 577 LYS cc_start: 0.9462 (tppt) cc_final: 0.9227 (tppt) REVERT: L 81 ARG cc_start: 0.5996 (mtm110) cc_final: 0.5041 (ptp90) REVERT: L 139 ASP cc_start: 0.8148 (m-30) cc_final: 0.7706 (m-30) REVERT: L 144 LYS cc_start: 0.7328 (tptt) cc_final: 0.7074 (tptt) REVERT: L 152 ASP cc_start: 0.9051 (m-30) cc_final: 0.8606 (m-30) REVERT: L 198 MET cc_start: 0.9061 (tpt) cc_final: 0.8545 (tpt) REVERT: L 359 ASP cc_start: 0.8924 (m-30) cc_final: 0.8598 (t0) REVERT: M 159 GLU cc_start: 0.8866 (mp0) cc_final: 0.8622 (pm20) REVERT: N 161 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8969 (tt) REVERT: N 172 ASP cc_start: 0.8730 (m-30) cc_final: 0.8320 (t0) REVERT: N 203 MET cc_start: 0.8007 (mmp) cc_final: 0.7642 (mmp) REVERT: N 233 MET cc_start: 0.9536 (mmm) cc_final: 0.9290 (mmm) REVERT: N 338 ASN cc_start: 0.8813 (m-40) cc_final: 0.8490 (p0) REVERT: N 543 MET cc_start: 0.8618 (mmp) cc_final: 0.8131 (mpp) outliers start: 97 outliers final: 44 residues processed: 553 average time/residue: 0.5961 time to fit residues: 581.7881 Evaluate side-chains 491 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 438 time to evaluate : 5.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 554 ASP Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 539 LEU Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 380 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 233 MET Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 154 CYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 505 VAL Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 196 MET Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 430 optimal weight: 0.8980 chunk 778 optimal weight: 9.9990 chunk 142 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 215 optimal weight: 5.9990 chunk 398 optimal weight: 3.9990 chunk 624 optimal weight: 0.8980 chunk 674 optimal weight: 0.2980 chunk 205 optimal weight: 0.4980 chunk 741 optimal weight: 0.0370 chunk 591 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 ASN I 487 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.056949 restraints weight = 200821.763| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.97 r_work: 0.2906 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 67144 Z= 0.143 Angle : 0.459 13.853 90986 Z= 0.238 Chirality : 0.042 0.246 9982 Planarity : 0.003 0.039 11676 Dihedral : 3.679 17.044 8764 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 11.33 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 8050 helix: 1.36 (0.10), residues: 2772 sheet: -0.23 (0.17), residues: 966 loop : 0.23 (0.10), residues: 4312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 183 HIS 0.004 0.000 HIS M 208 PHE 0.023 0.001 PHE C 572 TYR 0.013 0.001 TYR D 112 ARG 0.006 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 472 time to evaluate : 5.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6715 (mtt) cc_final: 0.6267 (mpp) REVERT: A 198 MET cc_start: 0.9272 (ttm) cc_final: 0.8703 (mmm) REVERT: A 465 MET cc_start: 0.8585 (mmm) cc_final: 0.8179 (mmm) REVERT: A 473 MET cc_start: 0.9046 (tpp) cc_final: 0.8037 (mmm) REVERT: A 501 GLU cc_start: 0.8636 (tp30) cc_final: 0.8356 (tp30) REVERT: A 560 LYS cc_start: 0.9361 (pttm) cc_final: 0.9129 (tptt) REVERT: B 129 LYS cc_start: 0.9204 (mmtp) cc_final: 0.8996 (mmtp) REVERT: B 198 MET cc_start: 0.8038 (tpp) cc_final: 0.7814 (tpt) REVERT: B 329 PHE cc_start: 0.8684 (m-10) cc_final: 0.8384 (m-10) REVERT: B 472 PHE cc_start: 0.8944 (m-10) cc_final: 0.8664 (m-10) REVERT: B 473 MET cc_start: 0.8539 (mmm) cc_final: 0.7693 (mtp) REVERT: B 516 MET cc_start: 0.8470 (tmm) cc_final: 0.8211 (tmm) REVERT: C 82 GLU cc_start: 0.7407 (pm20) cc_final: 0.7150 (mp0) REVERT: C 328 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8764 (pt0) REVERT: C 465 MET cc_start: 0.9580 (mtm) cc_final: 0.9313 (mtm) REVERT: C 564 MET cc_start: 0.8271 (mpp) cc_final: 0.7672 (ttt) REVERT: C 577 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8863 (mmtp) REVERT: D 82 GLU cc_start: 0.8325 (pp20) cc_final: 0.7997 (pm20) REVERT: D 173 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8808 (t70) REVERT: D 465 MET cc_start: 0.9218 (ptp) cc_final: 0.8715 (ptp) REVERT: D 557 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8713 (mp0) REVERT: E 359 ASP cc_start: 0.9078 (m-30) cc_final: 0.8637 (m-30) REVERT: E 564 MET cc_start: 0.8923 (mmp) cc_final: 0.8250 (ptt) REVERT: F 1 MET cc_start: 0.8464 (ppp) cc_final: 0.8147 (ptt) REVERT: F 39 CYS cc_start: 0.9282 (m) cc_final: 0.8950 (m) REVERT: F 128 GLU cc_start: 0.8840 (pm20) cc_final: 0.8264 (pm20) REVERT: F 173 ASP cc_start: 0.9025 (t0) cc_final: 0.8667 (t0) REVERT: F 198 MET cc_start: 0.9384 (tpp) cc_final: 0.9015 (tpt) REVERT: F 471 TYR cc_start: 0.8303 (p90) cc_final: 0.7972 (p90) REVERT: F 506 PHE cc_start: 0.9287 (t80) cc_final: 0.9086 (t80) REVERT: F 582 GLU cc_start: 0.9028 (tt0) cc_final: 0.8693 (tt0) REVERT: G 152 ASP cc_start: 0.9003 (m-30) cc_final: 0.8522 (m-30) REVERT: G 159 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8290 (pm20) REVERT: G 557 GLU cc_start: 0.8732 (mp0) cc_final: 0.8389 (mp0) REVERT: G 564 MET cc_start: 0.7230 (OUTLIER) cc_final: 0.6947 (tpp) REVERT: H 56 GLU cc_start: 0.8669 (pt0) cc_final: 0.8307 (pm20) REVERT: H 83 MET cc_start: 0.8142 (OUTLIER) cc_final: 0.7762 (mtm) REVERT: H 380 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8814 (mt) REVERT: I 471 TYR cc_start: 0.8537 (p90) cc_final: 0.7971 (p90) REVERT: I 506 PHE cc_start: 0.9222 (t80) cc_final: 0.8812 (t80) REVERT: I 577 LYS cc_start: 0.9201 (tppt) cc_final: 0.8607 (mmtm) REVERT: I 582 GLU cc_start: 0.9113 (tt0) cc_final: 0.8804 (tt0) REVERT: J 152 ASP cc_start: 0.8989 (m-30) cc_final: 0.8364 (m-30) REVERT: J 349 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8852 (p) REVERT: J 564 MET cc_start: 0.9016 (mmp) cc_final: 0.8804 (pmm) REVERT: J 577 LYS cc_start: 0.9394 (tptm) cc_final: 0.9117 (tppt) REVERT: K 152 ASP cc_start: 0.9181 (m-30) cc_final: 0.8743 (m-30) REVERT: K 172 ASP cc_start: 0.8953 (p0) cc_final: 0.8673 (p0) REVERT: K 198 MET cc_start: 0.8918 (tpt) cc_final: 0.8403 (tpp) REVERT: K 334 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8850 (tttt) REVERT: K 473 MET cc_start: 0.9077 (mmm) cc_final: 0.8584 (mtp) REVERT: K 501 GLU cc_start: 0.9009 (pt0) cc_final: 0.8694 (pm20) REVERT: K 516 MET cc_start: 0.8447 (ttp) cc_final: 0.7905 (mtp) REVERT: K 557 GLU cc_start: 0.9083 (mt-10) cc_final: 0.8815 (mt-10) REVERT: L 139 ASP cc_start: 0.8099 (m-30) cc_final: 0.7553 (m-30) REVERT: L 144 LYS cc_start: 0.7244 (tptt) cc_final: 0.6990 (tptt) REVERT: L 152 ASP cc_start: 0.9037 (m-30) cc_final: 0.8581 (m-30) REVERT: L 198 MET cc_start: 0.9136 (tpt) cc_final: 0.8594 (tpt) REVERT: L 359 ASP cc_start: 0.8975 (m-30) cc_final: 0.8624 (t0) REVERT: M 159 GLU cc_start: 0.8864 (mp0) cc_final: 0.8618 (pm20) REVERT: M 349 THR cc_start: 0.7619 (OUTLIER) cc_final: 0.7322 (p) REVERT: M 356 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: N 1 MET cc_start: 0.7096 (ppp) cc_final: 0.6861 (ppp) REVERT: N 161 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8927 (tt) REVERT: N 172 ASP cc_start: 0.8700 (m-30) cc_final: 0.8309 (t0) REVERT: N 203 MET cc_start: 0.8016 (mmp) cc_final: 0.7648 (mmp) REVERT: N 233 MET cc_start: 0.9531 (mmm) cc_final: 0.9299 (mmm) REVERT: N 338 ASN cc_start: 0.8775 (m-40) cc_final: 0.8459 (p0) REVERT: N 465 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8456 (pmm) REVERT: N 590 LEU cc_start: 0.8056 (mm) cc_final: 0.7698 (mm) outliers start: 86 outliers final: 43 residues processed: 533 average time/residue: 0.5985 time to fit residues: 561.8939 Evaluate side-chains 488 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 433 time to evaluate : 5.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 447 THR Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 407 ILE Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 539 LEU Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 380 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 465 MET Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 154 CYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 505 VAL Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 196 MET Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 465 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 538 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 645 optimal weight: 2.9990 chunk 497 optimal weight: 0.0070 chunk 711 optimal weight: 9.9990 chunk 708 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 157 optimal weight: 7.9990 chunk 265 optimal weight: 2.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 178 ASN G 208 HIS G 240 HIS ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN I 338 ASN ** J 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 HIS L 405 ASN M 388 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.079164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.051867 restraints weight = 202114.857| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.91 r_work: 0.2779 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 67144 Z= 0.337 Angle : 0.548 13.845 90986 Z= 0.286 Chirality : 0.045 0.250 9982 Planarity : 0.003 0.046 11676 Dihedral : 4.089 18.140 8764 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.50 % Allowed : 11.48 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.10), residues: 8050 helix: 1.21 (0.10), residues: 2856 sheet: -0.56 (0.17), residues: 994 loop : 0.23 (0.10), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 410 HIS 0.004 0.001 HIS L 207 PHE 0.035 0.001 PHE H 506 TYR 0.026 0.002 TYR H 471 ARG 0.010 0.001 ARG F 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 403 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 465 MET cc_start: 0.8745 (mmm) cc_final: 0.8289 (mmm) REVERT: A 473 MET cc_start: 0.9211 (tpp) cc_final: 0.8244 (mmm) REVERT: B 83 MET cc_start: 0.7650 (mpp) cc_final: 0.7261 (mpp) REVERT: B 198 MET cc_start: 0.8027 (tpp) cc_final: 0.7818 (tpt) REVERT: B 329 PHE cc_start: 0.8731 (m-10) cc_final: 0.8414 (m-10) REVERT: B 472 PHE cc_start: 0.8901 (m-10) cc_final: 0.8645 (m-10) REVERT: B 473 MET cc_start: 0.8493 (mmm) cc_final: 0.7758 (mtp) REVERT: B 506 PHE cc_start: 0.7739 (t80) cc_final: 0.7380 (t80) REVERT: C 47 MET cc_start: 0.8896 (ttp) cc_final: 0.8689 (ttp) REVERT: C 82 GLU cc_start: 0.7601 (pm20) cc_final: 0.7310 (mp0) REVERT: C 328 GLU cc_start: 0.9046 (OUTLIER) cc_final: 0.8816 (pt0) REVERT: C 564 MET cc_start: 0.8368 (mpp) cc_final: 0.8155 (pmm) REVERT: C 577 LYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8913 (mmtm) REVERT: D 82 GLU cc_start: 0.8448 (pp20) cc_final: 0.8077 (pp20) REVERT: D 173 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8859 (t70) REVERT: D 557 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8737 (mp0) REVERT: D 564 MET cc_start: 0.8727 (ptt) cc_final: 0.8436 (pmm) REVERT: D 567 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8919 (mm) REVERT: E 81 ARG cc_start: 0.7503 (mmt90) cc_final: 0.7270 (mmt90) REVERT: E 359 ASP cc_start: 0.9200 (m-30) cc_final: 0.8734 (m-30) REVERT: E 564 MET cc_start: 0.9081 (mmp) cc_final: 0.8801 (mpp) REVERT: F 1 MET cc_start: 0.8859 (ppp) cc_final: 0.8477 (ptt) REVERT: F 173 ASP cc_start: 0.9054 (t0) cc_final: 0.8638 (t0) REVERT: F 198 MET cc_start: 0.9319 (tpp) cc_final: 0.8868 (tpt) REVERT: F 270 ASP cc_start: 0.8561 (t0) cc_final: 0.8274 (t0) REVERT: F 582 GLU cc_start: 0.9065 (tt0) cc_final: 0.8668 (tt0) REVERT: F 586 LYS cc_start: 0.9345 (mtmt) cc_final: 0.9083 (mttt) REVERT: G 198 MET cc_start: 0.9268 (ttt) cc_final: 0.8888 (ttt) REVERT: G 382 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8527 (mm) REVERT: G 557 GLU cc_start: 0.8803 (mp0) cc_final: 0.8307 (mp0) REVERT: H 83 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7937 (mtm) REVERT: H 110 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8775 (tt0) REVERT: I 382 ILE cc_start: 0.8896 (OUTLIER) cc_final: 0.8519 (mm) REVERT: I 471 TYR cc_start: 0.8696 (p90) cc_final: 0.8278 (p90) REVERT: I 506 PHE cc_start: 0.9287 (t80) cc_final: 0.8889 (t80) REVERT: I 577 LYS cc_start: 0.9248 (tppt) cc_final: 0.8636 (mmtp) REVERT: J 144 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.7933 (tmtt) REVERT: J 577 LYS cc_start: 0.9420 (tptm) cc_final: 0.9122 (tppt) REVERT: K 152 ASP cc_start: 0.9253 (m-30) cc_final: 0.8843 (m-30) REVERT: K 382 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8450 (mp) REVERT: K 473 MET cc_start: 0.9124 (mmm) cc_final: 0.8710 (mtp) REVERT: K 557 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8780 (mt-10) REVERT: L 139 ASP cc_start: 0.8452 (m-30) cc_final: 0.7930 (m-30) REVERT: L 144 LYS cc_start: 0.7185 (tptt) cc_final: 0.6901 (tptt) REVERT: L 198 MET cc_start: 0.9141 (tpt) cc_final: 0.8689 (tpt) REVERT: L 212 LEU cc_start: 0.9314 (tp) cc_final: 0.8998 (tt) REVERT: L 405 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7859 (p0) REVERT: M 159 GLU cc_start: 0.8934 (mp0) cc_final: 0.8667 (pm20) REVERT: M 212 LEU cc_start: 0.9069 (mt) cc_final: 0.8839 (pp) REVERT: M 349 THR cc_start: 0.7685 (OUTLIER) cc_final: 0.7380 (p) REVERT: M 356 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: M 543 MET cc_start: 0.9208 (mpp) cc_final: 0.8933 (mpp) REVERT: N 1 MET cc_start: 0.7451 (ppp) cc_final: 0.7153 (ppp) REVERT: N 161 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8857 (tt) REVERT: N 172 ASP cc_start: 0.8735 (m-30) cc_final: 0.8316 (t0) REVERT: N 203 MET cc_start: 0.8115 (mmp) cc_final: 0.7754 (mmp) REVERT: N 338 ASN cc_start: 0.8825 (m-40) cc_final: 0.8521 (p0) REVERT: N 543 MET cc_start: 0.8638 (mmp) cc_final: 0.8427 (mmt) outliers start: 109 outliers final: 54 residues processed: 489 average time/residue: 0.5974 time to fit residues: 513.5492 Evaluate side-chains 439 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 371 time to evaluate : 5.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 39 CYS Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 539 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 524 ASN Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 141 THR Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 234 VAL Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 465 MET Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 47 MET Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 154 CYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 405 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain M residue 551 ASP Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 253 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 772 optimal weight: 8.9990 chunk 649 optimal weight: 0.8980 chunk 730 optimal weight: 7.9990 chunk 250 optimal weight: 0.6980 chunk 416 optimal weight: 0.5980 chunk 503 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 329 optimal weight: 0.0570 chunk 466 optimal weight: 0.7980 chunk 662 optimal weight: 3.9990 chunk 632 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 405 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.055451 restraints weight = 200205.638| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.96 r_work: 0.2856 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 67144 Z= 0.156 Angle : 0.475 13.331 90986 Z= 0.245 Chirality : 0.043 0.218 9982 Planarity : 0.003 0.063 11676 Dihedral : 3.788 19.958 8764 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.20 % Allowed : 12.17 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 8050 helix: 1.43 (0.10), residues: 2772 sheet: -0.24 (0.17), residues: 924 loop : 0.17 (0.10), residues: 4354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 183 HIS 0.002 0.000 HIS G 486 PHE 0.024 0.001 PHE C 572 TYR 0.024 0.001 TYR B 412 ARG 0.012 0.000 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 434 time to evaluate : 5.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6806 (mtt) cc_final: 0.6375 (mpp) REVERT: A 198 MET cc_start: 0.9287 (ttm) cc_final: 0.8585 (tpt) REVERT: A 465 MET cc_start: 0.8718 (mmm) cc_final: 0.8286 (mmm) REVERT: A 473 MET cc_start: 0.9230 (tpp) cc_final: 0.8817 (mmt) REVERT: B 83 MET cc_start: 0.7706 (mpp) cc_final: 0.7272 (mpp) REVERT: B 198 MET cc_start: 0.8148 (tpp) cc_final: 0.7948 (tpt) REVERT: B 329 PHE cc_start: 0.8737 (m-10) cc_final: 0.8386 (m-10) REVERT: B 473 MET cc_start: 0.8598 (mmm) cc_final: 0.7816 (mtp) REVERT: B 506 PHE cc_start: 0.7765 (t80) cc_final: 0.7327 (t80) REVERT: C 198 MET cc_start: 0.9405 (tpp) cc_final: 0.9155 (tpp) REVERT: C 328 GLU cc_start: 0.9005 (OUTLIER) cc_final: 0.8770 (pt0) REVERT: C 465 MET cc_start: 0.9569 (mtm) cc_final: 0.9364 (mtm) REVERT: C 572 PHE cc_start: 0.9092 (t80) cc_final: 0.8819 (t80) REVERT: C 577 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8877 (mmtp) REVERT: D 83 MET cc_start: 0.8216 (mtm) cc_final: 0.7915 (mtt) REVERT: D 173 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8813 (t70) REVERT: D 557 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8731 (mp0) REVERT: D 564 MET cc_start: 0.8781 (ptt) cc_final: 0.8461 (pmm) REVERT: D 567 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8870 (mm) REVERT: E 359 ASP cc_start: 0.9137 (m-30) cc_final: 0.8665 (m-30) REVERT: E 564 MET cc_start: 0.9040 (mmp) cc_final: 0.8808 (mpp) REVERT: F 1 MET cc_start: 0.8609 (ppp) cc_final: 0.8300 (ptt) REVERT: F 39 CYS cc_start: 0.9325 (m) cc_final: 0.9029 (m) REVERT: F 173 ASP cc_start: 0.9024 (t0) cc_final: 0.8643 (t0) REVERT: F 198 MET cc_start: 0.9303 (tpp) cc_final: 0.8874 (tpt) REVERT: F 270 ASP cc_start: 0.8554 (t0) cc_final: 0.8352 (t0) REVERT: F 582 GLU cc_start: 0.8991 (tt0) cc_final: 0.8691 (tt0) REVERT: G 152 ASP cc_start: 0.9102 (m-30) cc_final: 0.8592 (m-30) REVERT: G 159 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: G 557 GLU cc_start: 0.8828 (mp0) cc_final: 0.8365 (mp0) REVERT: G 564 MET cc_start: 0.7658 (pmm) cc_final: 0.7340 (tmm) REVERT: H 144 LYS cc_start: 0.7436 (tptt) cc_final: 0.7107 (tptt) REVERT: I 83 MET cc_start: 0.8052 (mtt) cc_final: 0.7760 (mtt) REVERT: I 382 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8416 (mm) REVERT: I 471 TYR cc_start: 0.8552 (p90) cc_final: 0.7841 (p90) REVERT: I 506 PHE cc_start: 0.9225 (t80) cc_final: 0.8984 (t80) REVERT: I 577 LYS cc_start: 0.9228 (tppt) cc_final: 0.8572 (mmtp) REVERT: J 82 GLU cc_start: 0.7923 (mp0) cc_final: 0.7638 (mp0) REVERT: J 173 ASP cc_start: 0.9040 (t0) cc_final: 0.8838 (t0) REVERT: J 563 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8164 (mmtt) REVERT: J 564 MET cc_start: 0.7837 (pmm) cc_final: 0.7367 (ptt) REVERT: J 577 LYS cc_start: 0.9399 (tptm) cc_final: 0.9084 (tppt) REVERT: K 152 ASP cc_start: 0.9225 (m-30) cc_final: 0.9015 (m-30) REVERT: K 334 LYS cc_start: 0.9125 (mmmm) cc_final: 0.8883 (tttt) REVERT: K 382 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8275 (mp) REVERT: K 473 MET cc_start: 0.9118 (mmm) cc_final: 0.8649 (mtp) REVERT: K 557 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8816 (mt-10) REVERT: L 81 ARG cc_start: 0.6370 (mtm110) cc_final: 0.5537 (ptp90) REVERT: L 139 ASP cc_start: 0.8471 (m-30) cc_final: 0.8026 (m-30) REVERT: L 144 LYS cc_start: 0.7107 (tptt) cc_final: 0.6831 (tptt) REVERT: L 198 MET cc_start: 0.9147 (tpt) cc_final: 0.8607 (tpt) REVERT: L 212 LEU cc_start: 0.9307 (tp) cc_final: 0.8973 (tt) REVERT: M 156 THR cc_start: 0.7962 (OUTLIER) cc_final: 0.7720 (t) REVERT: M 159 GLU cc_start: 0.8925 (mp0) cc_final: 0.8665 (pm20) REVERT: M 198 MET cc_start: 0.7365 (mmm) cc_final: 0.7098 (mmm) REVERT: M 349 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.7224 (p) REVERT: M 356 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: M 543 MET cc_start: 0.9180 (mpp) cc_final: 0.8960 (mpp) REVERT: N 161 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8910 (tt) REVERT: N 172 ASP cc_start: 0.8724 (m-30) cc_final: 0.8215 (t0) REVERT: N 176 ASN cc_start: 0.8789 (m-40) cc_final: 0.8005 (p0) REVERT: N 203 MET cc_start: 0.8035 (mmp) cc_final: 0.7677 (mmp) REVERT: N 233 MET cc_start: 0.9438 (mmm) cc_final: 0.9000 (mmp) REVERT: N 338 ASN cc_start: 0.8840 (m-40) cc_final: 0.8529 (p0) outliers start: 87 outliers final: 44 residues processed: 503 average time/residue: 0.6040 time to fit residues: 534.5389 Evaluate side-chains 449 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 394 time to evaluate : 5.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 253 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 127 optimal weight: 0.8980 chunk 268 optimal weight: 3.9990 chunk 404 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 643 optimal weight: 4.9990 chunk 252 optimal weight: 2.9990 chunk 229 optimal weight: 0.0170 chunk 528 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 395 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 402 GLN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 550 ASN M 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.080333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053257 restraints weight = 201208.007| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.91 r_work: 0.2822 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 67144 Z= 0.225 Angle : 0.501 15.127 90986 Z= 0.258 Chirality : 0.044 0.294 9982 Planarity : 0.003 0.045 11676 Dihedral : 3.824 16.541 8764 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.14 % Allowed : 12.54 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.10), residues: 8050 helix: 1.36 (0.10), residues: 2856 sheet: -0.24 (0.17), residues: 924 loop : 0.20 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 439 HIS 0.004 0.001 HIS D 442 PHE 0.027 0.001 PHE E 506 TYR 0.024 0.001 TYR B 412 ARG 0.010 0.000 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 392 time to evaluate : 7.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6782 (mtt) cc_final: 0.6380 (mpp) REVERT: A 198 MET cc_start: 0.9306 (ttm) cc_final: 0.8595 (tpt) REVERT: A 465 MET cc_start: 0.8757 (mmm) cc_final: 0.8307 (mmm) REVERT: A 506 PHE cc_start: 0.8989 (t80) cc_final: 0.8363 (m-80) REVERT: B 83 MET cc_start: 0.7802 (mpp) cc_final: 0.7311 (mpp) REVERT: B 198 MET cc_start: 0.8125 (tpp) cc_final: 0.7910 (tpt) REVERT: B 329 PHE cc_start: 0.8723 (m-10) cc_final: 0.8374 (m-10) REVERT: B 473 MET cc_start: 0.8485 (mmm) cc_final: 0.7671 (mtp) REVERT: B 506 PHE cc_start: 0.8008 (t80) cc_final: 0.7624 (t80) REVERT: C 328 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8792 (pt0) REVERT: C 465 MET cc_start: 0.9571 (mtm) cc_final: 0.9349 (mtm) REVERT: C 572 PHE cc_start: 0.9127 (t80) cc_final: 0.8867 (t80) REVERT: C 577 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8907 (mmtp) REVERT: D 82 GLU cc_start: 0.8355 (pp20) cc_final: 0.7973 (pp20) REVERT: D 173 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8847 (t70) REVERT: D 352 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8806 (p) REVERT: D 364 ILE cc_start: 0.9367 (tp) cc_final: 0.9117 (tp) REVERT: D 557 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8735 (mp0) REVERT: D 564 MET cc_start: 0.8779 (ptt) cc_final: 0.8505 (pmm) REVERT: D 567 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8913 (mm) REVERT: E 359 ASP cc_start: 0.9137 (m-30) cc_final: 0.8653 (m-30) REVERT: E 564 MET cc_start: 0.8979 (mmp) cc_final: 0.8539 (pmm) REVERT: F 1 MET cc_start: 0.8709 (ppp) cc_final: 0.8356 (ptt) REVERT: F 173 ASP cc_start: 0.9016 (t0) cc_final: 0.8601 (t0) REVERT: F 198 MET cc_start: 0.9321 (tpp) cc_final: 0.8910 (tpt) REVERT: F 270 ASP cc_start: 0.8504 (t0) cc_final: 0.8220 (t0) REVERT: F 582 GLU cc_start: 0.9019 (tt0) cc_final: 0.8610 (tt0) REVERT: F 586 LYS cc_start: 0.9367 (mtmt) cc_final: 0.9065 (mttp) REVERT: G 152 ASP cc_start: 0.9125 (m-30) cc_final: 0.8631 (m-30) REVERT: G 159 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8341 (pm20) REVERT: G 382 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8591 (mp) REVERT: G 557 GLU cc_start: 0.8802 (mp0) cc_final: 0.8306 (mp0) REVERT: G 564 MET cc_start: 0.7716 (pmm) cc_final: 0.7293 (tmm) REVERT: H 83 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8011 (mtm) REVERT: H 110 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8771 (tt0) REVERT: I 382 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8457 (mm) REVERT: I 471 TYR cc_start: 0.8626 (p90) cc_final: 0.8036 (p90) REVERT: I 506 PHE cc_start: 0.9205 (t80) cc_final: 0.8808 (t80) REVERT: I 582 GLU cc_start: 0.9140 (tt0) cc_final: 0.8612 (pt0) REVERT: J 82 GLU cc_start: 0.7942 (mp0) cc_final: 0.7594 (mp0) REVERT: J 144 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.7939 (tmtt) REVERT: J 577 LYS cc_start: 0.9399 (tptm) cc_final: 0.9089 (tppt) REVERT: K 152 ASP cc_start: 0.9263 (m-30) cc_final: 0.8828 (m-30) REVERT: K 334 LYS cc_start: 0.9081 (mmmm) cc_final: 0.8740 (tttt) REVERT: K 382 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8389 (mp) REVERT: K 473 MET cc_start: 0.9141 (mmm) cc_final: 0.8683 (mtp) REVERT: L 28 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9040 (mp) REVERT: L 81 ARG cc_start: 0.6523 (mtm110) cc_final: 0.5701 (ptp90) REVERT: L 139 ASP cc_start: 0.8463 (m-30) cc_final: 0.7969 (m-30) REVERT: L 144 LYS cc_start: 0.7179 (tptt) cc_final: 0.6876 (tptt) REVERT: L 198 MET cc_start: 0.9155 (tpt) cc_final: 0.8632 (tpt) REVERT: L 212 LEU cc_start: 0.9297 (tp) cc_final: 0.9042 (tt) REVERT: M 156 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7744 (t) REVERT: M 159 GLU cc_start: 0.8923 (mp0) cc_final: 0.8663 (pm20) REVERT: M 198 MET cc_start: 0.7384 (mmm) cc_final: 0.7087 (mmm) REVERT: M 349 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7248 (p) REVERT: M 356 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: M 543 MET cc_start: 0.9235 (mpp) cc_final: 0.8962 (mpp) REVERT: N 161 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8926 (tt) REVERT: N 172 ASP cc_start: 0.8750 (m-30) cc_final: 0.8364 (t0) REVERT: N 203 MET cc_start: 0.8053 (mmp) cc_final: 0.7687 (mmp) REVERT: N 338 ASN cc_start: 0.8825 (m-40) cc_final: 0.8532 (p0) REVERT: N 590 LEU cc_start: 0.8163 (mm) cc_final: 0.7730 (mm) outliers start: 83 outliers final: 48 residues processed: 462 average time/residue: 0.6299 time to fit residues: 515.4132 Evaluate side-chains 444 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 5.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 253 ILE Chi-restraints excluded: chain N residue 581 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 222 optimal weight: 0.6980 chunk 256 optimal weight: 1.9990 chunk 792 optimal weight: 0.9990 chunk 504 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 438 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 422 optimal weight: 2.9990 chunk 551 optimal weight: 0.6980 chunk 453 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 524 ASN ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.080530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.053579 restraints weight = 201312.895| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.92 r_work: 0.2829 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2829 r_free = 0.2829 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 67144 Z= 0.209 Angle : 0.498 14.566 90986 Z= 0.256 Chirality : 0.043 0.308 9982 Planarity : 0.003 0.056 11676 Dihedral : 3.797 16.392 8764 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.07 % Allowed : 12.75 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.10), residues: 8050 helix: 1.36 (0.10), residues: 2856 sheet: -0.22 (0.17), residues: 924 loop : 0.22 (0.10), residues: 4270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 410 HIS 0.003 0.001 HIS L 207 PHE 0.029 0.001 PHE E 506 TYR 0.024 0.001 TYR H 471 ARG 0.009 0.000 ARG L 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 5.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6862 (mtt) cc_final: 0.6438 (mpp) REVERT: A 198 MET cc_start: 0.9304 (ttm) cc_final: 0.8604 (tpt) REVERT: A 465 MET cc_start: 0.8751 (mmm) cc_final: 0.8293 (mmm) REVERT: A 506 PHE cc_start: 0.8989 (t80) cc_final: 0.8385 (m-80) REVERT: B 83 MET cc_start: 0.7817 (mpp) cc_final: 0.7250 (mpp) REVERT: B 149 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8804 (tt0) REVERT: B 329 PHE cc_start: 0.8678 (m-10) cc_final: 0.8345 (m-10) REVERT: B 473 MET cc_start: 0.8474 (mmm) cc_final: 0.7599 (mtp) REVERT: B 506 PHE cc_start: 0.8146 (t80) cc_final: 0.7729 (t80) REVERT: C 328 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (pt0) REVERT: C 465 MET cc_start: 0.9570 (mtm) cc_final: 0.9366 (mtm) REVERT: C 572 PHE cc_start: 0.9140 (t80) cc_final: 0.8891 (t80) REVERT: C 577 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8913 (mmtp) REVERT: D 82 GLU cc_start: 0.8346 (pp20) cc_final: 0.7971 (pp20) REVERT: D 173 ASP cc_start: 0.9129 (OUTLIER) cc_final: 0.8832 (t70) REVERT: D 352 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8825 (p) REVERT: D 364 ILE cc_start: 0.9336 (tp) cc_final: 0.9074 (tp) REVERT: D 557 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8718 (mp0) REVERT: D 564 MET cc_start: 0.8758 (ptt) cc_final: 0.8285 (pmm) REVERT: D 567 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8900 (mm) REVERT: E 359 ASP cc_start: 0.9143 (m-30) cc_final: 0.8664 (m-30) REVERT: E 564 MET cc_start: 0.8935 (mmp) cc_final: 0.8659 (pmm) REVERT: F 1 MET cc_start: 0.8694 (ppp) cc_final: 0.8360 (ptt) REVERT: F 173 ASP cc_start: 0.9014 (t0) cc_final: 0.8599 (t0) REVERT: F 198 MET cc_start: 0.9325 (tpp) cc_final: 0.8893 (tpt) REVERT: F 270 ASP cc_start: 0.8525 (t0) cc_final: 0.8262 (t0) REVERT: F 582 GLU cc_start: 0.9007 (tt0) cc_final: 0.8699 (tt0) REVERT: G 152 ASP cc_start: 0.9091 (m-30) cc_final: 0.8617 (m-30) REVERT: G 159 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8317 (pm20) REVERT: G 557 GLU cc_start: 0.8831 (mp0) cc_final: 0.8293 (mp0) REVERT: G 564 MET cc_start: 0.7785 (pmm) cc_final: 0.7468 (tmm) REVERT: H 110 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8766 (tt0) REVERT: H 144 LYS cc_start: 0.7403 (tptt) cc_final: 0.7139 (tptt) REVERT: I 382 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8433 (mm) REVERT: I 471 TYR cc_start: 0.8609 (p90) cc_final: 0.7999 (p90) REVERT: I 506 PHE cc_start: 0.9197 (t80) cc_final: 0.8802 (t80) REVERT: I 582 GLU cc_start: 0.9116 (tt0) cc_final: 0.8566 (pt0) REVERT: J 82 GLU cc_start: 0.7903 (mp0) cc_final: 0.7543 (mp0) REVERT: J 144 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.7766 (tmtt) REVERT: J 577 LYS cc_start: 0.9396 (tptm) cc_final: 0.9089 (tppt) REVERT: K 152 ASP cc_start: 0.9254 (m-30) cc_final: 0.9045 (m-30) REVERT: K 334 LYS cc_start: 0.9094 (mmmm) cc_final: 0.8866 (tttt) REVERT: K 382 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8358 (mp) REVERT: K 473 MET cc_start: 0.9142 (mmm) cc_final: 0.8668 (mtp) REVERT: K 582 GLU cc_start: 0.9024 (tt0) cc_final: 0.8611 (mt-10) REVERT: L 28 ILE cc_start: 0.9386 (OUTLIER) cc_final: 0.9001 (mp) REVERT: L 81 ARG cc_start: 0.6655 (mtm110) cc_final: 0.5838 (ptp90) REVERT: L 139 ASP cc_start: 0.8460 (m-30) cc_final: 0.7952 (m-30) REVERT: L 144 LYS cc_start: 0.7145 (tptt) cc_final: 0.6815 (tptt) REVERT: L 198 MET cc_start: 0.9148 (tpt) cc_final: 0.8620 (tpt) REVERT: L 212 LEU cc_start: 0.9288 (tp) cc_final: 0.9058 (tt) REVERT: M 156 THR cc_start: 0.7989 (OUTLIER) cc_final: 0.7749 (t) REVERT: M 159 GLU cc_start: 0.8930 (mp0) cc_final: 0.8692 (pm20) REVERT: M 349 THR cc_start: 0.7528 (OUTLIER) cc_final: 0.7226 (p) REVERT: M 356 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8041 (tm-30) REVERT: M 543 MET cc_start: 0.9231 (mpp) cc_final: 0.8998 (mpp) REVERT: M 567 LEU cc_start: 0.9206 (mm) cc_final: 0.8836 (tp) REVERT: N 161 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8937 (tt) REVERT: N 172 ASP cc_start: 0.8758 (m-30) cc_final: 0.8374 (t0) REVERT: N 203 MET cc_start: 0.8042 (mmp) cc_final: 0.7686 (mmp) REVERT: N 338 ASN cc_start: 0.8839 (m-40) cc_final: 0.8554 (p0) outliers start: 78 outliers final: 52 residues processed: 459 average time/residue: 0.6140 time to fit residues: 498.3311 Evaluate side-chains 442 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 375 time to evaluate : 5.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 294 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 144 LYS Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 253 ILE Chi-restraints excluded: chain N residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 544 optimal weight: 0.6980 chunk 775 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 424 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 246 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 304 optimal weight: 0.0980 chunk 694 optimal weight: 1.9990 chunk 200 optimal weight: 0.2980 chunk 33 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.080932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.053890 restraints weight = 201815.542| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.94 r_work: 0.2841 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 67144 Z= 0.176 Angle : 0.493 14.453 90986 Z= 0.252 Chirality : 0.043 0.303 9982 Planarity : 0.003 0.121 11676 Dihedral : 3.735 16.032 8764 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.10 % Allowed : 12.80 % Favored : 86.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.10), residues: 8050 helix: 1.35 (0.10), residues: 2870 sheet: -0.18 (0.17), residues: 924 loop : 0.23 (0.10), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 387 HIS 0.002 0.001 HIS L 207 PHE 0.029 0.001 PHE L 572 TYR 0.028 0.001 TYR B 412 ARG 0.009 0.000 ARG L 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16100 Ramachandran restraints generated. 8050 Oldfield, 0 Emsley, 8050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 408 time to evaluate : 5.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 MET cc_start: 0.6947 (mtt) cc_final: 0.6440 (mpp) REVERT: A 198 MET cc_start: 0.9309 (ttm) cc_final: 0.8679 (tpt) REVERT: A 465 MET cc_start: 0.8743 (mmm) cc_final: 0.8273 (mmm) REVERT: A 506 PHE cc_start: 0.8950 (t80) cc_final: 0.8362 (m-80) REVERT: B 83 MET cc_start: 0.7924 (mpp) cc_final: 0.7364 (mpp) REVERT: B 329 PHE cc_start: 0.8685 (m-10) cc_final: 0.8346 (m-10) REVERT: B 349 THR cc_start: 0.7269 (OUTLIER) cc_final: 0.7023 (p) REVERT: B 473 MET cc_start: 0.8498 (mmm) cc_final: 0.7675 (mtp) REVERT: B 506 PHE cc_start: 0.8143 (t80) cc_final: 0.7777 (t80) REVERT: C 328 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8762 (pt0) REVERT: C 572 PHE cc_start: 0.9142 (t80) cc_final: 0.8904 (t80) REVERT: C 577 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8907 (mmtp) REVERT: D 82 GLU cc_start: 0.8337 (pp20) cc_final: 0.7962 (pp20) REVERT: D 173 ASP cc_start: 0.9122 (OUTLIER) cc_final: 0.8820 (t70) REVERT: D 356 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8645 (pm20) REVERT: D 364 ILE cc_start: 0.9263 (tp) cc_final: 0.8996 (tp) REVERT: D 557 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8720 (mp0) REVERT: D 564 MET cc_start: 0.8760 (ptt) cc_final: 0.8303 (pmm) REVERT: D 567 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8931 (mm) REVERT: E 359 ASP cc_start: 0.9142 (m-30) cc_final: 0.8664 (m-30) REVERT: E 564 MET cc_start: 0.8908 (mmp) cc_final: 0.8662 (pmm) REVERT: F 1 MET cc_start: 0.8673 (ppp) cc_final: 0.8346 (ptt) REVERT: F 173 ASP cc_start: 0.9024 (t0) cc_final: 0.8623 (t0) REVERT: F 198 MET cc_start: 0.9316 (tpp) cc_final: 0.8887 (tpt) REVERT: F 270 ASP cc_start: 0.8526 (t0) cc_final: 0.8276 (t0) REVERT: F 582 GLU cc_start: 0.8987 (tt0) cc_final: 0.8696 (tt0) REVERT: G 152 ASP cc_start: 0.9036 (m-30) cc_final: 0.8605 (m-30) REVERT: G 159 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: G 382 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8607 (mp) REVERT: G 557 GLU cc_start: 0.8828 (mp0) cc_final: 0.8292 (mp0) REVERT: G 564 MET cc_start: 0.7865 (pmm) cc_final: 0.7523 (tmm) REVERT: G 574 LYS cc_start: 0.9048 (tppt) cc_final: 0.8843 (ttmt) REVERT: H 110 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8772 (tt0) REVERT: H 144 LYS cc_start: 0.7345 (tptt) cc_final: 0.7063 (tptt) REVERT: H 577 LYS cc_start: 0.9530 (tptm) cc_final: 0.9217 (mmmm) REVERT: I 382 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8412 (mm) REVERT: I 471 TYR cc_start: 0.8598 (p90) cc_final: 0.7997 (p90) REVERT: I 506 PHE cc_start: 0.9171 (t80) cc_final: 0.8863 (t80) REVERT: I 577 LYS cc_start: 0.9192 (tppt) cc_final: 0.8656 (mmtm) REVERT: I 582 GLU cc_start: 0.9135 (tt0) cc_final: 0.8554 (pt0) REVERT: J 82 GLU cc_start: 0.7836 (mp0) cc_final: 0.7471 (mp0) REVERT: J 577 LYS cc_start: 0.9399 (tptm) cc_final: 0.9086 (tppt) REVERT: K 152 ASP cc_start: 0.9243 (m-30) cc_final: 0.9027 (m-30) REVERT: K 334 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8844 (tttt) REVERT: K 382 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8321 (mp) REVERT: K 473 MET cc_start: 0.9143 (mmm) cc_final: 0.8662 (mtp) REVERT: K 582 GLU cc_start: 0.9023 (tt0) cc_final: 0.8538 (mt-10) REVERT: L 28 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8994 (mp) REVERT: L 139 ASP cc_start: 0.8460 (m-30) cc_final: 0.7955 (m-30) REVERT: L 144 LYS cc_start: 0.7213 (tptt) cc_final: 0.6954 (tptt) REVERT: L 152 ASP cc_start: 0.9155 (m-30) cc_final: 0.8728 (m-30) REVERT: L 198 MET cc_start: 0.9162 (tpt) cc_final: 0.8642 (tpt) REVERT: L 212 LEU cc_start: 0.9286 (tp) cc_final: 0.9060 (tt) REVERT: M 156 THR cc_start: 0.7980 (OUTLIER) cc_final: 0.7741 (t) REVERT: M 159 GLU cc_start: 0.8999 (mp0) cc_final: 0.8754 (pm20) REVERT: M 349 THR cc_start: 0.7443 (OUTLIER) cc_final: 0.7101 (p) REVERT: M 356 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8045 (tm-30) REVERT: M 471 TYR cc_start: 0.6776 (p90) cc_final: 0.6556 (p90) REVERT: M 543 MET cc_start: 0.9182 (mpp) cc_final: 0.8948 (mpp) REVERT: M 567 LEU cc_start: 0.9195 (mm) cc_final: 0.8799 (tp) REVERT: N 161 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8943 (tt) REVERT: N 172 ASP cc_start: 0.8756 (m-30) cc_final: 0.8243 (t0) REVERT: N 176 ASN cc_start: 0.8790 (m-40) cc_final: 0.7934 (p0) REVERT: N 203 MET cc_start: 0.8041 (mmp) cc_final: 0.7685 (mmp) REVERT: N 338 ASN cc_start: 0.8846 (m-40) cc_final: 0.8557 (p0) outliers start: 80 outliers final: 56 residues processed: 473 average time/residue: 0.6047 time to fit residues: 505.3540 Evaluate side-chains 458 residues out of total 7280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 386 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 508 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 356 GLU Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain D residue 550 ASN Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 145 THR Chi-restraints excluded: chain E residue 203 MET Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 ILE Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 382 ILE Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 110 GLU Chi-restraints excluded: chain I residue 135 VAL Chi-restraints excluded: chain I residue 163 ASP Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 357 ILE Chi-restraints excluded: chain I residue 382 ILE Chi-restraints excluded: chain I residue 407 ILE Chi-restraints excluded: chain I residue 524 ASN Chi-restraints excluded: chain I residue 539 LEU Chi-restraints excluded: chain J residue 60 LYS Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 277 SER Chi-restraints excluded: chain J residue 278 ILE Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain J residue 350 SER Chi-restraints excluded: chain J residue 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 382 ILE Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 156 THR Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 356 GLU Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 161 LEU Chi-restraints excluded: chain N residue 253 ILE Chi-restraints excluded: chain N residue 581 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 123 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 344 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 472 optimal weight: 1.9990 chunk 662 optimal weight: 5.9990 chunk 309 optimal weight: 2.9990 chunk 340 optimal weight: 2.9990 chunk 797 optimal weight: 0.9980 chunk 355 optimal weight: 0.1980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 ASN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.081074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054545 restraints weight = 200928.546| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.88 r_work: 0.2836 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 67144 Z= 0.196 Angle : 0.494 12.055 90986 Z= 0.254 Chirality : 0.043 0.305 9982 Planarity : 0.003 0.046 11676 Dihedral : 3.744 16.662 8764 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.00 % Allowed : 13.10 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.10), residues: 8050 helix: 1.35 (0.10), residues: 2870 sheet: -0.16 (0.17), residues: 924 loop : 0.23 (0.10), residues: 4256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP M 180 HIS 0.003 0.001 HIS L 207 PHE 0.026 0.001 PHE E 506 TYR 0.031 0.001 TYR B 412 ARG 0.013 0.000 ARG L 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32232.54 seconds wall clock time: 556 minutes 2.23 seconds (33362.23 seconds total)