Starting phenix.real_space_refine on Sun Oct 13 08:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_43965.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_43965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_43965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_43965.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axe_43965/10_2024/9axe_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-5477/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: 33.50, per 1000 atoms: 0.51 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: 14.02 Conformation dependent library (CDL) restraints added in 6.5 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: 6.63 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: 31.52 Time building geometry restraints manager: 16.46 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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: 22.790 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: 0.110 Extract box with map and model: 3.010 Check model and map are aligned: 0.500 Set scattering table: 0.650 Process input model: 138.970 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.010 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 1335 time to evaluate : 6.027 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: 0.7768 time to fit residues: 1759.7400 Evaluate side-chains 622 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 622 time to evaluate : 7.333 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 fitting. rotamer outliers: 74 poor density : 682 time to evaluate : 7.440 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 142 LEU cc_start: 0.8531 (mt) cc_final: 0.8053 (mt) REVERT: A 439 TRP cc_start: 0.7960 (t60) cc_final: 0.7737 (t60) REVERT: A 506 PHE cc_start: 0.8735 (t80) cc_final: 0.8471 (t80) REVERT: A 560 LYS cc_start: 0.9393 (pttm) cc_final: 0.9123 (tptt) REVERT: B 238 LYS cc_start: 0.9225 (mttt) cc_final: 0.9023 (mmmt) REVERT: B 471 TYR cc_start: 0.7503 (p90) cc_final: 0.7039 (p90) REVERT: B 472 PHE cc_start: 0.8827 (m-10) cc_final: 0.8392 (m-10) REVERT: B 473 MET cc_start: 0.8703 (mmm) cc_final: 0.8226 (mtp) REVERT: D 587 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7671 (tp30) REVERT: E 564 MET cc_start: 0.8711 (mmp) cc_final: 0.8198 (ptm) REVERT: F 380 ILE cc_start: 0.8159 (mm) cc_final: 0.7852 (mt) REVERT: F 564 MET cc_start: 0.7785 (pmm) cc_final: 0.7312 (ptt) REVERT: F 575 LYS cc_start: 0.8638 (mmtm) cc_final: 0.8423 (tptt) REVERT: G 450 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8216 (tt) REVERT: H 564 MET cc_start: 0.8655 (mmp) cc_final: 0.8360 (tmm) REVERT: J 144 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8167 (tmtt) REVERT: J 152 ASP cc_start: 0.7500 (m-30) cc_final: 0.7293 (m-30) REVERT: J 564 MET cc_start: 0.9147 (mmp) cc_final: 0.8824 (ttt) REVERT: K 141 THR cc_start: 0.8781 (p) cc_final: 0.8548 (t) REVERT: K 565 GLN cc_start: 0.7952 (mm110) cc_final: 0.7751 (mp10) REVERT: M 1 MET cc_start: 0.5920 (ppp) cc_final: 0.5706 (ppp) REVERT: M 501 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6960 (pt0) REVERT: M 564 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7812 (pmm) REVERT: N 389 MET cc_start: 0.7721 (tmm) cc_final: 0.7422 (tmm) REVERT: N 564 MET cc_start: 0.6887 (pmm) cc_final: 0.6675 (pmm) REVERT: N 577 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8341 (mttp) outliers start: 74 outliers final: 37 residues processed: 729 average time/residue: 0.7509 time to fit residues: 952.9930 Evaluate side-chains 549 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 508 time to evaluate : 7.493 ------------------------------------------------------------------------------- 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 145 THR 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 450 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 402 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 603 optimal weight: 4.9990 chunk 493 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 725 optimal weight: 0.0170 chunk 784 optimal weight: 5.9990 chunk 646 optimal weight: 3.9990 chunk 719 optimal weight: 0.6980 chunk 247 optimal weight: 3.9990 chunk 582 optimal weight: 5.9990 overall best weight: 1.8822 ------------------------------------------------------------------------------- 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 B 402 GLN ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 402 GLN F 402 GLN F 496 ASN ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 486 HIS ** 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 K 496 ASN L 402 GLN ** L 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 402 GLN N 338 ASN N 405 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 67144 Z= 0.339 Angle : 0.591 12.395 90986 Z= 0.310 Chirality : 0.046 0.169 9982 Planarity : 0.004 0.048 11676 Dihedral : 4.364 17.914 8764 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.83 % Allowed : 9.35 % Favored : 88.82 % 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: 0.26 (0.09), residues: 8050 helix: 0.75 (0.10), residues: 2842 sheet: -0.49 (0.17), residues: 994 loop : 0.07 (0.10), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP A 410 HIS 0.006 0.001 HIS G 486 PHE 0.040 0.002 PHE J 506 TYR 0.024 0.002 TYR K 226 ARG 0.008 0.001 ARG K 475 *********************** 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 610 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 477 time to evaluate : 7.172 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: A 439 TRP cc_start: 0.7928 (t60) cc_final: 0.7657 (t60) REVERT: A 560 LYS cc_start: 0.9345 (pttm) cc_final: 0.9071 (tptt) REVERT: B 473 MET cc_start: 0.8753 (mmm) cc_final: 0.8329 (mtp) REVERT: B 516 MET cc_start: 0.8585 (tmm) cc_final: 0.8324 (tmm) REVERT: C 564 MET cc_start: 0.8512 (mpp) cc_final: 0.7869 (ttt) REVERT: D 468 ILE cc_start: 0.8233 (tp) cc_final: 0.7883 (tp) REVERT: E 564 MET cc_start: 0.9138 (mmp) cc_final: 0.8597 (ptm) REVERT: F 1 MET cc_start: 0.7542 (ppp) cc_final: 0.7037 (ptt) REVERT: F 198 MET cc_start: 0.7849 (tpt) cc_final: 0.7623 (tpt) REVERT: F 582 GLU cc_start: 0.7607 (tt0) cc_final: 0.7372 (tt0) REVERT: G 564 MET cc_start: 0.7796 (OUTLIER) cc_final: 0.7378 (tpp) REVERT: I 577 LYS cc_start: 0.8872 (tppt) cc_final: 0.8497 (mmtm) REVERT: J 198 MET cc_start: 0.7059 (ttt) cc_final: 0.6811 (ttt) REVERT: J 564 MET cc_start: 0.9151 (mmp) cc_final: 0.8938 (pmm) REVERT: K 152 ASP cc_start: 0.8706 (m-30) cc_final: 0.8501 (m-30) REVERT: K 582 GLU cc_start: 0.8076 (tt0) cc_final: 0.7651 (tt0) REVERT: M 356 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8452 (tm-30) REVERT: N 196 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8884 (mmm) REVERT: N 233 MET cc_start: 0.8981 (mmm) cc_final: 0.8702 (mmp) REVERT: N 389 MET cc_start: 0.7708 (tmm) cc_final: 0.7313 (tmm) REVERT: N 411 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8309 (tt) REVERT: N 543 MET cc_start: 0.8744 (mmp) cc_final: 0.8524 (mmp) outliers start: 133 outliers final: 60 residues processed: 576 average time/residue: 0.7243 time to fit residues: 733.5282 Evaluate side-chains 443 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 379 time to evaluate : 7.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 326 SER 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 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 554 ASP 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 539 LEU Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 277 SER Chi-restraints excluded: chain F residue 278 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 G residue 539 LEU Chi-restraints excluded: chain G residue 564 MET Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 447 THR Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain H residue 529 ILE 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 356 GLU Chi-restraints excluded: chain J residue 58 LEU 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 346 VAL Chi-restraints excluded: chain J residue 364 ILE Chi-restraints excluded: chain J residue 451 GLU Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 334 LYS 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 154 CYS Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 346 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain L residue 569 LEU Chi-restraints excluded: chain M residue 346 VAL 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 196 MET Chi-restraints excluded: chain N residue 411 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 717 optimal weight: 8.9990 chunk 545 optimal weight: 0.9980 chunk 376 optimal weight: 0.5980 chunk 80 optimal weight: 10.0000 chunk 346 optimal weight: 0.7980 chunk 487 optimal weight: 0.6980 chunk 728 optimal weight: 7.9990 chunk 771 optimal weight: 5.9990 chunk 380 optimal weight: 4.9990 chunk 690 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- 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** G 208 HIS G 240 HIS ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 496 ASN H 550 ASN I 338 ASN I 550 ASN ** L 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 67144 Z= 0.281 Angle : 0.527 12.060 90986 Z= 0.275 Chirality : 0.044 0.163 9982 Planarity : 0.003 0.041 11676 Dihedral : 4.103 18.821 8764 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.57 % Allowed : 10.30 % Favored : 88.13 % 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: 0.44 (0.10), residues: 8050 helix: 0.99 (0.10), residues: 2856 sheet: -0.58 (0.17), residues: 994 loop : 0.16 (0.10), residues: 4200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 192 HIS 0.005 0.001 HIS D 588 PHE 0.029 0.001 PHE J 506 TYR 0.020 0.001 TYR B 471 ARG 0.005 0.000 ARG I 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 519 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 405 time to evaluate : 7.454 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 560 LYS cc_start: 0.9338 (pttm) cc_final: 0.9074 (tptt) REVERT: B 83 MET cc_start: 0.7388 (mpp) cc_final: 0.7009 (mpp) REVERT: B 473 MET cc_start: 0.8723 (mmm) cc_final: 0.8310 (mtp) REVERT: C 564 MET cc_start: 0.8638 (mpp) cc_final: 0.7986 (ttt) REVERT: D 359 ASP cc_start: 0.8702 (m-30) cc_final: 0.8491 (m-30) REVERT: D 465 MET cc_start: 0.8602 (ptp) cc_final: 0.8395 (ptp) REVERT: D 564 MET cc_start: 0.8972 (ptm) cc_final: 0.8537 (pmm) REVERT: D 587 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7848 (tp30) REVERT: E 564 MET cc_start: 0.9157 (mmp) cc_final: 0.8622 (ptt) REVERT: F 1 MET cc_start: 0.7395 (ppp) cc_final: 0.6929 (ptt) REVERT: H 110 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: I 382 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8252 (mm) REVERT: I 577 LYS cc_start: 0.8752 (tppt) cc_final: 0.8350 (mmtm) REVERT: K 152 ASP cc_start: 0.8760 (m-30) cc_final: 0.8518 (m-30) REVERT: L 152 ASP cc_start: 0.8599 (m-30) cc_final: 0.8320 (m-30) REVERT: L 359 ASP cc_start: 0.9051 (m-30) cc_final: 0.8849 (p0) REVERT: M 349 THR cc_start: 0.8128 (OUTLIER) cc_final: 0.7842 (p) REVERT: N 1 MET cc_start: 0.7379 (ppp) cc_final: 0.7074 (ppp) REVERT: N 233 MET cc_start: 0.8923 (mmm) cc_final: 0.8718 (mmp) REVERT: N 389 MET cc_start: 0.7961 (tmm) cc_final: 0.7622 (tmm) REVERT: N 411 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8353 (tt) REVERT: N 543 MET cc_start: 0.8675 (mmp) cc_final: 0.8430 (mmt) outliers start: 114 outliers final: 56 residues processed: 496 average time/residue: 0.7955 time to fit residues: 697.5524 Evaluate side-chains 421 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 361 time to evaluate : 7.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER 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 C residue 550 ASN Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 145 THR 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 554 ASP Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 589 LYS 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 84 GLU Chi-restraints excluded: chain G residue 159 GLU Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 370 LEU 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 J residue 20 VAL 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 357 ILE Chi-restraints excluded: chain J residue 451 GLU 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 20 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 550 ASN Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 407 ILE Chi-restraints excluded: chain N residue 411 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 642 optimal weight: 4.9990 chunk 437 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 574 optimal weight: 0.9980 chunk 318 optimal weight: 3.9990 chunk 658 optimal weight: 0.6980 chunk 533 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 393 optimal weight: 0.9990 chunk 692 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 338 ASN L 240 HIS ** M 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 67144 Z= 0.271 Angle : 0.518 14.307 90986 Z= 0.269 Chirality : 0.044 0.176 9982 Planarity : 0.003 0.041 11676 Dihedral : 4.054 16.828 8764 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.61 % Allowed : 11.14 % Favored : 87.25 % 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: 0.51 (0.10), residues: 8050 helix: 1.09 (0.10), residues: 2856 sheet: -0.49 (0.17), residues: 966 loop : 0.15 (0.10), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 192 HIS 0.004 0.001 HIS D 588 PHE 0.027 0.001 PHE J 506 TYR 0.017 0.001 TYR B 471 ARG 0.006 0.000 ARG I 204 *********************** 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 506 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 389 time to evaluate : 7.576 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: A 560 LYS cc_start: 0.9345 (pttm) cc_final: 0.9101 (tptt) REVERT: B 473 MET cc_start: 0.8742 (mmm) cc_final: 0.8372 (mtp) REVERT: D 564 MET cc_start: 0.8964 (ptm) cc_final: 0.8609 (pmm) REVERT: F 1 MET cc_start: 0.7422 (ppp) cc_final: 0.6984 (ptt) REVERT: G 564 MET cc_start: 0.8146 (pmm) cc_final: 0.7633 (tmm) REVERT: I 57 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8637 (tp30) REVERT: I 382 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (mm) REVERT: L 152 ASP cc_start: 0.8676 (m-30) cc_final: 0.8356 (m-30) REVERT: M 349 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7810 (p) REVERT: M 356 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: M 473 MET cc_start: 0.7950 (mmm) cc_final: 0.7174 (mmm) REVERT: M 564 MET cc_start: 0.8046 (pmm) cc_final: 0.7810 (pmm) REVERT: N 172 ASP cc_start: 0.8788 (m-30) cc_final: 0.8458 (t0) REVERT: N 389 MET cc_start: 0.7964 (tmm) cc_final: 0.7663 (tmm) REVERT: N 411 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8305 (tt) REVERT: N 543 MET cc_start: 0.8635 (mmp) cc_final: 0.8404 (mmt) outliers start: 117 outliers final: 63 residues processed: 484 average time/residue: 0.6009 time to fit residues: 514.0739 Evaluate side-chains 422 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 354 time to evaluate : 5.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 326 SER 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 376 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain C residue 550 ASN 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 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 550 ASN Chi-restraints excluded: chain D residue 554 ASP 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 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 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 505 VAL Chi-restraints excluded: chain I residue 57 GLU 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 J residue 20 VAL Chi-restraints excluded: chain J residue 234 VAL 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 483 VAL Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 253 ILE 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 20 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 505 VAL Chi-restraints excluded: chain L residue 539 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 411 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 259 optimal weight: 1.9990 chunk 694 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 452 optimal weight: 3.9990 chunk 190 optimal weight: 0.9990 chunk 772 optimal weight: 2.9990 chunk 640 optimal weight: 0.8980 chunk 357 optimal weight: 0.0070 chunk 64 optimal weight: 10.0000 chunk 255 optimal weight: 0.6980 chunk 405 optimal weight: 5.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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** C 321 ASN ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 ASN M 402 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67144 Z= 0.168 Angle : 0.482 14.420 90986 Z= 0.250 Chirality : 0.043 0.259 9982 Planarity : 0.003 0.041 11676 Dihedral : 3.856 16.489 8764 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.24 % Allowed : 12.05 % Favored : 86.72 % 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: 1.22 (0.10), residues: 2856 sheet: -0.45 (0.17), residues: 966 loop : 0.19 (0.10), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 183 HIS 0.003 0.001 HIS H 442 PHE 0.022 0.001 PHE L 572 TYR 0.014 0.001 TYR G 112 ARG 0.008 0.000 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 498 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 408 time to evaluate : 5.762 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 560 LYS cc_start: 0.9327 (pttm) cc_final: 0.9078 (tptt) REVERT: B 57 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: B 83 MET cc_start: 0.8081 (mpp) cc_final: 0.7733 (mpp) REVERT: B 198 MET cc_start: 0.8736 (tpp) cc_final: 0.8489 (tpt) REVERT: B 473 MET cc_start: 0.8739 (mmm) cc_final: 0.8373 (mtp) REVERT: D 359 ASP cc_start: 0.8681 (m-30) cc_final: 0.8472 (m-30) REVERT: D 564 MET cc_start: 0.8947 (ptm) cc_final: 0.8609 (pmm) REVERT: E 564 MET cc_start: 0.8280 (mpp) cc_final: 0.7724 (ptt) REVERT: F 1 MET cc_start: 0.7257 (ppp) cc_final: 0.6875 (ptt) REVERT: F 128 GLU cc_start: 0.8383 (pm20) cc_final: 0.8155 (pm20) REVERT: G 564 MET cc_start: 0.8301 (pmm) cc_final: 0.7696 (tmm) REVERT: I 382 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8200 (mm) REVERT: I 577 LYS cc_start: 0.8657 (tppt) cc_final: 0.8424 (mmtm) REVERT: J 564 MET cc_start: 0.8366 (pmm) cc_final: 0.7818 (ptt) REVERT: L 152 ASP cc_start: 0.8621 (m-30) cc_final: 0.8310 (m-30) REVERT: M 349 THR cc_start: 0.8190 (OUTLIER) cc_final: 0.7823 (p) REVERT: M 356 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8432 (tm-30) REVERT: M 473 MET cc_start: 0.8172 (mmm) cc_final: 0.7478 (mmm) REVERT: N 172 ASP cc_start: 0.8790 (m-30) cc_final: 0.8463 (t0) REVERT: N 389 MET cc_start: 0.7978 (tmm) cc_final: 0.7701 (tmm) REVERT: N 411 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8315 (tt) outliers start: 90 outliers final: 53 residues processed: 478 average time/residue: 0.5744 time to fit residues: 482.3728 Evaluate side-chains 428 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 370 time to evaluate : 5.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 539 LEU 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 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 550 ASN Chi-restraints excluded: chain D residue 554 ASP 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 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 370 LEU 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 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 J residue 20 VAL Chi-restraints excluded: chain J residue 159 GLU Chi-restraints excluded: chain J residue 234 VAL 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 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 389 MET Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 539 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 N residue 411 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 744 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 439 optimal weight: 2.9990 chunk 563 optimal weight: 1.9990 chunk 436 optimal weight: 0.8980 chunk 649 optimal weight: 0.7980 chunk 431 optimal weight: 0.9990 chunk 769 optimal weight: 0.4980 chunk 481 optimal weight: 0.9990 chunk 468 optimal weight: 4.9990 chunk 355 optimal weight: 0.7980 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** C 321 ASN ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 67144 Z= 0.176 Angle : 0.484 12.920 90986 Z= 0.250 Chirality : 0.043 0.201 9982 Planarity : 0.003 0.042 11676 Dihedral : 3.795 17.978 8764 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.21 % Allowed : 12.60 % Favored : 86.20 % 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: 0.67 (0.10), residues: 8050 helix: 1.27 (0.10), residues: 2856 sheet: -0.40 (0.17), residues: 966 loop : 0.20 (0.10), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 183 HIS 0.003 0.001 HIS G 442 PHE 0.033 0.001 PHE B 472 TYR 0.013 0.001 TYR F 471 ARG 0.006 0.000 ARG F 199 *********************** 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 483 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 395 time to evaluate : 5.722 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 560 LYS cc_start: 0.9338 (pttm) cc_final: 0.9066 (tptt) REVERT: B 57 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7924 (mm-30) REVERT: B 83 MET cc_start: 0.8181 (mpp) cc_final: 0.7791 (mpp) REVERT: B 198 MET cc_start: 0.8745 (tpp) cc_final: 0.8526 (tpt) REVERT: B 465 MET cc_start: 0.7778 (mmm) cc_final: 0.7556 (mmt) REVERT: B 473 MET cc_start: 0.8745 (mmm) cc_final: 0.8340 (mtp) REVERT: D 356 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8444 (pm20) REVERT: D 359 ASP cc_start: 0.8696 (m-30) cc_final: 0.8472 (m-30) REVERT: D 564 MET cc_start: 0.8936 (ptm) cc_final: 0.8608 (pmm) REVERT: E 564 MET cc_start: 0.8300 (mpp) cc_final: 0.7767 (ptt) REVERT: F 1 MET cc_start: 0.7271 (ppp) cc_final: 0.6898 (ptt) REVERT: F 128 GLU cc_start: 0.8350 (pm20) cc_final: 0.8143 (pm20) REVERT: G 159 GLU cc_start: 0.8142 (pm20) cc_final: 0.7914 (pm20) REVERT: G 564 MET cc_start: 0.8339 (pmm) cc_final: 0.7695 (tmm) REVERT: H 144 LYS cc_start: 0.7784 (tptt) cc_final: 0.7548 (tptt) REVERT: I 382 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8255 (mm) REVERT: I 577 LYS cc_start: 0.8633 (tppt) cc_final: 0.8317 (mmtm) REVERT: J 564 MET cc_start: 0.8348 (pmm) cc_final: 0.7800 (ptt) REVERT: L 152 ASP cc_start: 0.8652 (m-30) cc_final: 0.8372 (m-30) REVERT: M 349 THR cc_start: 0.8172 (OUTLIER) cc_final: 0.7784 (p) REVERT: M 356 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8394 (tm-30) REVERT: M 473 MET cc_start: 0.8213 (mmm) cc_final: 0.7574 (mmm) REVERT: N 172 ASP cc_start: 0.8846 (m-30) cc_final: 0.8513 (t0) REVERT: N 389 MET cc_start: 0.8001 (tmm) cc_final: 0.7770 (tmm) REVERT: N 411 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8288 (tt) REVERT: N 590 LEU cc_start: 0.7935 (mm) cc_final: 0.7667 (mm) outliers start: 88 outliers final: 62 residues processed: 467 average time/residue: 0.5981 time to fit residues: 491.2009 Evaluate side-chains 439 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 371 time to evaluate : 6.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU 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 376 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 225 GLN 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 539 LEU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain E residue 268 LEU 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 349 THR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain H residue 203 MET Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 447 THR 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 J residue 159 GLU Chi-restraints excluded: chain J residue 234 VAL 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 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 196 MET Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 389 MET Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 539 LEU Chi-restraints excluded: chain L residue 550 ASN 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 411 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 475 optimal weight: 3.9990 chunk 307 optimal weight: 0.9980 chunk 459 optimal weight: 3.9990 chunk 231 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 149 optimal weight: 0.0570 chunk 488 optimal weight: 0.9990 chunk 524 optimal weight: 5.9990 chunk 380 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 604 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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** D 524 ASN E 388 GLN ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 67144 Z= 0.162 Angle : 0.482 15.401 90986 Z= 0.247 Chirality : 0.043 0.236 9982 Planarity : 0.003 0.042 11676 Dihedral : 3.737 17.403 8764 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.14 % Allowed : 13.02 % Favored : 85.84 % 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: 0.72 (0.10), residues: 8050 helix: 1.30 (0.10), residues: 2856 sheet: -0.33 (0.17), residues: 966 loop : 0.23 (0.10), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 183 HIS 0.003 0.000 HIS G 442 PHE 0.025 0.001 PHE L 572 TYR 0.013 0.001 TYR G 112 ARG 0.005 0.000 ARG I 204 *********************** 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 478 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 395 time to evaluate : 5.897 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: B 57 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7933 (mm-30) REVERT: B 83 MET cc_start: 0.8121 (mpp) cc_final: 0.7709 (mpp) REVERT: B 198 MET cc_start: 0.8767 (tpp) cc_final: 0.8528 (tpt) REVERT: B 349 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7755 (p) REVERT: B 473 MET cc_start: 0.8788 (mmm) cc_final: 0.8393 (mtp) REVERT: D 356 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8412 (pm20) REVERT: D 359 ASP cc_start: 0.8634 (m-30) cc_final: 0.8370 (m-30) REVERT: D 564 MET cc_start: 0.8932 (ptm) cc_final: 0.8594 (pmm) REVERT: E 564 MET cc_start: 0.8319 (mpp) cc_final: 0.7794 (ptt) REVERT: F 1 MET cc_start: 0.7218 (ppp) cc_final: 0.6893 (ptt) REVERT: F 575 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8866 (tptt) REVERT: G 564 MET cc_start: 0.8377 (pmm) cc_final: 0.7712 (tmm) REVERT: I 83 MET cc_start: 0.6849 (mtt) cc_final: 0.6642 (mtt) REVERT: I 382 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8215 (mm) REVERT: I 389 MET cc_start: 0.7679 (ttp) cc_final: 0.7394 (mtp) REVERT: I 577 LYS cc_start: 0.8595 (tppt) cc_final: 0.8261 (mmtt) REVERT: J 564 MET cc_start: 0.8322 (pmm) cc_final: 0.7760 (ptt) REVERT: L 152 ASP cc_start: 0.8562 (m-30) cc_final: 0.8323 (m-30) REVERT: M 356 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8361 (tm-30) REVERT: M 473 MET cc_start: 0.8209 (mmm) cc_final: 0.7180 (mtp) REVERT: N 172 ASP cc_start: 0.8846 (m-30) cc_final: 0.8518 (t0) REVERT: N 411 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8283 (tt) REVERT: N 590 LEU cc_start: 0.7813 (mm) cc_final: 0.7574 (mm) outliers start: 83 outliers final: 58 residues processed: 458 average time/residue: 0.6172 time to fit residues: 497.0827 Evaluate side-chains 434 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 370 time to evaluate : 5.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 CYS Chi-restraints excluded: chain B residue 471 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain D residue 145 THR 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 539 LEU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 124 CYS Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain G residue 558 ILE Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 447 THR 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 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 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 389 MET Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 539 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 253 ILE Chi-restraints excluded: chain N residue 411 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 798 random chunks: chunk 699 optimal weight: 7.9990 chunk 736 optimal weight: 0.9990 chunk 672 optimal weight: 4.9990 chunk 716 optimal weight: 6.9990 chunk 431 optimal weight: 0.9980 chunk 312 optimal weight: 0.8980 chunk 562 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 647 optimal weight: 0.9980 chunk 677 optimal weight: 2.9990 chunk 714 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** A 521 GLN ** D 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.5468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 67144 Z= 0.194 Angle : 0.502 21.048 90986 Z= 0.255 Chirality : 0.043 0.267 9982 Planarity : 0.003 0.042 11676 Dihedral : 3.762 17.217 8764 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.09 % Allowed : 13.17 % Favored : 85.74 % 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: 0.75 (0.10), residues: 8050 helix: 1.32 (0.10), residues: 2856 sheet: -0.33 (0.17), residues: 966 loop : 0.25 (0.10), residues: 4228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP M 180 HIS 0.003 0.001 HIS G 442 PHE 0.025 0.001 PHE H 506 TYR 0.024 0.001 TYR H 471 ARG 0.008 0.000 ARG J 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 461 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 382 time to evaluate : 5.913 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 172 ASP cc_start: 0.9511 (m-30) cc_final: 0.9307 (t0) REVERT: A 473 MET cc_start: 0.8701 (mmm) cc_final: 0.8480 (mtt) REVERT: B 57 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: B 83 MET cc_start: 0.8089 (mpp) cc_final: 0.7684 (mpp) REVERT: B 349 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7765 (p) REVERT: B 473 MET cc_start: 0.8709 (mmm) cc_final: 0.8303 (mtp) REVERT: D 356 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8461 (pm20) REVERT: D 564 MET cc_start: 0.8934 (ptm) cc_final: 0.8551 (pmm) REVERT: F 1 MET cc_start: 0.7291 (ppp) cc_final: 0.6928 (ptt) REVERT: G 564 MET cc_start: 0.8415 (pmm) cc_final: 0.7715 (tmm) REVERT: H 144 LYS cc_start: 0.7769 (tptt) cc_final: 0.7549 (tptt) REVERT: I 382 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8241 (mm) REVERT: I 577 LYS cc_start: 0.8663 (tppt) cc_final: 0.8332 (mmtm) REVERT: L 152 ASP cc_start: 0.8712 (m-30) cc_final: 0.8352 (m-30) REVERT: M 349 THR cc_start: 0.8052 (OUTLIER) cc_final: 0.7660 (p) REVERT: M 356 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8368 (tm-30) REVERT: M 473 MET cc_start: 0.8253 (mmm) cc_final: 0.7255 (mtp) REVERT: N 172 ASP cc_start: 0.8856 (m-30) cc_final: 0.8532 (t0) REVERT: N 590 LEU cc_start: 0.7774 (mm) cc_final: 0.7548 (mm) outliers start: 79 outliers final: 61 residues processed: 443 average time/residue: 0.5947 time to fit residues: 466.9817 Evaluate side-chains 433 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 366 time to evaluate : 5.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU 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 471 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain D residue 145 THR 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 539 LEU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 349 THR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 447 THR 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 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 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 389 MET Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 151 LEU Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 539 LEU Chi-restraints excluded: chain L residue 550 ASN 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 253 ILE Chi-restraints excluded: chain N residue 465 MET 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 470 optimal weight: 0.5980 chunk 757 optimal weight: 10.0000 chunk 462 optimal weight: 5.9990 chunk 359 optimal weight: 1.9990 chunk 526 optimal weight: 0.7980 chunk 795 optimal weight: 0.8980 chunk 731 optimal weight: 2.9990 chunk 633 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 489 optimal weight: 0.9980 chunk 388 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 67144 Z= 0.176 Angle : 0.499 14.358 90986 Z= 0.253 Chirality : 0.043 0.309 9982 Planarity : 0.003 0.056 11676 Dihedral : 3.737 16.851 8764 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.04 % Allowed : 13.13 % Favored : 85.82 % 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: 0.75 (0.10), residues: 8050 helix: 1.30 (0.10), residues: 2870 sheet: -0.31 (0.17), residues: 966 loop : 0.26 (0.10), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP M 180 HIS 0.003 0.001 HIS L 207 PHE 0.026 0.001 PHE L 572 TYR 0.017 0.001 TYR G 471 ARG 0.005 0.000 ARG L 199 ********************** 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 468 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 392 time to evaluate : 5.830 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 473 MET cc_start: 0.8740 (mmm) cc_final: 0.8498 (mtt) REVERT: B 57 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7960 (mm-30) REVERT: B 83 MET cc_start: 0.8098 (mpp) cc_final: 0.7684 (mpp) REVERT: B 349 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7729 (p) REVERT: B 473 MET cc_start: 0.8718 (mmm) cc_final: 0.8325 (mtp) REVERT: D 356 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8436 (pm20) REVERT: D 564 MET cc_start: 0.8898 (ptm) cc_final: 0.8526 (pmm) REVERT: F 1 MET cc_start: 0.7253 (ppp) cc_final: 0.6905 (ptt) REVERT: G 564 MET cc_start: 0.8429 (pmm) cc_final: 0.7830 (tmm) REVERT: H 144 LYS cc_start: 0.7762 (tptt) cc_final: 0.7543 (tptt) REVERT: I 382 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8218 (mm) REVERT: I 389 MET cc_start: 0.7674 (ttp) cc_final: 0.7414 (mtp) REVERT: I 577 LYS cc_start: 0.8660 (tppt) cc_final: 0.8337 (mmtm) REVERT: L 152 ASP cc_start: 0.8641 (m-30) cc_final: 0.8283 (m-30) REVERT: M 349 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7659 (p) REVERT: M 356 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8369 (tm-30) REVERT: M 473 MET cc_start: 0.8229 (mmm) cc_final: 0.7248 (mtp) REVERT: N 172 ASP cc_start: 0.8867 (m-30) cc_final: 0.8506 (t0) outliers start: 76 outliers final: 63 residues processed: 447 average time/residue: 0.5756 time to fit residues: 457.8286 Evaluate side-chains 443 residues out of total 7280 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 374 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 SER Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 57 GLU 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 471 TYR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain C residue 550 ASN Chi-restraints excluded: chain D residue 145 THR 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 539 LEU Chi-restraints excluded: chain D residue 554 ASP Chi-restraints excluded: chain D residue 567 LEU Chi-restraints excluded: chain D residue 585 LEU Chi-restraints excluded: chain E residue 550 ASN Chi-restraints excluded: chain E residue 554 ASP Chi-restraints excluded: chain F residue 221 THR 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 82 GLU Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 389 MET Chi-restraints excluded: chain G residue 465 MET Chi-restraints excluded: chain H residue 278 ILE Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 447 THR 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 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 357 ILE Chi-restraints excluded: chain J residue 483 VAL Chi-restraints excluded: chain K residue 253 ILE Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 389 MET Chi-restraints excluded: chain K residue 550 ASN Chi-restraints excluded: chain K residue 569 LEU Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 169 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain L residue 539 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 253 ILE Chi-restraints excluded: chain N residue 465 MET 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 502 optimal weight: 2.9990 chunk 674 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 583 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 634 optimal weight: 3.9990 chunk 265 optimal weight: 0.5980 chunk 651 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 402 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 = 0.3617 r_free = 0.3617 target = 0.081260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.054162 restraints weight = 203162.574| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.93 r_work: 0.2839 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 67144 Z= 0.179 Angle : 0.500 14.109 90986 Z= 0.255 Chirality : 0.043 0.308 9982 Planarity : 0.003 0.041 11676 Dihedral : 3.737 22.386 8764 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.06 % Allowed : 13.19 % Favored : 85.76 % 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: 1.30 (0.10), residues: 2870 sheet: -0.30 (0.17), residues: 966 loop : 0.27 (0.10), residues: 4214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.001 TRP M 180 HIS 0.003 0.001 HIS I 552 PHE 0.026 0.001 PHE E 506 TYR 0.021 0.001 TYR G 471 ARG 0.005 0.000 ARG L 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14376.24 seconds wall clock time: 277 minutes 37.62 seconds (16657.62 seconds total)