Starting phenix.real_space_refine on Tue Dec 31 01:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.map" model { file = "/net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wuc_37853/12_2024/8wuc_37853.cif" } resolution = 2.5 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= 0.015 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: 6 Type Number sf(0) Gaussians P 28 5.49 5 Mg 14 5.21 5 S 252 5.16 5 C 40712 2.51 5 N 11424 2.21 5 O 12908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 209 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 65338 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "a" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "b" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "C" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "c" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "d" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "E" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "e" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "f" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "G" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "g" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "H" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "h" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "I" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "i" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "J" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "j" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "K" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "k" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "L" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "l" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "M" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "m" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "N" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3923 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "n" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 716 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.63, per 1000 atoms: 0.44 Number of scatterers: 65338 At special positions: 0 Unit cell: (152.04, 151.2, 256.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 252 16.00 P 28 15.00 Mg 14 11.99 O 12908 8.00 N 11424 7.00 C 40712 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: 12.52 Conformation dependent library (CDL) restraints added in 6.7 seconds 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15820 Finding SS restraints... Secondary structure from input PDB file: 281 helices and 110 sheets defined 50.6% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.21 Creating SS restraints... Processing helix chain 'A' and resid 9 through 29 removed outlier: 3.713A pdb=" N ARG A 15 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 removed outlier: 3.674A pdb=" N GLU A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 85 removed outlier: 3.574A pdb=" N GLY A 70 " --> pdb=" O PHE A 66 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 109 removed outlier: 3.747A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 135 Processing helix chain 'A' and resid 140 through 152 Processing helix chain 'A' and resid 155 through 170 Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 229 through 244 removed outlier: 4.147A pdb=" N LEU A 233 " --> pdb=" O ASN A 229 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.542A pdb=" N LYS A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.521A pdb=" N LEU A 259 " --> pdb=" O GLU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 297 removed outlier: 3.605A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 356 removed outlier: 3.741A pdb=" N GLU A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 374 removed outlier: 3.504A pdb=" N ARG A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 410 Processing helix chain 'A' and resid 416 through 429 Processing helix chain 'A' and resid 435 through 449 Processing helix chain 'A' and resid 450 through 461 Processing helix chain 'A' and resid 463 through 474 Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.517A pdb=" N LEU A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR A 518 " --> pdb=" O GLY A 514 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 80 Processing helix chain 'a' and resid 86 through 90 removed outlier: 3.568A pdb=" N ASP a 89 " --> pdb=" O ARG a 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 29 removed outlier: 3.597A pdb=" N THR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 59 removed outlier: 3.696A pdb=" N GLU B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 85 removed outlier: 3.553A pdb=" N GLY B 70 " --> pdb=" O PHE B 66 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 77 " --> pdb=" O MET B 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 109 removed outlier: 3.769A pdb=" N LYS B 105 " --> pdb=" O ARG B 101 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 106 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 removed outlier: 3.570A pdb=" N LYS B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA B 243 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 282 through 297 removed outlier: 3.628A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.627A pdb=" N GLU B 354 " --> pdb=" O ARG B 350 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 355 " --> pdb=" O VAL B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 374 Processing helix chain 'B' and resid 385 through 410 Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 450 through 461 Processing helix chain 'B' and resid 463 through 474 Processing helix chain 'B' and resid 499 through 518 removed outlier: 3.537A pdb=" N LEU B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR B 518 " --> pdb=" O GLY B 514 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 80 Processing helix chain 'C' and resid 9 through 29 removed outlier: 3.580A pdb=" N THR C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.682A pdb=" N GLU C 59 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 85 removed outlier: 3.670A pdb=" N GLY C 70 " --> pdb=" O PHE C 66 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 109 removed outlier: 3.766A pdb=" N LYS C 105 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 135 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'C' and resid 155 through 170 Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 229 through 244 removed outlier: 4.220A pdb=" N LEU C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Proline residue: C 235 - end of helix removed outlier: 3.504A pdb=" N GLN C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 268 removed outlier: 3.577A pdb=" N LEU C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 297 removed outlier: 3.638A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 317 Processing helix chain 'C' and resid 338 through 354 removed outlier: 3.614A pdb=" N GLU C 354 " --> pdb=" O ARG C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 374 removed outlier: 3.794A pdb=" N ARG C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 363 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 410 Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 435 through 449 removed outlier: 3.523A pdb=" N VAL C 445 " --> pdb=" O GLY C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 461 Processing helix chain 'C' and resid 463 through 474 Processing helix chain 'C' and resid 499 through 518 removed outlier: 3.525A pdb=" N LEU C 515 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) Processing helix chain 'c' and resid 76 through 80 removed outlier: 3.735A pdb=" N GLY c 79 " --> pdb=" O LYS c 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 removed outlier: 3.584A pdb=" N THR D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 removed outlier: 3.677A pdb=" N GLU D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 85 removed outlier: 3.548A pdb=" N GLY D 70 " --> pdb=" O PHE D 66 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU D 76 " --> pdb=" O GLN D 72 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 77 " --> pdb=" O MET D 73 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 78 " --> pdb=" O VAL D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 109 removed outlier: 3.737A pdb=" N LYS D 105 " --> pdb=" O ARG D 101 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 135 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 201 through 205 Processing helix chain 'D' and resid 233 through 244 Processing helix chain 'D' and resid 256 through 268 Processing helix chain 'D' and resid 282 through 297 removed outlier: 3.591A pdb=" N LYS D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.758A pdb=" N GLU D 355 " --> pdb=" O VAL D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 374 removed outlier: 3.637A pdb=" N ARG D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 410 Processing helix chain 'D' and resid 416 through 429 Processing helix chain 'D' and resid 435 through 449 Processing helix chain 'D' and resid 450 through 461 Processing helix chain 'D' and resid 463 through 474 Processing helix chain 'D' and resid 499 through 518 removed outlier: 3.541A pdb=" N LEU D 515 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR D 518 " --> pdb=" O GLY D 514 " (cutoff:3.500A) Processing helix chain 'd' and resid 76 through 80 removed outlier: 3.727A pdb=" N GLY d 79 " --> pdb=" O LYS d 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 29 removed outlier: 3.676A pdb=" N ARG E 15 " --> pdb=" O SER E 11 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 58 Processing helix chain 'E' and resid 64 through 85 removed outlier: 3.520A pdb=" N GLY E 70 " --> pdb=" O PHE E 66 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 109 removed outlier: 3.729A pdb=" N LYS E 105 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N TYR E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 135 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 155 through 170 Processing helix chain 'E' and resid 201 through 205 Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.617A pdb=" N GLN E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 282 through 297 removed outlier: 3.589A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 354 removed outlier: 3.626A pdb=" N GLU E 354 " --> pdb=" O ARG E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 374 removed outlier: 4.055A pdb=" N ARG E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 363 " --> pdb=" O ASP E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 410 Processing helix chain 'E' and resid 416 through 429 Processing helix chain 'E' and resid 435 through 449 Processing helix chain 'E' and resid 450 through 461 Processing helix chain 'E' and resid 463 through 474 Processing helix chain 'E' and resid 490 through 494 Processing helix chain 'E' and resid 499 through 518 removed outlier: 3.567A pdb=" N LEU E 515 " --> pdb=" O SER E 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 518 " --> pdb=" O GLY E 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 29 removed outlier: 3.679A pdb=" N ARG F 15 " --> pdb=" O SER F 11 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 59 removed outlier: 3.743A pdb=" N GLU F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 85 removed outlier: 3.764A pdb=" N GLY F 70 " --> pdb=" O PHE F 66 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL F 77 " --> pdb=" O MET F 73 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 78 " --> pdb=" O VAL F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 109 removed outlier: 3.757A pdb=" N LYS F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR F 106 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 135 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 155 through 170 Processing helix chain 'F' and resid 201 through 205 Processing helix chain 'F' and resid 232 through 244 removed outlier: 4.647A pdb=" N VAL F 236 " --> pdb=" O ASP F 232 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 255 through 269 removed outlier: 3.529A pdb=" N LEU F 259 " --> pdb=" O GLU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 removed outlier: 3.634A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 356 removed outlier: 3.543A pdb=" N GLU F 355 " --> pdb=" O VAL F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 removed outlier: 3.644A pdb=" N ARG F 362 " --> pdb=" O SER F 358 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU F 363 " --> pdb=" O ASP F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 410 Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'F' and resid 435 through 449 Processing helix chain 'F' and resid 450 through 461 Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'F' and resid 499 through 518 removed outlier: 3.559A pdb=" N LEU F 515 " --> pdb=" O SER F 511 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR F 518 " --> pdb=" O GLY F 514 " (cutoff:3.500A) Processing helix chain 'f' and resid 76 through 80 removed outlier: 3.787A pdb=" N GLY f 79 " --> pdb=" O LYS f 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.640A pdb=" N ARG G 15 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 59 removed outlier: 3.640A pdb=" N GLU G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 85 removed outlier: 3.613A pdb=" N GLY G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 109 removed outlier: 3.745A pdb=" N LYS G 105 " --> pdb=" O ARG G 101 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR G 106 " --> pdb=" O GLU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 135 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 155 through 170 Processing helix chain 'G' and resid 201 through 205 Processing helix chain 'G' and resid 233 through 244 removed outlier: 3.624A pdb=" N GLN G 239 " --> pdb=" O PRO G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 255 through 268 removed outlier: 3.569A pdb=" N LEU G 259 " --> pdb=" O GLU G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 282 through 297 removed outlier: 3.629A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 354 removed outlier: 3.730A pdb=" N GLU G 354 " --> pdb=" O ARG G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 358 through 374 removed outlier: 3.757A pdb=" N ARG G 362 " --> pdb=" O SER G 358 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU G 363 " --> pdb=" O ASP G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 410 Processing helix chain 'G' and resid 416 through 430 Processing helix chain 'G' and resid 435 through 449 Processing helix chain 'G' and resid 450 through 461 Processing helix chain 'G' and resid 463 through 474 Processing helix chain 'G' and resid 499 through 518 removed outlier: 3.531A pdb=" N LEU G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR G 518 " --> pdb=" O GLY G 514 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 80 removed outlier: 3.519A pdb=" N GLY g 79 " --> pdb=" O LYS g 76 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU g 80 " --> pdb=" O VAL g 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 76 through 80' Processing helix chain 'H' and resid 9 through 29 removed outlier: 3.553A pdb=" N THR H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 58 Processing helix chain 'H' and resid 64 through 85 removed outlier: 3.921A pdb=" N GLY H 70 " --> pdb=" O PHE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 109 removed outlier: 3.749A pdb=" N LYS H 105 " --> pdb=" O ARG H 101 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 135 Processing helix chain 'H' and resid 140 through 152 Processing helix chain 'H' and resid 155 through 170 Processing helix chain 'H' and resid 201 through 205 Processing helix chain 'H' and resid 229 through 243 removed outlier: 4.233A pdb=" N LEU H 233 " --> pdb=" O ASN H 229 " (cutoff:3.500A) Proline residue: H 235 - end of helix Processing helix chain 'H' and resid 255 through 268 Processing helix chain 'H' and resid 282 through 297 removed outlier: 3.665A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 356 removed outlier: 3.588A pdb=" N GLU H 354 " --> pdb=" O ARG H 350 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU H 355 " --> pdb=" O VAL H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 358 through 374 Processing helix chain 'H' and resid 385 through 410 Processing helix chain 'H' and resid 416 through 430 Processing helix chain 'H' and resid 435 through 449 Processing helix chain 'H' and resid 450 through 461 Processing helix chain 'H' and resid 463 through 474 Processing helix chain 'H' and resid 499 through 518 removed outlier: 3.543A pdb=" N LEU H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR H 518 " --> pdb=" O GLY H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 29 removed outlier: 3.582A pdb=" N THR I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 60 removed outlier: 3.711A pdb=" N GLU I 59 " --> pdb=" O THR I 55 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 85 removed outlier: 3.547A pdb=" N GLY I 70 " --> pdb=" O PHE I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 109 removed outlier: 3.737A pdb=" N LYS I 105 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR I 106 " --> pdb=" O GLU I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 135 Processing helix chain 'I' and resid 140 through 152 Processing helix chain 'I' and resid 155 through 170 Processing helix chain 'I' and resid 201 through 205 Processing helix chain 'I' and resid 232 through 244 removed outlier: 4.726A pdb=" N VAL I 236 " --> pdb=" O ASP I 232 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS I 242 " --> pdb=" O GLU I 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA I 243 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 255 through 268 removed outlier: 3.512A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 282 through 297 removed outlier: 3.605A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 355 removed outlier: 3.604A pdb=" N GLU I 354 " --> pdb=" O ARG I 350 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU I 355 " --> pdb=" O VAL I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 374 removed outlier: 3.913A pdb=" N ARG I 362 " --> pdb=" O SER I 358 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLU I 363 " --> pdb=" O ASP I 359 " (cutoff:3.500A) Processing helix chain 'I' and resid 385 through 410 Processing helix chain 'I' and resid 416 through 430 Processing helix chain 'I' and resid 435 through 449 removed outlier: 3.504A pdb=" N VAL I 445 " --> pdb=" O GLY I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 460 Processing helix chain 'I' and resid 463 through 474 Processing helix chain 'I' and resid 490 through 494 Processing helix chain 'I' and resid 499 through 518 removed outlier: 3.557A pdb=" N LEU I 515 " --> pdb=" O SER I 511 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR I 518 " --> pdb=" O GLY I 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 29 removed outlier: 3.595A pdb=" N THR J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 60 removed outlier: 3.665A pdb=" N GLU J 59 " --> pdb=" O THR J 55 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 85 removed outlier: 3.609A pdb=" N GLY J 70 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL J 77 " --> pdb=" O MET J 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 109 removed outlier: 3.728A pdb=" N LYS J 105 " --> pdb=" O ARG J 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR J 106 " --> pdb=" O GLU J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 135 Processing helix chain 'J' and resid 140 through 152 Processing helix chain 'J' and resid 155 through 170 Processing helix chain 'J' and resid 201 through 205 Processing helix chain 'J' and resid 232 through 244 removed outlier: 4.607A pdb=" N VAL J 236 " --> pdb=" O ASP J 232 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS J 242 " --> pdb=" O GLU J 238 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA J 243 " --> pdb=" O GLN J 239 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY J 244 " --> pdb=" O VAL J 240 " (cutoff:3.500A) Processing helix chain 'J' and resid 255 through 268 removed outlier: 3.579A pdb=" N LEU J 259 " --> pdb=" O GLU J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 removed outlier: 3.624A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 356 removed outlier: 3.710A pdb=" N GLU J 355 " --> pdb=" O VAL J 351 " (cutoff:3.500A) Processing helix chain 'J' and resid 358 through 374 removed outlier: 4.094A pdb=" N ARG J 362 " --> pdb=" O SER J 358 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU J 363 " --> pdb=" O ASP J 359 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU J 367 " --> pdb=" O GLU J 363 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG J 368 " --> pdb=" O LYS J 364 " (cutoff:3.500A) Processing helix chain 'J' and resid 385 through 410 Processing helix chain 'J' and resid 416 through 429 Processing helix chain 'J' and resid 435 through 449 Processing helix chain 'J' and resid 450 through 461 Processing helix chain 'J' and resid 463 through 474 Processing helix chain 'J' and resid 499 through 518 removed outlier: 3.515A pdb=" N LEU J 515 " --> pdb=" O SER J 511 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR J 518 " --> pdb=" O GLY J 514 " (cutoff:3.500A) Processing helix chain 'j' and resid 76 through 80 Processing helix chain 'K' and resid 9 through 29 removed outlier: 3.580A pdb=" N THR K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 59 removed outlier: 3.607A pdb=" N GLU K 59 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 85 removed outlier: 3.684A pdb=" N GLY K 70 " --> pdb=" O PHE K 66 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 109 removed outlier: 3.771A pdb=" N LYS K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR K 106 " --> pdb=" O GLU K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 135 Processing helix chain 'K' and resid 140 through 152 Processing helix chain 'K' and resid 155 through 170 Processing helix chain 'K' and resid 201 through 205 Processing helix chain 'K' and resid 229 through 244 removed outlier: 3.920A pdb=" N LEU K 233 " --> pdb=" O ASN K 229 " (cutoff:3.500A) Proline residue: K 235 - end of helix removed outlier: 3.531A pdb=" N GLN K 239 " --> pdb=" O PRO K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 268 removed outlier: 3.570A pdb=" N LEU K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 removed outlier: 3.642A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 356 Processing helix chain 'K' and resid 358 through 374 Processing helix chain 'K' and resid 385 through 410 Processing helix chain 'K' and resid 416 through 430 Processing helix chain 'K' and resid 435 through 449 removed outlier: 3.527A pdb=" N VAL K 445 " --> pdb=" O GLY K 441 " (cutoff:3.500A) Processing helix chain 'K' and resid 450 through 461 Processing helix chain 'K' and resid 463 through 474 Processing helix chain 'K' and resid 499 through 518 removed outlier: 3.514A pdb=" N LEU K 515 " --> pdb=" O SER K 511 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR K 518 " --> pdb=" O GLY K 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 29 removed outlier: 3.589A pdb=" N THR L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 59 removed outlier: 3.651A pdb=" N GLU L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 64 through 85 removed outlier: 3.510A pdb=" N GLY L 70 " --> pdb=" O PHE L 66 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL L 77 " --> pdb=" O MET L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 109 removed outlier: 3.752A pdb=" N LYS L 105 " --> pdb=" O ARG L 101 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 135 Processing helix chain 'L' and resid 140 through 152 Processing helix chain 'L' and resid 155 through 170 Processing helix chain 'L' and resid 201 through 205 Processing helix chain 'L' and resid 233 through 244 removed outlier: 3.682A pdb=" N ALA L 243 " --> pdb=" O GLN L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 255 through 268 removed outlier: 3.629A pdb=" N LEU L 259 " --> pdb=" O GLU L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 removed outlier: 3.618A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 356 removed outlier: 3.544A pdb=" N ILE L 342 " --> pdb=" O ASP L 338 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU L 354 " --> pdb=" O ARG L 350 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU L 355 " --> pdb=" O VAL L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 358 through 374 removed outlier: 3.715A pdb=" N ARG L 362 " --> pdb=" O SER L 358 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU L 363 " --> pdb=" O ASP L 359 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS L 364 " --> pdb=" O TYR L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 385 through 410 Processing helix chain 'L' and resid 416 through 429 Processing helix chain 'L' and resid 435 through 449 Processing helix chain 'L' and resid 450 through 461 Processing helix chain 'L' and resid 463 through 474 Processing helix chain 'L' and resid 499 through 518 removed outlier: 3.519A pdb=" N LEU L 515 " --> pdb=" O SER L 511 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR L 518 " --> pdb=" O GLY L 514 " (cutoff:3.500A) Processing helix chain 'l' and resid 76 through 80 removed outlier: 3.648A pdb=" N GLY l 79 " --> pdb=" O LYS l 76 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU l 80 " --> pdb=" O VAL l 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 76 through 80' Processing helix chain 'M' and resid 9 through 29 removed outlier: 3.521A pdb=" N ARG M 15 " --> pdb=" O SER M 11 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 59 removed outlier: 3.658A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 85 removed outlier: 3.548A pdb=" N GLY M 70 " --> pdb=" O PHE M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 88 through 109 removed outlier: 3.739A pdb=" N LYS M 105 " --> pdb=" O ARG M 101 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR M 106 " --> pdb=" O GLU M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 135 Processing helix chain 'M' and resid 140 through 152 Processing helix chain 'M' and resid 155 through 170 Processing helix chain 'M' and resid 201 through 205 Processing helix chain 'M' and resid 229 through 244 removed outlier: 4.211A pdb=" N LEU M 233 " --> pdb=" O ASN M 229 " (cutoff:3.500A) Proline residue: M 235 - end of helix removed outlier: 3.622A pdb=" N LYS M 242 " --> pdb=" O GLU M 238 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA M 243 " --> pdb=" O GLN M 239 " (cutoff:3.500A) Processing helix chain 'M' and resid 256 through 268 Processing helix chain 'M' and resid 282 through 297 removed outlier: 3.601A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 356 removed outlier: 3.695A pdb=" N GLU M 354 " --> pdb=" O ARG M 350 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU M 355 " --> pdb=" O VAL M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 358 through 374 Processing helix chain 'M' and resid 385 through 410 Processing helix chain 'M' and resid 416 through 429 Processing helix chain 'M' and resid 435 through 449 Processing helix chain 'M' and resid 450 through 461 Processing helix chain 'M' and resid 463 through 474 Processing helix chain 'M' and resid 499 through 518 removed outlier: 3.540A pdb=" N LEU M 515 " --> pdb=" O SER M 511 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR M 518 " --> pdb=" O GLY M 514 " (cutoff:3.500A) Processing helix chain 'm' and resid 76 through 80 removed outlier: 3.753A pdb=" N GLY m 79 " --> pdb=" O LYS m 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU m 80 " --> pdb=" O VAL m 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 76 through 80' Processing helix chain 'm' and resid 86 through 90 removed outlier: 3.655A pdb=" N ASP m 89 " --> pdb=" O ARG m 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 29 removed outlier: 3.563A pdb=" N ARG N 15 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR N 29 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 59 removed outlier: 3.631A pdb=" N GLU N 59 " --> pdb=" O THR N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 85 removed outlier: 3.618A pdb=" N GLY N 70 " --> pdb=" O PHE N 66 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL N 77 " --> pdb=" O MET N 73 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 78 " --> pdb=" O VAL N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 109 removed outlier: 3.729A pdb=" N LYS N 105 " --> pdb=" O ARG N 101 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR N 106 " --> pdb=" O GLU N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 135 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 155 through 170 Processing helix chain 'N' and resid 201 through 205 Processing helix chain 'N' and resid 229 through 244 removed outlier: 4.095A pdb=" N LEU N 233 " --> pdb=" O ASN N 229 " (cutoff:3.500A) Proline residue: N 235 - end of helix removed outlier: 3.608A pdb=" N LYS N 242 " --> pdb=" O GLU N 238 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA N 243 " --> pdb=" O GLN N 239 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY N 244 " --> pdb=" O VAL N 240 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 268 Processing helix chain 'N' and resid 282 through 297 removed outlier: 3.613A pdb=" N LYS N 286 " --> pdb=" O GLY N 282 " (cutoff:3.500A) Processing helix chain 'N' and resid 338 through 354 removed outlier: 3.575A pdb=" N GLU N 354 " --> pdb=" O ARG N 350 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 374 removed outlier: 3.763A pdb=" N ARG N 362 " --> pdb=" O SER N 358 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU N 363 " --> pdb=" O ASP N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 385 through 410 Processing helix chain 'N' and resid 416 through 430 Processing helix chain 'N' and resid 435 through 449 Processing helix chain 'N' and resid 450 through 461 Processing helix chain 'N' and resid 463 through 474 Processing helix chain 'N' and resid 499 through 518 removed outlier: 3.568A pdb=" N LEU N 515 " --> pdb=" O SER N 511 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR N 518 " --> pdb=" O GLY N 514 " (cutoff:3.500A) Processing helix chain 'n' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.078A pdb=" N ASN G 37 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N CYS A 521 " --> pdb=" O ASN G 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 6.925A pdb=" N ASN A 37 " --> pdb=" O CYS B 521 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N ILE B 523 " --> pdb=" O ASN A 37 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 39 " --> pdb=" O ILE B 523 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N GLU B 525 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179 removed outlier: 6.292A pdb=" N VAL A 174 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE A 379 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A 176 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N VAL A 381 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLU A 178 " --> pdb=" O VAL A 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 194 Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.313A pdb=" N TYR A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 250 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 277 removed outlier: 6.313A pdb=" N TYR A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE A 250 " --> pdb=" O TYR A 219 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413 Processing sheet with id=AA8, first strand: chain 'A' and resid 478 through 481 Processing sheet with id=AA9, first strand: chain 'a' and resid 3 through 5 removed outlier: 4.115A pdb=" N LYS b 64 " --> pdb=" O ILE b 94 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL b 11 " --> pdb=" O LEU b 41 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N VAL b 43 " --> pdb=" O ARG b 9 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ARG b 9 " --> pdb=" O VAL b 43 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU b 82 " --> pdb=" O VAL b 75 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'a' and resid 73 through 75 removed outlier: 4.100A pdb=" N LEU a 82 " --> pdb=" O VAL a 75 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA a 42 " --> pdb=" O VAL a 11 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS a 13 " --> pdb=" O VAL a 40 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL a 40 " --> pdb=" O LYS a 13 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS a 64 " --> pdb=" O ILE a 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 48 through 49 removed outlier: 4.143A pdb=" N LEU a 49 " --> pdb=" O GLY a 52 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 48 through 50 removed outlier: 6.709A pdb=" N ASN B 37 " --> pdb=" O CYS C 521 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE C 523 " --> pdb=" O ASN B 37 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B 39 " --> pdb=" O ILE C 523 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLU C 525 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.280A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 193 through 194 Processing sheet with id=AB6, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.139A pdb=" N LEU B 247 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 250 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.139A pdb=" N LEU B 247 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N TYR B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 250 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AB9, first strand: chain 'B' and resid 478 through 481 Processing sheet with id=AC1, first strand: chain 'b' and resid 3 through 5 removed outlier: 3.638A pdb=" N ALA c 92 " --> pdb=" O LEU c 66 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS c 64 " --> pdb=" O ILE c 94 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL c 11 " --> pdb=" O LEU c 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU c 82 " --> pdb=" O VAL c 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.838A pdb=" N ASN C 37 " --> pdb=" O CYS D 521 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ILE D 523 " --> pdb=" O ASN C 37 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL C 39 " --> pdb=" O ILE D 523 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N GLU D 525 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 174 through 179 removed outlier: 6.288A pdb=" N VAL C 174 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE C 379 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 176 " --> pdb=" O ILE C 379 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL C 381 " --> pdb=" O THR C 176 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLU C 178 " --> pdb=" O VAL C 381 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 193 through 194 Processing sheet with id=AC5, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.183A pdb=" N LEU C 247 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE C 250 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE C 301 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU C 222 " --> pdb=" O ILE C 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.183A pdb=" N LEU C 247 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL C 276 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE C 249 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N TYR C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE C 250 " --> pdb=" O TYR C 219 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AC8, first strand: chain 'C' and resid 478 through 481 Processing sheet with id=AC9, first strand: chain 'c' and resid 3 through 5 removed outlier: 4.229A pdb=" N LYS d 64 " --> pdb=" O ILE d 94 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL d 40 " --> pdb=" O LYS d 13 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LYS d 13 " --> pdb=" O VAL d 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA d 42 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU d 82 " --> pdb=" O VAL d 75 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 48 through 50 removed outlier: 6.931A pdb=" N ASN D 37 " --> pdb=" O CYS E 521 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ILE E 523 " --> pdb=" O ASN D 37 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL D 39 " --> pdb=" O ILE E 523 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLU E 525 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 174 through 179 removed outlier: 6.301A pdb=" N VAL D 174 " --> pdb=" O ALA D 377 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE D 379 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N THR D 176 " --> pdb=" O ILE D 379 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL D 381 " --> pdb=" O THR D 176 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU D 178 " --> pdb=" O VAL D 381 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 193 through 194 Processing sheet with id=AD4, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.112A pdb=" N LEU D 247 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL D 276 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ILE D 249 " --> pdb=" O VAL D 276 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE D 250 " --> pdb=" O TYR D 219 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 411 through 413 Processing sheet with id=AD6, first strand: chain 'D' and resid 478 through 481 Processing sheet with id=AD7, first strand: chain 'd' and resid 3 through 5 removed outlier: 3.648A pdb=" N ALA e 92 " --> pdb=" O LEU e 66 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LYS e 64 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL e 11 " --> pdb=" O LEU e 41 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL e 43 " --> pdb=" O ARG e 9 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ARG e 9 " --> pdb=" O VAL e 43 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU e 82 " --> pdb=" O VAL e 75 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.779A pdb=" N ASN E 37 " --> pdb=" O CYS F 521 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ILE F 523 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL E 39 " --> pdb=" O ILE F 523 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLU F 525 " --> pdb=" O VAL E 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 174 through 179 removed outlier: 6.313A pdb=" N VAL E 174 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE E 379 " --> pdb=" O VAL E 174 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR E 176 " --> pdb=" O ILE E 379 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N VAL E 381 " --> pdb=" O THR E 176 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLU E 178 " --> pdb=" O VAL E 381 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 193 through 194 Processing sheet with id=AE2, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.152A pdb=" N LEU E 247 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE E 250 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'E' and resid 273 through 277 removed outlier: 6.152A pdb=" N LEU E 247 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL E 276 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ILE E 249 " --> pdb=" O VAL E 276 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ILE E 250 " --> pdb=" O TYR E 219 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 411 through 413 Processing sheet with id=AE5, first strand: chain 'E' and resid 478 through 481 Processing sheet with id=AE6, first strand: chain 'e' and resid 3 through 5 removed outlier: 4.224A pdb=" N LYS f 64 " --> pdb=" O ILE f 94 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL f 11 " --> pdb=" O LEU f 41 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N VAL f 43 " --> pdb=" O ARG f 9 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ARG f 9 " --> pdb=" O VAL f 43 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 48 through 50 removed outlier: 6.836A pdb=" N ASN F 37 " --> pdb=" O CYS G 521 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N ILE G 523 " --> pdb=" O ASN F 37 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL F 39 " --> pdb=" O ILE G 523 " (cutoff:3.500A) removed outlier: 8.518A pdb=" N GLU G 525 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 174 through 179 removed outlier: 6.255A pdb=" N VAL F 174 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE F 379 " --> pdb=" O VAL F 174 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N THR F 176 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N VAL F 381 " --> pdb=" O THR F 176 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU F 178 " --> pdb=" O VAL F 381 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 193 through 194 Processing sheet with id=AF1, first strand: chain 'F' and resid 273 through 277 removed outlier: 6.201A pdb=" N LEU F 247 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N VAL F 276 " --> pdb=" O LEU F 247 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE F 249 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE F 250 " --> pdb=" O TYR F 219 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 411 through 413 Processing sheet with id=AF3, first strand: chain 'F' and resid 478 through 481 Processing sheet with id=AF4, first strand: chain 'f' and resid 3 through 5 removed outlier: 3.619A pdb=" N ALA g 92 " --> pdb=" O LEU g 66 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS g 64 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL g 11 " --> pdb=" O LEU g 41 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N VAL g 43 " --> pdb=" O ARG g 9 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG g 9 " --> pdb=" O VAL g 43 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU g 82 " --> pdb=" O VAL g 75 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 174 through 179 removed outlier: 6.260A pdb=" N VAL G 174 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE G 379 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR G 176 " --> pdb=" O ILE G 379 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N VAL G 381 " --> pdb=" O THR G 176 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLU G 178 " --> pdb=" O VAL G 381 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 193 through 194 Processing sheet with id=AF7, first strand: chain 'G' and resid 273 through 277 removed outlier: 6.084A pdb=" N LEU G 247 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N VAL G 276 " --> pdb=" O LEU G 247 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE G 249 " --> pdb=" O VAL G 276 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N TYR G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ILE G 250 " --> pdb=" O TYR G 219 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 411 through 413 Processing sheet with id=AF9, first strand: chain 'G' and resid 478 through 481 Processing sheet with id=AG1, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.092A pdb=" N ASN I 37 " --> pdb=" O THR H 519 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N CYS H 521 " --> pdb=" O ASN I 37 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 48 through 50 removed outlier: 6.765A pdb=" N ASN H 37 " --> pdb=" O CYS N 521 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE N 523 " --> pdb=" O ASN H 37 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL H 39 " --> pdb=" O ILE N 523 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N GLU N 525 " --> pdb=" O VAL H 39 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 174 through 179 removed outlier: 6.281A pdb=" N VAL H 174 " --> pdb=" O ALA H 377 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE H 379 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR H 176 " --> pdb=" O ILE H 379 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL H 381 " --> pdb=" O THR H 176 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N GLU H 178 " --> pdb=" O VAL H 381 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 193 through 194 Processing sheet with id=AG5, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.246A pdb=" N LEU H 247 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE H 250 " --> pdb=" O TYR H 219 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'H' and resid 273 through 277 removed outlier: 6.246A pdb=" N LEU H 247 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL H 276 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE H 249 " --> pdb=" O VAL H 276 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE H 250 " --> pdb=" O TYR H 219 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 411 through 413 Processing sheet with id=AG8, first strand: chain 'H' and resid 478 through 481 Processing sheet with id=AG9, first strand: chain 'h' and resid 3 through 5 removed outlier: 3.629A pdb=" N ALA n 92 " --> pdb=" O LEU n 66 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 64 " --> pdb=" O ILE n 94 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL n 11 " --> pdb=" O LEU n 41 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL n 43 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG n 9 " --> pdb=" O VAL n 43 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU n 82 " --> pdb=" O VAL n 75 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'h' and resid 73 through 75 removed outlier: 3.708A pdb=" N LEU h 82 " --> pdb=" O VAL h 75 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ARG h 9 " --> pdb=" O VAL h 43 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N VAL h 43 " --> pdb=" O ARG h 9 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N VAL h 11 " --> pdb=" O LEU h 41 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU h 39 " --> pdb=" O LYS h 13 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS h 64 " --> pdb=" O ILE h 94 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.123A pdb=" N ASN J 37 " --> pdb=" O THR I 519 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS I 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 174 through 179 removed outlier: 6.308A pdb=" N VAL I 174 " --> pdb=" O ALA I 377 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ILE I 379 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR I 176 " --> pdb=" O ILE I 379 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL I 381 " --> pdb=" O THR I 176 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU I 178 " --> pdb=" O VAL I 381 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 193 through 194 Processing sheet with id=AH5, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.116A pdb=" N LEU I 247 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE I 250 " --> pdb=" O TYR I 219 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'I' and resid 273 through 277 removed outlier: 6.116A pdb=" N LEU I 247 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL I 276 " --> pdb=" O LEU I 247 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE I 249 " --> pdb=" O VAL I 276 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N TYR I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ILE I 250 " --> pdb=" O TYR I 219 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'I' and resid 411 through 413 Processing sheet with id=AH8, first strand: chain 'I' and resid 478 through 481 Processing sheet with id=AH9, first strand: chain 'i' and resid 73 through 75 removed outlier: 3.988A pdb=" N LEU i 82 " --> pdb=" O VAL i 75 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ARG i 9 " --> pdb=" O VAL i 43 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N VAL i 43 " --> pdb=" O ARG i 9 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL i 11 " --> pdb=" O LEU i 41 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS i 64 " --> pdb=" O ILE i 94 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.078A pdb=" N ASN K 37 " --> pdb=" O THR J 519 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N CYS J 521 " --> pdb=" O ASN K 37 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 174 through 179 removed outlier: 6.306A pdb=" N VAL J 174 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ILE J 379 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N THR J 176 " --> pdb=" O ILE J 379 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL J 381 " --> pdb=" O THR J 176 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU J 178 " --> pdb=" O VAL J 381 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'J' and resid 193 through 194 Processing sheet with id=AI4, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.189A pdb=" N LEU J 247 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE J 250 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI4 Processing sheet with id=AI5, first strand: chain 'J' and resid 273 through 277 removed outlier: 6.189A pdb=" N LEU J 247 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL J 276 " --> pdb=" O LEU J 247 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE J 249 " --> pdb=" O VAL J 276 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N TYR J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ILE J 250 " --> pdb=" O TYR J 219 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 411 through 413 Processing sheet with id=AI7, first strand: chain 'J' and resid 478 through 481 Processing sheet with id=AI8, first strand: chain 'j' and resid 73 through 74 removed outlier: 6.927A pdb=" N ARG j 9 " --> pdb=" O VAL j 43 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL j 43 " --> pdb=" O ARG j 9 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N VAL j 11 " --> pdb=" O LEU j 41 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS j 64 " --> pdb=" O ILE j 94 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.112A pdb=" N ASN L 37 " --> pdb=" O THR K 519 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS K 521 " --> pdb=" O ASN L 37 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'K' and resid 174 through 179 removed outlier: 6.292A pdb=" N VAL K 174 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE K 379 " --> pdb=" O VAL K 174 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR K 176 " --> pdb=" O ILE K 379 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL K 381 " --> pdb=" O THR K 176 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU K 178 " --> pdb=" O VAL K 381 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'K' and resid 193 through 194 Processing sheet with id=AJ3, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.262A pdb=" N LEU K 247 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE K 250 " --> pdb=" O TYR K 219 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'K' and resid 273 through 277 removed outlier: 6.262A pdb=" N LEU K 247 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL K 276 " --> pdb=" O LEU K 247 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE K 249 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE K 250 " --> pdb=" O TYR K 219 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'K' and resid 411 through 413 Processing sheet with id=AJ6, first strand: chain 'K' and resid 478 through 481 Processing sheet with id=AJ7, first strand: chain 'k' and resid 74 through 75 removed outlier: 3.998A pdb=" N LEU k 82 " --> pdb=" O VAL k 75 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA k 42 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS k 13 " --> pdb=" O VAL k 40 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N VAL k 40 " --> pdb=" O LYS k 13 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS k 64 " --> pdb=" O ILE k 94 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.067A pdb=" N ASN M 37 " --> pdb=" O THR L 519 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS L 521 " --> pdb=" O ASN M 37 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'L' and resid 174 through 179 removed outlier: 6.298A pdb=" N VAL L 174 " --> pdb=" O ALA L 377 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ILE L 379 " --> pdb=" O VAL L 174 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR L 176 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL L 381 " --> pdb=" O THR L 176 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU L 178 " --> pdb=" O VAL L 381 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'L' and resid 193 through 194 Processing sheet with id=AK2, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.277A pdb=" N LEU L 247 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE L 250 " --> pdb=" O TYR L 219 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'L' and resid 273 through 277 removed outlier: 6.277A pdb=" N LEU L 247 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N VAL L 276 " --> pdb=" O LEU L 247 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE L 249 " --> pdb=" O VAL L 276 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE L 250 " --> pdb=" O TYR L 219 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'L' and resid 411 through 413 Processing sheet with id=AK5, first strand: chain 'L' and resid 478 through 481 Processing sheet with id=AK6, first strand: chain 'l' and resid 73 through 75 removed outlier: 4.090A pdb=" N LEU l 82 " --> pdb=" O VAL l 75 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N VAL l 11 " --> pdb=" O LEU l 41 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LYS l 64 " --> pdb=" O ILE l 94 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA l 92 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.044A pdb=" N ASN N 37 " --> pdb=" O THR M 519 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS M 521 " --> pdb=" O ASN N 37 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'M' and resid 174 through 179 removed outlier: 6.313A pdb=" N VAL M 174 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ILE M 379 " --> pdb=" O VAL M 174 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR M 176 " --> pdb=" O ILE M 379 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL M 381 " --> pdb=" O THR M 176 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLU M 178 " --> pdb=" O VAL M 381 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'M' and resid 193 through 194 Processing sheet with id=AL1, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.368A pdb=" N TYR M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE M 250 " --> pdb=" O TYR M 219 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'M' and resid 273 through 277 removed outlier: 6.368A pdb=" N TYR M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N ILE M 250 " --> pdb=" O TYR M 219 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'M' and resid 411 through 413 Processing sheet with id=AL4, first strand: chain 'M' and resid 478 through 481 Processing sheet with id=AL5, first strand: chain 'm' and resid 73 through 75 removed outlier: 4.344A pdb=" N LEU m 82 " --> pdb=" O VAL m 75 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA m 42 " --> pdb=" O VAL m 11 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LYS m 13 " --> pdb=" O VAL m 40 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL m 40 " --> pdb=" O LYS m 13 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LYS m 64 " --> pdb=" O ILE m 94 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA m 92 " --> pdb=" O LEU m 66 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'N' and resid 174 through 179 removed outlier: 6.239A pdb=" N VAL N 174 " --> pdb=" O ALA N 377 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ILE N 379 " --> pdb=" O VAL N 174 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR N 176 " --> pdb=" O ILE N 379 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL N 381 " --> pdb=" O THR N 176 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLU N 178 " --> pdb=" O VAL N 381 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'N' and resid 193 through 194 Processing sheet with id=AL8, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.240A pdb=" N LEU N 247 " --> pdb=" O CYS N 274 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE N 250 " --> pdb=" O TYR N 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'N' and resid 273 through 277 removed outlier: 6.240A pdb=" N LEU N 247 " --> pdb=" O CYS N 274 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL N 276 " --> pdb=" O LEU N 247 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE N 249 " --> pdb=" O VAL N 276 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ILE N 250 " --> pdb=" O TYR N 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'N' and resid 411 through 413 Processing sheet with id=AM2, first strand: chain 'N' and resid 478 through 481 3727 hydrogen bonds defined for protein. 10746 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: 31.54 Time building geometry restraints manager: 14.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22524 1.34 - 1.46: 10365 1.46 - 1.58: 32519 1.58 - 1.70: 42 1.70 - 1.82: 462 Bond restraints: 65912 Sorted by residual: bond pdb=" N GLU i 78 " pdb=" CA GLU i 78 " ideal model delta sigma weight residual 1.457 1.484 -0.027 1.29e-02 6.01e+03 4.40e+00 bond pdb=" CB GLU e 16 " pdb=" CG GLU e 16 " ideal model delta sigma weight residual 1.520 1.564 -0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB LYS b 69 " pdb=" CG LYS b 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.09e+00 bond pdb=" CB GLU n 16 " pdb=" CG GLU n 16 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CB GLU l 16 " pdb=" CG GLU l 16 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.04e+00 ... (remaining 65907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 87846 2.66 - 5.33: 931 5.33 - 7.99: 171 7.99 - 10.66: 33 10.66 - 13.32: 3 Bond angle restraints: 88984 Sorted by residual: angle pdb=" CA LYS E 210 " pdb=" CB LYS E 210 " pdb=" CG LYS E 210 " ideal model delta sigma weight residual 114.10 125.86 -11.76 2.00e+00 2.50e-01 3.46e+01 angle pdb=" CA GLU f 81 " pdb=" CB GLU f 81 " pdb=" CG GLU f 81 " ideal model delta sigma weight residual 114.10 123.95 -9.85 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CA GLU i 78 " pdb=" CB GLU i 78 " pdb=" CG GLU i 78 " ideal model delta sigma weight residual 114.10 123.91 -9.81 2.00e+00 2.50e-01 2.40e+01 angle pdb=" N VAL M 305 " pdb=" CA VAL M 305 " pdb=" C VAL M 305 " ideal model delta sigma weight residual 113.42 108.31 5.11 1.17e+00 7.31e-01 1.91e+01 angle pdb=" C VAL l 77 " pdb=" N GLU l 78 " pdb=" CA GLU l 78 " ideal model delta sigma weight residual 121.54 129.77 -8.23 1.91e+00 2.74e-01 1.86e+01 ... (remaining 88979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 39808 35.77 - 71.53: 1176 71.53 - 107.30: 76 107.30 - 143.07: 3 143.07 - 178.84: 13 Dihedral angle restraints: 41076 sinusoidal: 16464 harmonic: 24612 Sorted by residual: dihedral pdb=" O2A ADP I 601 " pdb=" O3A ADP I 601 " pdb=" PA ADP I 601 " pdb=" PB ADP I 601 " ideal model delta sinusoidal sigma weight residual -60.00 118.84 -178.84 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP H 601 " pdb=" O3A ADP H 601 " pdb=" PA ADP H 601 " pdb=" PB ADP H 601 " ideal model delta sinusoidal sigma weight residual -60.00 115.42 -175.42 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP J 601 " pdb=" O3A ADP J 601 " pdb=" PA ADP J 601 " pdb=" PB ADP J 601 " ideal model delta sinusoidal sigma weight residual -60.00 114.77 -174.77 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 41073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 8699 0.053 - 0.106: 1654 0.106 - 0.159: 308 0.159 - 0.211: 6 0.211 - 0.264: 1 Chirality restraints: 10668 Sorted by residual: chirality pdb=" CA GLU i 78 " pdb=" N GLU i 78 " pdb=" C GLU i 78 " pdb=" CB GLU i 78 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA GLU b 78 " pdb=" N GLU b 78 " pdb=" C GLU b 78 " pdb=" CB GLU b 78 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 chirality pdb=" CB ILE i 94 " pdb=" CA ILE i 94 " pdb=" CG1 ILE i 94 " pdb=" CG2 ILE i 94 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.94e-01 ... (remaining 10665 not shown) Planarity restraints: 11578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 210 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C LYS E 210 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS E 210 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN E 211 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE f 48 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C ILE f 48 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE f 48 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU f 49 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU l 78 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.50e+00 pdb=" C GLU l 78 " -0.041 2.00e-02 2.50e+03 pdb=" O GLU l 78 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY l 79 " 0.014 2.00e-02 2.50e+03 ... (remaining 11575 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 487 2.53 - 3.12: 49884 3.12 - 3.72: 108052 3.72 - 4.31: 148946 4.31 - 4.90: 249891 Nonbonded interactions: 557260 Sorted by model distance: nonbonded pdb=" O3B ADP F 601 " pdb="MG MG F 602 " model vdw 1.940 2.170 nonbonded pdb=" O2A ADP E 601 " pdb="MG MG E 602 " model vdw 2.023 2.170 nonbonded pdb=" O2A ADP G 601 " pdb="MG MG G 602 " model vdw 2.042 2.170 nonbonded pdb=" O1A ADP N 601 " pdb="MG MG N 602 " model vdw 2.043 2.170 nonbonded pdb=" O1A ADP L 601 " pdb="MG MG L 602 " model vdw 2.054 2.170 ... (remaining 557255 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' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.030 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: 0.050 Extract box with map and model: 2.080 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 122.780 Find NCS groups from input model: 2.790 Set up NCS constraints: 0.600 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:10.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 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 : 0.004 0.044 65912 Z= 0.235 Angle : 0.667 13.322 88984 Z= 0.327 Chirality : 0.043 0.264 10668 Planarity : 0.003 0.051 11578 Dihedral : 16.600 178.837 25256 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % Rotamer: Outliers : 1.01 % Allowed : 21.44 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.08), residues: 8652 helix: 1.25 (0.08), residues: 4214 sheet: 0.79 (0.17), residues: 896 loop : -0.33 (0.09), residues: 3542 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS M 329 PHE 0.010 0.001 PHE M 195 TYR 0.025 0.001 TYR g 70 ARG 0.010 0.000 ARG L 268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 998 time to evaluate : 5.748 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 15 ILE cc_start: 0.8673 (pt) cc_final: 0.8308 (pp) REVERT: a 63 ASP cc_start: 0.7674 (m-30) cc_final: 0.6781 (m-30) REVERT: C 226 LYS cc_start: 0.9090 (mppt) cc_final: 0.8836 (ttmm) REVERT: c 15 ILE cc_start: 0.8781 (pt) cc_final: 0.8481 (pp) REVERT: D 268 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8631 (mtt90) REVERT: e 15 ILE cc_start: 0.8645 (pt) cc_final: 0.8235 (pp) REVERT: F 178 GLU cc_start: 0.8796 (pt0) cc_final: 0.8500 (pt0) REVERT: f 60 LYS cc_start: 0.8075 (pptt) cc_final: 0.7836 (pmtt) REVERT: g 15 ILE cc_start: 0.8872 (pt) cc_final: 0.8600 (pp) REVERT: g 82 LEU cc_start: 0.8557 (mt) cc_final: 0.8262 (mp) REVERT: H 362 ARG cc_start: 0.7633 (ptp90) cc_final: 0.7253 (ptp90) REVERT: I 321 LYS cc_start: 0.8173 (mppt) cc_final: 0.7904 (mppt) REVERT: i 57 MET cc_start: 0.7787 (mmm) cc_final: 0.7520 (mmm) REVERT: i 89 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7894 (m-30) REVERT: j 15 ILE cc_start: 0.8618 (pt) cc_final: 0.8263 (pp) REVERT: j 63 ASP cc_start: 0.7616 (p0) cc_final: 0.7257 (p0) REVERT: k 15 ILE cc_start: 0.8536 (pt) cc_final: 0.8221 (pp) REVERT: k 89 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: l 15 ILE cc_start: 0.8571 (pt) cc_final: 0.8255 (pp) REVERT: l 60 LYS cc_start: 0.8173 (mppt) cc_final: 0.7877 (mmpt) REVERT: m 15 ILE cc_start: 0.8565 (pt) cc_final: 0.8289 (pp) REVERT: n 15 ILE cc_start: 0.8773 (pt) cc_final: 0.8508 (pp) outliers start: 69 outliers final: 54 residues processed: 1051 average time/residue: 1.6484 time to fit residues: 2170.9430 Evaluate side-chains 991 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 935 time to evaluate : 5.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 51 ASP Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain d residue 13 LYS Chi-restraints excluded: chain E residue 176 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 216 ASP Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 216 ASP Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain h residue 51 ASP Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 222 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain i residue 51 ASP Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 13 LYS Chi-restraints excluded: chain K residue 216 ASP Chi-restraints excluded: chain K residue 334 ASP Chi-restraints excluded: chain k residue 89 ASP Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 216 ASP Chi-restraints excluded: chain m residue 89 ASP Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 176 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 721 optimal weight: 1.9990 chunk 647 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 221 optimal weight: 0.0980 chunk 436 optimal weight: 0.6980 chunk 345 optimal weight: 1.9990 chunk 669 optimal weight: 20.0000 chunk 259 optimal weight: 0.0060 chunk 407 optimal weight: 0.9990 chunk 498 optimal weight: 1.9990 chunk 775 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN b 37 GLN c 37 GLN h 37 GLN i 37 GLN j 37 GLN M 37 ASN m 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 65912 Z= 0.216 Angle : 0.672 10.597 88984 Z= 0.334 Chirality : 0.045 0.173 10668 Planarity : 0.004 0.048 11578 Dihedral : 9.251 177.282 9481 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.59 % Allowed : 19.94 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.08), residues: 8652 helix: 1.71 (0.08), residues: 4270 sheet: 0.54 (0.16), residues: 924 loop : -0.47 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS f 7 PHE 0.014 0.001 PHE A 195 TYR 0.006 0.001 TYR h 70 ARG 0.009 0.001 ARG c 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1209 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1032 time to evaluate : 5.931 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 80 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7517 (mm-30) REVERT: B 362 ARG cc_start: 0.7946 (ttm110) cc_final: 0.7435 (ptp-110) REVERT: C 226 LYS cc_start: 0.9114 (mppt) cc_final: 0.8868 (ttmm) REVERT: C 268 ARG cc_start: 0.8720 (mtt-85) cc_final: 0.8432 (mtt90) REVERT: c 82 LEU cc_start: 0.8513 (mm) cc_final: 0.8108 (mp) REVERT: c 87 GLU cc_start: 0.8006 (tt0) cc_final: 0.7610 (tt0) REVERT: D 268 ARG cc_start: 0.8908 (mtt-85) cc_final: 0.8676 (mtt90) REVERT: D 321 LYS cc_start: 0.8023 (mmtm) cc_final: 0.7785 (mmtm) REVERT: d 55 ARG cc_start: 0.7850 (ptm160) cc_final: 0.7440 (ttp80) REVERT: d 91 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7629 (mtm) REVERT: E 73 MET cc_start: 0.8492 (mtp) cc_final: 0.8275 (mtp) REVERT: F 178 GLU cc_start: 0.8786 (pt0) cc_final: 0.8535 (pt0) REVERT: h 55 ARG cc_start: 0.7770 (ptm160) cc_final: 0.7382 (ttp80) REVERT: I 268 ARG cc_start: 0.8780 (mtt90) cc_final: 0.8535 (mtt90) REVERT: I 321 LYS cc_start: 0.8276 (mppt) cc_final: 0.8060 (mppt) REVERT: J 362 ARG cc_start: 0.7593 (mpp80) cc_final: 0.7323 (mtm-85) REVERT: j 15 ILE cc_start: 0.8773 (pt) cc_final: 0.8449 (pp) REVERT: j 55 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7276 (ttp80) REVERT: k 55 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7319 (ttp80) REVERT: k 57 MET cc_start: 0.7867 (mmt) cc_final: 0.7471 (tpt) REVERT: l 87 GLU cc_start: 0.7984 (tt0) cc_final: 0.7665 (tt0) REVERT: M 486 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7907 (pp20) REVERT: m 2 LYS cc_start: 0.8176 (tptm) cc_final: 0.7664 (tttm) REVERT: m 55 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7570 (ttp80) REVERT: N 216 ASP cc_start: 0.8552 (m-30) cc_final: 0.8346 (p0) REVERT: n 55 ARG cc_start: 0.7876 (ptm160) cc_final: 0.7623 (ttp80) REVERT: n 80 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7029 (mp0) REVERT: n 87 GLU cc_start: 0.7741 (tt0) cc_final: 0.7457 (tt0) outliers start: 177 outliers final: 48 residues processed: 1145 average time/residue: 1.6594 time to fit residues: 2384.3807 Evaluate side-chains 1018 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 968 time to evaluate : 5.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 272 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain F residue 142 LYS Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain i residue 81 GLU Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 88 ASP Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 334 ASP Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 81 GLU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain l residue 13 LYS Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 19 ARG Chi-restraints excluded: chain N residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 431 optimal weight: 3.9990 chunk 240 optimal weight: 20.0000 chunk 645 optimal weight: 9.9990 chunk 528 optimal weight: 0.7980 chunk 213 optimal weight: 2.9990 chunk 776 optimal weight: 0.8980 chunk 839 optimal weight: 1.9990 chunk 691 optimal weight: 0.0370 chunk 770 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 623 optimal weight: 1.9990 overall best weight: 1.1462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 65912 Z= 0.236 Angle : 0.648 9.140 88984 Z= 0.319 Chirality : 0.044 0.163 10668 Planarity : 0.004 0.045 11578 Dihedral : 8.907 170.435 9427 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.44 % Allowed : 20.32 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.08), residues: 8652 helix: 1.73 (0.08), residues: 4256 sheet: 0.47 (0.16), residues: 924 loop : -0.47 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 223 PHE 0.012 0.001 PHE A 195 TYR 0.011 0.001 TYR b 70 ARG 0.014 0.001 ARG d 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1019 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 VAL cc_start: 0.8688 (t) cc_final: 0.8483 (m) REVERT: A 324 GLU cc_start: 0.7647 (pp20) cc_final: 0.7387 (pp20) REVERT: A 362 ARG cc_start: 0.7392 (pmm-80) cc_final: 0.7153 (pmm-80) REVERT: a 80 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7368 (mm-30) REVERT: b 13 LYS cc_start: 0.8838 (tppp) cc_final: 0.8637 (tppt) REVERT: b 55 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7274 (ttp80) REVERT: b 63 ASP cc_start: 0.7679 (p0) cc_final: 0.7466 (p0) REVERT: C 226 LYS cc_start: 0.9099 (mppt) cc_final: 0.8891 (ttmm) REVERT: C 397 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8239 (mm-30) REVERT: c 21 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8296 (p) REVERT: c 87 GLU cc_start: 0.7937 (tt0) cc_final: 0.7637 (tt0) REVERT: D 321 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7859 (mmtm) REVERT: D 341 LYS cc_start: 0.9424 (mtpp) cc_final: 0.9182 (mtpt) REVERT: d 19 ARG cc_start: 0.7666 (mmp80) cc_final: 0.7437 (mmp-170) REVERT: d 47 LYS cc_start: 0.8707 (ptpp) cc_final: 0.8276 (ptpp) REVERT: d 80 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7151 (mm-30) REVERT: d 87 GLU cc_start: 0.7934 (tt0) cc_final: 0.7566 (tt0) REVERT: d 91 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7700 (mtm) REVERT: E 73 MET cc_start: 0.8505 (mtp) cc_final: 0.8280 (mtp) REVERT: E 272 LYS cc_start: 0.9079 (ptpp) cc_final: 0.8831 (pttm) REVERT: E 516 MET cc_start: 0.9216 (mtm) cc_final: 0.8945 (mtp) REVERT: F 178 GLU cc_start: 0.8775 (pt0) cc_final: 0.8541 (pt0) REVERT: f 88 ASP cc_start: 0.8490 (p0) cc_final: 0.8282 (p0) REVERT: f 91 MET cc_start: 0.7969 (mpp) cc_final: 0.7623 (mtt) REVERT: h 87 GLU cc_start: 0.8128 (tt0) cc_final: 0.7873 (tt0) REVERT: h 91 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7583 (mpp) REVERT: I 321 LYS cc_start: 0.8280 (mppt) cc_final: 0.8028 (mppt) REVERT: i 21 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.8105 (p) REVERT: J 76 GLU cc_start: 0.8259 (tt0) cc_final: 0.7977 (tm-30) REVERT: J 304 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8361 (mp0) REVERT: J 362 ARG cc_start: 0.7742 (mpp80) cc_final: 0.7220 (ptp90) REVERT: J 386 GLU cc_start: 0.7926 (pp20) cc_final: 0.7706 (tp30) REVERT: j 87 GLU cc_start: 0.8038 (tt0) cc_final: 0.7761 (tt0) REVERT: K 397 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8207 (mm-30) REVERT: k 63 ASP cc_start: 0.7763 (p0) cc_final: 0.7445 (p0) REVERT: k 87 GLU cc_start: 0.7774 (tt0) cc_final: 0.7541 (tt0) REVERT: k 89 ASP cc_start: 0.7796 (m-30) cc_final: 0.7509 (m-30) REVERT: L 242 LYS cc_start: 0.9303 (mtmm) cc_final: 0.9015 (pttp) REVERT: L 277 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: l 87 GLU cc_start: 0.7975 (tt0) cc_final: 0.7662 (tt0) REVERT: M 486 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7876 (pp20) REVERT: m 47 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8153 (ptpp) REVERT: N 321 LYS cc_start: 0.8072 (mppt) cc_final: 0.7514 (mppt) REVERT: N 386 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: n 13 LYS cc_start: 0.8811 (tppp) cc_final: 0.8569 (tppt) REVERT: n 87 GLU cc_start: 0.7814 (tt0) cc_final: 0.7547 (tt0) outliers start: 167 outliers final: 58 residues processed: 1140 average time/residue: 1.6440 time to fit residues: 2355.0856 Evaluate side-chains 1031 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 966 time to evaluate : 5.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain C residue 216 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 91 MET Chi-restraints excluded: chain I residue 216 ASP Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 334 ASP Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 81 GLU Chi-restraints excluded: chain L residue 186 GLU Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 411 ILE Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 386 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 767 optimal weight: 8.9990 chunk 584 optimal weight: 6.9990 chunk 403 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 370 optimal weight: 2.9990 chunk 521 optimal weight: 0.0970 chunk 779 optimal weight: 5.9990 chunk 825 optimal weight: 8.9990 chunk 407 optimal weight: 2.9990 chunk 738 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 65912 Z= 0.420 Angle : 0.701 8.766 88984 Z= 0.347 Chirality : 0.047 0.182 10668 Planarity : 0.004 0.049 11578 Dihedral : 8.900 177.593 9421 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.13 % Allowed : 19.88 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.08), residues: 8652 helix: 1.55 (0.08), residues: 4270 sheet: 0.30 (0.16), residues: 924 loop : -0.50 (0.09), residues: 3458 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 9 PHE 0.019 0.001 PHE e 67 TYR 0.010 0.001 TYR j 70 ARG 0.012 0.001 ARG m 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 989 time to evaluate : 5.866 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 324 GLU cc_start: 0.7702 (pp20) cc_final: 0.7430 (pp20) REVERT: A 362 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7276 (pmm-80) REVERT: a 63 ASP cc_start: 0.8015 (m-30) cc_final: 0.7659 (m-30) REVERT: a 80 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 277 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7990 (ttmm) REVERT: b 19 ARG cc_start: 0.7860 (mmp80) cc_final: 0.7441 (mmp-170) REVERT: b 47 LYS cc_start: 0.8716 (ptmm) cc_final: 0.8139 (ptmm) REVERT: b 63 ASP cc_start: 0.7654 (p0) cc_final: 0.7413 (p0) REVERT: C 214 VAL cc_start: 0.9123 (t) cc_final: 0.8919 (p) REVERT: C 226 LYS cc_start: 0.9119 (mppt) cc_final: 0.8857 (ttmm) REVERT: C 277 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8008 (mmmm) REVERT: C 397 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8284 (mm-30) REVERT: c 55 ARG cc_start: 0.7759 (ttp80) cc_final: 0.6915 (ttp80) REVERT: c 86 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8407 (mmm-85) REVERT: c 87 GLU cc_start: 0.7948 (tt0) cc_final: 0.7627 (tt0) REVERT: D 277 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8032 (ttmm) REVERT: D 321 LYS cc_start: 0.8206 (mmtm) cc_final: 0.7879 (mmtm) REVERT: D 463 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: d 80 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7217 (mm-30) REVERT: d 91 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7881 (mtm) REVERT: E 214 VAL cc_start: 0.9126 (t) cc_final: 0.8925 (p) REVERT: E 272 LYS cc_start: 0.9120 (ptpp) cc_final: 0.8918 (pttm) REVERT: E 341 LYS cc_start: 0.9401 (mtpt) cc_final: 0.9189 (mtpp) REVERT: e 63 ASP cc_start: 0.7881 (m-30) cc_final: 0.6770 (m-30) REVERT: f 13 LYS cc_start: 0.8478 (tppp) cc_final: 0.8260 (tppp) REVERT: f 88 ASP cc_start: 0.8447 (p0) cc_final: 0.8236 (p0) REVERT: f 91 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7604 (mtt) REVERT: G 277 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7934 (ttmm) REVERT: H 69 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8029 (mtt) REVERT: H 277 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7986 (ttmm) REVERT: h 91 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7690 (mpp) REVERT: I 321 LYS cc_start: 0.8252 (mppt) cc_final: 0.8020 (mppt) REVERT: I 367 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7889 (pt0) REVERT: i 63 ASP cc_start: 0.7803 (p0) cc_final: 0.7294 (p0) REVERT: i 88 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8115 (p0) REVERT: i 89 ASP cc_start: 0.8123 (m-30) cc_final: 0.7755 (m-30) REVERT: J 321 LYS cc_start: 0.8040 (mppt) cc_final: 0.7465 (mppt) REVERT: J 362 ARG cc_start: 0.7806 (mpp80) cc_final: 0.7372 (ptp90) REVERT: j 80 GLU cc_start: 0.7383 (mm-30) cc_final: 0.6859 (mm-30) REVERT: K 362 ARG cc_start: 0.7913 (ptp90) cc_final: 0.7698 (ptp90) REVERT: K 397 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8274 (mm-30) REVERT: L 242 LYS cc_start: 0.9277 (mtmm) cc_final: 0.8996 (pttm) REVERT: L 277 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.8027 (mmmm) REVERT: l 55 ARG cc_start: 0.7882 (ttp80) cc_final: 0.6593 (ttp80) REVERT: l 87 GLU cc_start: 0.7967 (tt0) cc_final: 0.7729 (tt0) REVERT: M 341 LYS cc_start: 0.9426 (mtpp) cc_final: 0.9200 (mtpt) REVERT: M 486 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7847 (pp20) REVERT: m 2 LYS cc_start: 0.8308 (tmtt) cc_final: 0.7987 (tttm) REVERT: m 55 ARG cc_start: 0.7716 (ttp80) cc_final: 0.7501 (ttp80) REVERT: N 171 LYS cc_start: 0.7918 (mmtm) cc_final: 0.7566 (mmpt) REVERT: n 55 ARG cc_start: 0.7703 (ptp-110) cc_final: 0.7448 (ttp80) outliers start: 214 outliers final: 82 residues processed: 1146 average time/residue: 1.6451 time to fit residues: 2366.6199 Evaluate side-chains 1045 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 948 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain c residue 14 ARG Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain d residue 91 MET Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 313 THR Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain e residue 90 ILE Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 212 VAL Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 277 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 334 ASP Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 91 MET Chi-restraints excluded: chain I residue 142 LYS Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain I residue 367 GLU Chi-restraints excluded: chain i residue 88 ASP Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 212 VAL Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 240 VAL Chi-restraints excluded: chain J residue 299 THR Chi-restraints excluded: chain J residue 309 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain K residue 186 GLU Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 411 ILE Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 37 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 687 optimal weight: 0.9990 chunk 468 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 614 optimal weight: 3.9990 chunk 340 optimal weight: 8.9990 chunk 704 optimal weight: 0.9990 chunk 570 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 421 optimal weight: 6.9990 chunk 740 optimal weight: 0.8980 chunk 208 optimal weight: 7.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 223 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 65912 Z= 0.225 Angle : 0.672 12.244 88984 Z= 0.329 Chirality : 0.045 0.344 10668 Planarity : 0.004 0.051 11578 Dihedral : 8.583 169.325 9414 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.60 % Favored : 98.39 % Rotamer: Outliers : 2.52 % Allowed : 20.61 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.08), residues: 8652 helix: 1.65 (0.08), residues: 4284 sheet: 0.28 (0.16), residues: 924 loop : -0.54 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 9 PHE 0.012 0.001 PHE A 195 TYR 0.009 0.001 TYR b 70 ARG 0.012 0.001 ARG b 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 991 time to evaluate : 5.820 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: A 321 LYS cc_start: 0.7950 (mppt) cc_final: 0.7722 (mppt) REVERT: A 324 GLU cc_start: 0.7708 (pp20) cc_final: 0.7397 (pp20) REVERT: a 63 ASP cc_start: 0.7915 (m-30) cc_final: 0.7310 (m-30) REVERT: a 80 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7400 (mm-30) REVERT: B 277 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7956 (ttmm) REVERT: B 321 LYS cc_start: 0.8033 (mppt) cc_final: 0.7528 (mppt) REVERT: b 13 LYS cc_start: 0.8868 (tppp) cc_final: 0.8661 (tppt) REVERT: C 214 VAL cc_start: 0.9107 (t) cc_final: 0.8878 (p) REVERT: C 226 LYS cc_start: 0.9127 (mppt) cc_final: 0.8870 (ttmm) REVERT: C 397 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8268 (mm-30) REVERT: c 21 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8359 (p) REVERT: c 47 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7941 (ptpp) REVERT: D 111 MET cc_start: 0.9132 (mtp) cc_final: 0.8908 (mtt) REVERT: D 217 ASN cc_start: 0.9112 (t0) cc_final: 0.8904 (t0) REVERT: D 277 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.7959 (ttmm) REVERT: D 321 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7884 (mmtm) REVERT: d 80 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7217 (mm-30) REVERT: E 463 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: F 277 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7953 (ttmm) REVERT: F 321 LYS cc_start: 0.8056 (mppt) cc_final: 0.7817 (mppt) REVERT: F 463 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: f 91 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7626 (mtt) REVERT: G 242 LYS cc_start: 0.9264 (tmmm) cc_final: 0.8946 (ptmm) REVERT: G 277 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7872 (ttmm) REVERT: H 277 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: h 87 GLU cc_start: 0.8083 (tt0) cc_final: 0.7796 (tt0) REVERT: I 321 LYS cc_start: 0.8305 (mppt) cc_final: 0.8048 (mppt) REVERT: J 76 GLU cc_start: 0.8400 (tt0) cc_final: 0.7958 (tm-30) REVERT: J 321 LYS cc_start: 0.7837 (mppt) cc_final: 0.7419 (mmtm) REVERT: J 362 ARG cc_start: 0.7842 (mpp80) cc_final: 0.7425 (ptp90) REVERT: j 80 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7144 (mp0) REVERT: j 91 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7777 (mpp) REVERT: K 397 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8251 (mm-30) REVERT: L 277 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7984 (mmmm) REVERT: L 463 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7679 (pm20) REVERT: l 47 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8209 (ptpp) REVERT: l 86 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8474 (mmm-85) REVERT: M 486 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7843 (pp20) REVERT: N 171 LYS cc_start: 0.7944 (mmtm) cc_final: 0.7549 (mmpt) REVERT: n 55 ARG cc_start: 0.7584 (ptp-110) cc_final: 0.7336 (ttp80) outliers start: 172 outliers final: 73 residues processed: 1109 average time/residue: 1.6429 time to fit residues: 2287.7925 Evaluate side-chains 1033 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 946 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 GLU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 23 SER Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 23 SER Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 186 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain e residue 23 SER Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 271 LEU Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 334 ASP Chi-restraints excluded: chain g residue 37 GLN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 277 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain J residue 234 LEU Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 91 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 3 LEU Chi-restraints excluded: chain k residue 23 SER Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 277 LYS Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 47 LYS Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 69 LYS Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 37 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 277 optimal weight: 7.9990 chunk 743 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 chunk 484 optimal weight: 5.9990 chunk 203 optimal weight: 0.0870 chunk 826 optimal weight: 9.9990 chunk 685 optimal weight: 3.9990 chunk 382 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 273 optimal weight: 0.9990 chunk 433 optimal weight: 0.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 65912 Z= 0.203 Angle : 0.672 13.332 88984 Z= 0.327 Chirality : 0.044 0.194 10668 Planarity : 0.004 0.056 11578 Dihedral : 8.297 168.504 9414 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.21 % Allowed : 22.03 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.00 (0.08), residues: 8652 helix: 1.72 (0.08), residues: 4284 sheet: 0.33 (0.16), residues: 924 loop : -0.57 (0.09), residues: 3444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 9 PHE 0.015 0.001 PHE e 67 TYR 0.008 0.001 TYR l 70 ARG 0.015 0.001 ARG c 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1147 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 996 time to evaluate : 6.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 321 LYS cc_start: 0.8001 (mppt) cc_final: 0.7795 (mppt) REVERT: A 324 GLU cc_start: 0.7711 (pp20) cc_final: 0.7396 (pp20) REVERT: a 80 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7409 (mm-30) REVERT: a 86 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8405 (mmm-85) REVERT: B 277 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7975 (ttmm) REVERT: B 321 LYS cc_start: 0.7882 (mppt) cc_final: 0.7400 (mppt) REVERT: b 13 LYS cc_start: 0.8797 (tppp) cc_final: 0.8592 (tppt) REVERT: b 47 LYS cc_start: 0.8522 (ptpp) cc_final: 0.8173 (ptpp) REVERT: C 214 VAL cc_start: 0.9113 (t) cc_final: 0.8901 (p) REVERT: C 226 LYS cc_start: 0.9114 (mppt) cc_final: 0.8865 (ttmm) REVERT: C 277 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7862 (ttmm) REVERT: C 397 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8295 (mm-30) REVERT: c 21 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8308 (p) REVERT: c 57 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7232 (mtm) REVERT: c 87 GLU cc_start: 0.7753 (tt0) cc_final: 0.7526 (tt0) REVERT: D 217 ASN cc_start: 0.9104 (t0) cc_final: 0.8892 (t0) REVERT: D 277 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7969 (ttmm) REVERT: D 321 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7814 (mmtm) REVERT: D 463 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: d 13 LYS cc_start: 0.9028 (tppp) cc_final: 0.8773 (tppt) REVERT: d 55 ARG cc_start: 0.7225 (ptm160) cc_final: 0.6949 (ptm160) REVERT: d 80 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7189 (mp0) REVERT: E 214 VAL cc_start: 0.9090 (t) cc_final: 0.8883 (p) REVERT: E 237 LEU cc_start: 0.9097 (mt) cc_final: 0.8884 (mp) REVERT: F 268 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8451 (mtm180) REVERT: F 277 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7992 (ttmm) REVERT: F 321 LYS cc_start: 0.8066 (mppt) cc_final: 0.7819 (mppt) REVERT: F 463 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7526 (pm20) REVERT: f 13 LYS cc_start: 0.8355 (tppp) cc_final: 0.8126 (tppt) REVERT: f 91 MET cc_start: 0.7926 (mpp) cc_final: 0.7628 (mtt) REVERT: G 277 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7832 (ttmm) REVERT: G 391 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: g 57 MET cc_start: 0.7796 (mmm) cc_final: 0.7368 (mtt) REVERT: H 277 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7975 (ttmm) REVERT: h 87 GLU cc_start: 0.8043 (tt0) cc_final: 0.7821 (tt0) REVERT: I 321 LYS cc_start: 0.8317 (mppt) cc_final: 0.8043 (mppt) REVERT: i 21 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (p) REVERT: i 86 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: i 88 ASP cc_start: 0.8503 (p0) cc_final: 0.8081 (p0) REVERT: J 321 LYS cc_start: 0.7963 (mppt) cc_final: 0.7654 (mmtm) REVERT: J 362 ARG cc_start: 0.7904 (mpp80) cc_final: 0.7523 (ptp90) REVERT: j 19 ARG cc_start: 0.7912 (mmp80) cc_final: 0.7632 (mmp80) REVERT: j 80 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7111 (mp0) REVERT: j 91 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7760 (mpp) REVERT: K 516 MET cc_start: 0.9147 (mtm) cc_final: 0.8934 (mtp) REVERT: k 47 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7673 (ptpp) REVERT: k 63 ASP cc_start: 0.7453 (p0) cc_final: 0.7224 (p0) REVERT: L 463 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.7591 (pm20) REVERT: l 47 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8195 (ptpp) REVERT: l 86 ARG cc_start: 0.8709 (mmm-85) cc_final: 0.8490 (mmm-85) REVERT: M 321 LYS cc_start: 0.8186 (mppt) cc_final: 0.7936 (mppt) REVERT: M 486 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: N 171 LYS cc_start: 0.7994 (mmtm) cc_final: 0.7582 (mmpt) REVERT: N 321 LYS cc_start: 0.8126 (mppt) cc_final: 0.7606 (mppt) REVERT: n 55 ARG cc_start: 0.7598 (ptp-110) cc_final: 0.7387 (ttp80) outliers start: 151 outliers final: 69 residues processed: 1101 average time/residue: 1.6441 time to fit residues: 2272.8567 Evaluate side-chains 1047 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 961 time to evaluate : 5.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain a residue 88 ASP Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 463 GLU Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 63 ASP Chi-restraints excluded: chain f residue 74 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain g residue 37 GLN Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 277 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 91 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 47 LYS Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 259 LEU Chi-restraints excluded: chain M residue 465 SER Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 37 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 796 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 470 optimal weight: 0.9990 chunk 603 optimal weight: 6.9990 chunk 467 optimal weight: 1.9990 chunk 695 optimal weight: 3.9990 chunk 461 optimal weight: 0.9990 chunk 823 optimal weight: 0.9990 chunk 515 optimal weight: 3.9990 chunk 501 optimal weight: 0.9990 chunk 380 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 223 HIS m 7 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 65912 Z= 0.229 Angle : 0.691 12.227 88984 Z= 0.337 Chirality : 0.045 0.235 10668 Planarity : 0.004 0.060 11578 Dihedral : 7.929 165.836 9407 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.99 % Allowed : 22.50 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.08), residues: 8652 helix: 1.73 (0.08), residues: 4284 sheet: 0.55 (0.16), residues: 896 loop : -0.61 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS f 7 PHE 0.011 0.001 PHE e 67 TYR 0.010 0.001 TYR l 70 ARG 0.014 0.001 ARG i 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 987 time to evaluate : 5.845 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 321 LYS cc_start: 0.8021 (mppt) cc_final: 0.7706 (mppt) REVERT: A 324 GLU cc_start: 0.7733 (pp20) cc_final: 0.7404 (pp20) REVERT: a 80 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7496 (mm-30) REVERT: a 86 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8399 (mmm-85) REVERT: B 277 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: B 321 LYS cc_start: 0.7925 (mppt) cc_final: 0.7636 (mmtm) REVERT: B 386 GLU cc_start: 0.7784 (mp0) cc_final: 0.7483 (mp0) REVERT: b 47 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8273 (pttp) REVERT: b 63 ASP cc_start: 0.7432 (p0) cc_final: 0.7092 (p0) REVERT: C 214 VAL cc_start: 0.9093 (t) cc_final: 0.8858 (p) REVERT: C 226 LYS cc_start: 0.9118 (mppt) cc_final: 0.8872 (ttmm) REVERT: C 277 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7783 (ttmm) REVERT: C 397 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8304 (mm-30) REVERT: c 21 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8314 (p) REVERT: c 87 GLU cc_start: 0.7753 (tt0) cc_final: 0.7488 (tt0) REVERT: D 217 ASN cc_start: 0.9112 (t0) cc_final: 0.8904 (t0) REVERT: D 321 LYS cc_start: 0.8217 (mmtm) cc_final: 0.7985 (mppt) REVERT: d 47 LYS cc_start: 0.8316 (ptpp) cc_final: 0.8066 (ptpp) REVERT: d 80 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 386 GLU cc_start: 0.7870 (mp0) cc_final: 0.7642 (mp0) REVERT: E 463 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.7790 (pm20) REVERT: F 277 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7967 (ttmm) REVERT: F 321 LYS cc_start: 0.8079 (mppt) cc_final: 0.7816 (mppt) REVERT: F 463 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: f 13 LYS cc_start: 0.8381 (tppp) cc_final: 0.8099 (tptt) REVERT: f 82 LEU cc_start: 0.8435 (mm) cc_final: 0.8100 (mm) REVERT: f 91 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7601 (mtt) REVERT: G 277 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7856 (ttmm) REVERT: G 391 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7621 (tm-30) REVERT: H 277 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.8026 (ttmm) REVERT: h 87 GLU cc_start: 0.8054 (tt0) cc_final: 0.7822 (tt0) REVERT: I 321 LYS cc_start: 0.8299 (mppt) cc_final: 0.8013 (mppt) REVERT: i 21 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8220 (p) REVERT: i 91 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7812 (mpp) REVERT: J 321 LYS cc_start: 0.8034 (mppt) cc_final: 0.7681 (mmtm) REVERT: J 362 ARG cc_start: 0.7950 (mpp80) cc_final: 0.7578 (ptp90) REVERT: j 80 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7041 (mp0) REVERT: j 91 MET cc_start: 0.8079 (OUTLIER) cc_final: 0.7694 (mpp) REVERT: K 397 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8224 (mm-30) REVERT: K 516 MET cc_start: 0.9137 (mtm) cc_final: 0.8916 (mtp) REVERT: L 463 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7586 (pm20) REVERT: l 87 GLU cc_start: 0.7984 (tt0) cc_final: 0.7770 (tt0) REVERT: M 486 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7837 (pp20) REVERT: M 516 MET cc_start: 0.9239 (mtm) cc_final: 0.8954 (mtp) REVERT: N 171 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7609 (mmpt) REVERT: N 268 ARG cc_start: 0.8958 (mtt90) cc_final: 0.8719 (mtt90) outliers start: 136 outliers final: 82 residues processed: 1083 average time/residue: 1.6466 time to fit residues: 2237.3179 Evaluate side-chains 1048 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 951 time to evaluate : 8.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 90 ILE Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 273 THR Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain D residue 186 GLU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 91 MET Chi-restraints excluded: chain G residue 186 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain g residue 37 GLN Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 277 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 234 LEU Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 299 THR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 91 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain l residue 37 GLN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 465 SER Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 509 optimal weight: 2.9990 chunk 328 optimal weight: 0.5980 chunk 491 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 159 optimal weight: 8.9990 chunk 523 optimal weight: 0.9980 chunk 560 optimal weight: 0.6980 chunk 406 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 646 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 65912 Z= 0.216 Angle : 0.701 11.109 88984 Z= 0.342 Chirality : 0.044 0.186 10668 Planarity : 0.004 0.067 11578 Dihedral : 7.645 153.908 9407 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.96 % Allowed : 22.95 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.08), residues: 8652 helix: 1.76 (0.08), residues: 4284 sheet: 0.56 (0.16), residues: 896 loop : -0.65 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS f 7 PHE 0.021 0.001 PHE c 67 TYR 0.008 0.001 TYR i 70 ARG 0.016 0.001 ARG m 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 979 time to evaluate : 5.948 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 324 GLU cc_start: 0.7690 (pp20) cc_final: 0.7396 (pp20) REVERT: A 362 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7188 (pmm-80) REVERT: a 55 ARG cc_start: 0.7840 (ttp80) cc_final: 0.7593 (ttp80) REVERT: a 80 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7546 (mm-30) REVERT: B 231 ARG cc_start: 0.9331 (ttp-110) cc_final: 0.9098 (ptp90) REVERT: B 277 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7976 (ttmm) REVERT: B 321 LYS cc_start: 0.7975 (mppt) cc_final: 0.7650 (mmtm) REVERT: b 47 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8255 (pttp) REVERT: b 63 ASP cc_start: 0.7383 (p0) cc_final: 0.7006 (p0) REVERT: b 88 ASP cc_start: 0.8467 (p0) cc_final: 0.8236 (p0) REVERT: C 214 VAL cc_start: 0.9093 (t) cc_final: 0.8858 (p) REVERT: C 226 LYS cc_start: 0.9117 (mppt) cc_final: 0.8874 (ttmm) REVERT: C 277 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7788 (ttmm) REVERT: C 397 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8279 (mm-30) REVERT: c 21 THR cc_start: 0.8524 (OUTLIER) cc_final: 0.8318 (p) REVERT: D 210 LYS cc_start: 0.8875 (ptpp) cc_final: 0.8425 (tptt) REVERT: D 277 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8013 (ttmm) REVERT: D 321 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7961 (mppt) REVERT: d 47 LYS cc_start: 0.8305 (ptpp) cc_final: 0.8067 (ptpp) REVERT: d 77 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8196 (p) REVERT: d 80 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7157 (mp0) REVERT: E 463 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: F 268 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8453 (mtm180) REVERT: F 277 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8006 (ttmm) REVERT: F 321 LYS cc_start: 0.8077 (mppt) cc_final: 0.7791 (mppt) REVERT: F 463 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: f 91 MET cc_start: 0.7917 (mpp) cc_final: 0.7526 (mtt) REVERT: G 277 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7828 (ttmm) REVERT: G 391 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: h 87 GLU cc_start: 0.8061 (tt0) cc_final: 0.7814 (tt0) REVERT: I 231 ARG cc_start: 0.9304 (ttp-110) cc_final: 0.9066 (ptp90) REVERT: I 321 LYS cc_start: 0.8292 (mppt) cc_final: 0.7999 (mppt) REVERT: i 21 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8187 (p) REVERT: i 88 ASP cc_start: 0.8468 (p0) cc_final: 0.8218 (p0) REVERT: i 91 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7699 (mpp) REVERT: J 321 LYS cc_start: 0.8063 (mppt) cc_final: 0.7648 (mmtm) REVERT: J 362 ARG cc_start: 0.7984 (mpp80) cc_final: 0.7611 (ptp90) REVERT: j 80 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7071 (mp0) REVERT: j 91 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7684 (mpp) REVERT: K 397 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8237 (mm-30) REVERT: K 516 MET cc_start: 0.9128 (mtm) cc_final: 0.8910 (mtp) REVERT: L 309 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8234 (tt) REVERT: L 463 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: M 321 LYS cc_start: 0.8241 (mppt) cc_final: 0.7975 (mppt) REVERT: M 486 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: M 516 MET cc_start: 0.9222 (mtm) cc_final: 0.8947 (mtp) REVERT: N 171 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7603 (mmpt) REVERT: N 268 ARG cc_start: 0.8959 (mtt90) cc_final: 0.8681 (mtt90) REVERT: N 321 LYS cc_start: 0.8118 (mppt) cc_final: 0.7752 (mppt) REVERT: N 367 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7843 (pt0) outliers start: 134 outliers final: 75 residues processed: 1075 average time/residue: 1.6594 time to fit residues: 2245.9586 Evaluate side-chains 1043 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 949 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain A residue 391 GLU Chi-restraints excluded: chain a residue 37 GLN Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 76 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain c residue 57 MET Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 88 ASP Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 37 GLN Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain F residue 330 THR Chi-restraints excluded: chain F residue 463 GLU Chi-restraints excluded: chain f residue 37 GLN Chi-restraints excluded: chain f residue 49 LEU Chi-restraints excluded: chain f residue 81 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain g residue 37 GLN Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain h residue 37 GLN Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 21 THR Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 299 THR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 91 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 GLN Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 259 LEU Chi-restraints excluded: chain L residue 309 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 465 SER Chi-restraints excluded: chain M residue 473 GLU Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain m residue 37 GLN Chi-restraints excluded: chain m residue 90 ILE Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain N residue 367 GLU Chi-restraints excluded: chain n residue 37 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 748 optimal weight: 0.9980 chunk 788 optimal weight: 3.9990 chunk 719 optimal weight: 2.9990 chunk 767 optimal weight: 6.9990 chunk 461 optimal weight: 0.9990 chunk 334 optimal weight: 5.9990 chunk 602 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 693 optimal weight: 6.9990 chunk 725 optimal weight: 6.9990 chunk 764 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 223 HIS m 7 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 65912 Z= 0.443 Angle : 0.779 11.155 88984 Z= 0.382 Chirality : 0.048 0.278 10668 Planarity : 0.005 0.070 11578 Dihedral : 7.803 151.366 9407 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.79 % Allowed : 23.19 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.08), residues: 8652 helix: 1.55 (0.08), residues: 4284 sheet: 0.43 (0.16), residues: 896 loop : -0.70 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 9 PHE 0.013 0.001 PHE A 66 TYR 0.010 0.001 TYR L 199 ARG 0.024 0.001 ARG e 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 976 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7781 (pp20) cc_final: 0.7460 (pp20) REVERT: a 13 LYS cc_start: 0.8673 (tppp) cc_final: 0.8380 (tppt) REVERT: a 80 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 231 ARG cc_start: 0.9352 (ttp-110) cc_final: 0.9071 (ptp90) REVERT: B 321 LYS cc_start: 0.8067 (mppt) cc_final: 0.7686 (mmtm) REVERT: B 386 GLU cc_start: 0.7836 (mp0) cc_final: 0.7575 (mp0) REVERT: b 47 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8214 (ptpp) REVERT: b 57 MET cc_start: 0.8183 (mmt) cc_final: 0.7904 (tpt) REVERT: b 88 ASP cc_start: 0.8498 (p0) cc_final: 0.8289 (p0) REVERT: C 214 VAL cc_start: 0.9093 (t) cc_final: 0.8870 (p) REVERT: C 226 LYS cc_start: 0.9139 (mppt) cc_final: 0.8836 (ttmm) REVERT: C 277 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7820 (ttmm) REVERT: C 397 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8323 (mm-30) REVERT: C 463 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: c 21 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (p) REVERT: c 63 ASP cc_start: 0.7574 (m-30) cc_final: 0.6455 (m-30) REVERT: D 277 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7984 (ttmm) REVERT: D 522 MET cc_start: 0.9414 (mtm) cc_final: 0.9206 (mtp) REVERT: d 77 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8260 (p) REVERT: d 80 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7200 (mp0) REVERT: E 386 GLU cc_start: 0.7942 (mp0) cc_final: 0.7645 (mp0) REVERT: E 463 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: e 81 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: F 268 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8447 (mtm180) REVERT: F 271 LEU cc_start: 0.9174 (pp) cc_final: 0.8920 (pp) REVERT: F 277 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8031 (ttmm) REVERT: F 321 LYS cc_start: 0.8058 (mppt) cc_final: 0.7703 (mppt) REVERT: f 19 ARG cc_start: 0.8101 (mmp80) cc_final: 0.7770 (mmp80) REVERT: f 91 MET cc_start: 0.7921 (mpp) cc_final: 0.7273 (mtt) REVERT: G 277 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.7922 (ttmm) REVERT: G 391 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: H 69 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8362 (mtt) REVERT: H 277 LYS cc_start: 0.8315 (OUTLIER) cc_final: 0.8025 (ttmm) REVERT: h 19 ARG cc_start: 0.8244 (mmp80) cc_final: 0.7870 (mmm160) REVERT: I 321 LYS cc_start: 0.8245 (mppt) cc_final: 0.7900 (mppt) REVERT: i 91 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.7740 (mpp) REVERT: J 76 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: J 321 LYS cc_start: 0.8127 (mppt) cc_final: 0.7703 (mmtm) REVERT: j 80 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7154 (mp0) REVERT: j 91 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7657 (mpp) REVERT: K 397 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8270 (mm-30) REVERT: K 516 MET cc_start: 0.9202 (mtm) cc_final: 0.8996 (mtp) REVERT: L 309 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8240 (tt) REVERT: L 463 GLU cc_start: 0.8644 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: M 486 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7886 (pp20) REVERT: M 516 MET cc_start: 0.9222 (mtm) cc_final: 0.8973 (mtp) REVERT: N 171 LYS cc_start: 0.8065 (mmtm) cc_final: 0.7685 (mmpt) REVERT: N 268 ARG cc_start: 0.8966 (mtt90) cc_final: 0.8679 (mtt90) REVERT: N 321 LYS cc_start: 0.8107 (mppt) cc_final: 0.7807 (mppt) outliers start: 122 outliers final: 66 residues processed: 1065 average time/residue: 1.6743 time to fit residues: 2232.6275 Evaluate side-chains 1030 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 945 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 91 MET Chi-restraints excluded: chain C residue 186 GLU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain c residue 3 LEU Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain e residue 81 GLU Chi-restraints excluded: chain F residue 186 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 LEU Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 277 LYS Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 236 VAL Chi-restraints excluded: chain I residue 273 THR Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain J residue 76 GLU Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 299 THR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain j residue 91 MET Chi-restraints excluded: chain K residue 234 LEU Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain K residue 473 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 309 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain M residue 186 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 236 VAL Chi-restraints excluded: chain M residue 465 SER Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 236 VAL Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain N residue 352 GLN Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 503 optimal weight: 1.9990 chunk 811 optimal weight: 1.9990 chunk 495 optimal weight: 0.7980 chunk 384 optimal weight: 2.9990 chunk 563 optimal weight: 0.9980 chunk 850 optimal weight: 8.9990 chunk 783 optimal weight: 0.8980 chunk 677 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 523 optimal weight: 9.9990 chunk 415 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 65912 Z= 0.237 Angle : 0.752 12.371 88984 Z= 0.368 Chirality : 0.045 0.294 10668 Planarity : 0.004 0.079 11578 Dihedral : 7.615 136.973 9407 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.30 % Allowed : 24.05 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.08), residues: 8652 helix: 1.64 (0.08), residues: 4284 sheet: 0.47 (0.16), residues: 896 loop : -0.72 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 7 PHE 0.012 0.001 PHE M 44 TYR 0.008 0.001 TYR l 70 ARG 0.017 0.001 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17304 Ramachandran restraints generated. 8652 Oldfield, 0 Emsley, 8652 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 972 time to evaluate : 5.952 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 324 GLU cc_start: 0.7735 (pp20) cc_final: 0.7416 (pp20) REVERT: a 13 LYS cc_start: 0.8705 (tppp) cc_final: 0.8474 (tppt) REVERT: a 36 ASP cc_start: 0.8026 (m-30) cc_final: 0.7793 (m-30) REVERT: a 80 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7609 (mm-30) REVERT: B 321 LYS cc_start: 0.8099 (mppt) cc_final: 0.7699 (mmtm) REVERT: B 386 GLU cc_start: 0.7789 (mp0) cc_final: 0.7541 (mp0) REVERT: b 47 LYS cc_start: 0.8542 (ptpp) cc_final: 0.8194 (ptpp) REVERT: b 88 ASP cc_start: 0.8472 (p0) cc_final: 0.8260 (p0) REVERT: C 214 VAL cc_start: 0.9093 (t) cc_final: 0.8868 (p) REVERT: C 226 LYS cc_start: 0.9124 (mppt) cc_final: 0.8822 (ttmm) REVERT: C 277 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7855 (ttmm) REVERT: C 397 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8302 (mm-30) REVERT: C 463 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7779 (pm20) REVERT: c 21 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8397 (p) REVERT: D 111 MET cc_start: 0.9036 (mtp) cc_final: 0.8823 (mtt) REVERT: D 210 LYS cc_start: 0.8877 (ptpp) cc_final: 0.8422 (tptt) REVERT: D 277 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8001 (ttmm) REVERT: D 321 LYS cc_start: 0.8235 (mmtm) cc_final: 0.7784 (mmtm) REVERT: D 385 THR cc_start: 0.8900 (OUTLIER) cc_final: 0.8668 (p) REVERT: D 522 MET cc_start: 0.9386 (mtm) cc_final: 0.9182 (mtp) REVERT: d 77 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8173 (p) REVERT: d 80 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7261 (mp0) REVERT: E 386 GLU cc_start: 0.7881 (mp0) cc_final: 0.7598 (mp0) REVERT: E 463 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: F 264 VAL cc_start: 0.9022 (t) cc_final: 0.8813 (t) REVERT: F 268 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8441 (mtm180) REVERT: F 271 LEU cc_start: 0.9149 (pp) cc_final: 0.8903 (pp) REVERT: F 277 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8014 (ttmm) REVERT: F 321 LYS cc_start: 0.8085 (mppt) cc_final: 0.7751 (mppt) REVERT: f 19 ARG cc_start: 0.8062 (mmp80) cc_final: 0.7768 (mmp80) REVERT: G 277 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7936 (ttmm) REVERT: G 391 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: g 13 LYS cc_start: 0.8704 (tppp) cc_final: 0.8485 (tppt) REVERT: g 19 ARG cc_start: 0.8153 (mmp80) cc_final: 0.7853 (mmp80) REVERT: H 69 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7425 (mmt) REVERT: h 19 ARG cc_start: 0.8179 (mmp80) cc_final: 0.7780 (mmm160) REVERT: h 20 LYS cc_start: 0.8990 (mppt) cc_final: 0.8782 (mppt) REVERT: h 86 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8267 (mmm-85) REVERT: I 321 LYS cc_start: 0.8271 (mppt) cc_final: 0.7996 (mppt) REVERT: i 91 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7678 (mpp) REVERT: J 76 GLU cc_start: 0.8329 (tt0) cc_final: 0.8118 (pt0) REVERT: J 321 LYS cc_start: 0.8145 (mppt) cc_final: 0.7675 (mmtm) REVERT: J 362 ARG cc_start: 0.7557 (mtm-85) cc_final: 0.7151 (ptp90) REVERT: j 13 LYS cc_start: 0.8704 (tppp) cc_final: 0.8357 (tppt) REVERT: K 397 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8231 (mm-30) REVERT: K 516 MET cc_start: 0.9177 (mtm) cc_final: 0.8941 (mtp) REVERT: L 309 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8182 (tt) REVERT: L 463 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: M 486 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7836 (pp20) REVERT: N 171 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7678 (mmpt) REVERT: N 321 LYS cc_start: 0.8118 (mppt) cc_final: 0.7839 (mppt) REVERT: n 47 LYS cc_start: 0.8214 (ptpp) cc_final: 0.7980 (ptpp) REVERT: n 55 ARG cc_start: 0.7251 (ptm160) cc_final: 0.7042 (ptp-110) outliers start: 89 outliers final: 51 residues processed: 1038 average time/residue: 1.6604 time to fit residues: 2157.5236 Evaluate side-chains 1026 residues out of total 6832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 959 time to evaluate : 6.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 ARG Chi-restraints excluded: chain a residue 75 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 300 VAL Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain b residue 37 GLN Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 463 GLU Chi-restraints excluded: chain C residue 465 SER Chi-restraints excluded: chain c residue 21 THR Chi-restraints excluded: chain c residue 37 GLN Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain D residue 385 THR Chi-restraints excluded: chain D residue 465 SER Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain E residue 76 GLU Chi-restraints excluded: chain E residue 216 ASP Chi-restraints excluded: chain E residue 330 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain e residue 30 THR Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 268 ARG Chi-restraints excluded: chain F residue 277 LYS Chi-restraints excluded: chain F residue 300 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 299 THR Chi-restraints excluded: chain G residue 391 GLU Chi-restraints excluded: chain g residue 69 LYS Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain H residue 186 GLU Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 236 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain H residue 330 THR Chi-restraints excluded: chain H residue 331 THR Chi-restraints excluded: chain H residue 473 GLU Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 330 THR Chi-restraints excluded: chain i residue 37 GLN Chi-restraints excluded: chain i residue 89 ASP Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain J residue 186 GLU Chi-restraints excluded: chain J residue 299 THR Chi-restraints excluded: chain J residue 330 THR Chi-restraints excluded: chain j residue 37 GLN Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain L residue 212 VAL Chi-restraints excluded: chain L residue 236 VAL Chi-restraints excluded: chain L residue 309 LEU Chi-restraints excluded: chain L residue 330 THR Chi-restraints excluded: chain L residue 463 GLU Chi-restraints excluded: chain M residue 212 VAL Chi-restraints excluded: chain M residue 465 SER Chi-restraints excluded: chain M residue 486 GLU Chi-restraints excluded: chain N residue 222 LEU Chi-restraints excluded: chain N residue 331 THR Chi-restraints excluded: chain n residue 37 GLN Chi-restraints excluded: chain n residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 854 random chunks: chunk 538 optimal weight: 0.5980 chunk 721 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 624 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 678 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 696 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 7 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.120523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.073214 restraints weight = 104081.480| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.21 r_work: 0.2801 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 65912 Z= 0.354 Angle : 0.780 12.626 88984 Z= 0.382 Chirality : 0.047 0.304 10668 Planarity : 0.005 0.075 11578 Dihedral : 7.659 142.057 9405 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.45 % Allowed : 23.84 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.08), residues: 8652 helix: 1.58 (0.08), residues: 4284 sheet: 0.46 (0.16), residues: 896 loop : -0.72 (0.09), residues: 3472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS h 7 PHE 0.023 0.001 PHE m 67 TYR 0.010 0.001 TYR B 219 ARG 0.017 0.001 ARG l 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29905.70 seconds wall clock time: 514 minutes 42.33 seconds (30882.33 seconds total)