Starting phenix.real_space_refine on Sun Aug 24 13:34:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590.map" model { file = "/net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do4_27590/08_2025/8do4_27590_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 12773 2.51 5 N 3303 2.21 5 O 3955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20163 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3348 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 16, 'TRANS': 419} Chain breaks: 1 Chain: "B" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3393 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain: "C" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Chain: "D" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3393 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 16, 'TRANS': 425} Chain: "E" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Chain: "G" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3343 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Time building chain proxies: 4.94, per 1000 atoms: 0.25 Number of scatterers: 20163 At special positions: 0 Unit cell: (156.04, 145.7, 99.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 3955 8.00 N 3303 7.00 C 12773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 71 " - pdb=" SG CYS A 192 " distance=2.02 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 114 " distance=2.04 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 71 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 114 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.04 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 71 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 104 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.02 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 71 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 340 " distance=2.03 Simple disulfide: pdb=" SG CYS D 355 " - pdb=" SG CYS D 363 " distance=2.03 Simple disulfide: pdb=" SG CYS D 387 " - pdb=" SG CYS D 392 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS E 71 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 104 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 331 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 355 " - pdb=" SG CYS E 363 " distance=2.03 Simple disulfide: pdb=" SG CYS E 387 " - pdb=" SG CYS E 392 " distance=2.03 Simple disulfide: pdb=" SG CYS E 394 " - pdb=" SG CYS E 417 " distance=2.04 Simple disulfide: pdb=" SG CYS G 71 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 331 " - pdb=" SG CYS G 340 " distance=2.03 Simple disulfide: pdb=" SG CYS G 355 " - pdb=" SG CYS G 363 " distance=2.03 Simple disulfide: pdb=" SG CYS G 387 " - pdb=" SG CYS G 392 " distance=2.03 Simple disulfide: pdb=" SG CYS G 394 " - pdb=" SG CYS G 417 " distance=2.03 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4958 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 33 sheets defined 38.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.933A pdb=" N CYS A 71 " --> pdb=" O MET A 68 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 68 through 72' Processing helix chain 'A' and resid 74 through 99 Proline residue: A 89 - end of helix removed outlier: 3.590A pdb=" N ILE A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.944A pdb=" N LYS A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASN A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 175 through 182 Processing helix chain 'A' and resid 191 through 211 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.933A pdb=" N LEU A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 437 through 441 removed outlier: 3.587A pdb=" N GLU A 441 " --> pdb=" O TYR A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 468 removed outlier: 3.981A pdb=" N SER A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.657A pdb=" N LYS B 35 " --> pdb=" O GLU B 31 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 72 removed outlier: 5.035A pdb=" N GLN B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N CYS B 71 " --> pdb=" O MET B 68 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 72 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 99 Proline residue: B 89 - end of helix removed outlier: 4.115A pdb=" N TYR B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.694A pdb=" N LYS B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 140 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 175 through 182 Processing helix chain 'B' and resid 191 through 211 removed outlier: 3.514A pdb=" N THR B 195 " --> pdb=" O PRO B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.762A pdb=" N LEU B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 349 through 357 Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 437 through 441 Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.926A pdb=" N SER B 457 " --> pdb=" O LYS B 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.937A pdb=" N CYS C 71 " --> pdb=" O MET C 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR C 72 " --> pdb=" O SER C 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 68 through 72' Processing helix chain 'C' and resid 74 through 99 removed outlier: 3.679A pdb=" N ASN C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Proline residue: C 89 - end of helix removed outlier: 3.872A pdb=" N ILE C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N TYR C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 125 through 146 removed outlier: 3.550A pdb=" N LYS C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN C 143 " --> pdb=" O LYS C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 153 Processing helix chain 'C' and resid 175 through 182 Processing helix chain 'C' and resid 191 through 211 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.896A pdb=" N LEU C 242 " --> pdb=" O ASN C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 328 through 331 Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.827A pdb=" N SER C 457 " --> pdb=" O LYS C 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 removed outlier: 3.556A pdb=" N LEU D 33 " --> pdb=" O HIS D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 74 through 99 Proline residue: D 89 - end of helix removed outlier: 3.586A pdb=" N ILE D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N TYR D 97 " --> pdb=" O ALA D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 125 through 147 removed outlier: 3.595A pdb=" N LYS D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASN D 143 " --> pdb=" O LYS D 139 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 176 through 182 Processing helix chain 'D' and resid 191 through 215 removed outlier: 4.360A pdb=" N PHE D 212 " --> pdb=" O SER D 208 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N VAL D 213 " --> pdb=" O ASP D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 238 through 247 removed outlier: 3.773A pdb=" N LEU D 242 " --> pdb=" O ASN D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 328 through 331 Processing helix chain 'D' and resid 349 through 358 Processing helix chain 'D' and resid 359 through 363 Processing helix chain 'D' and resid 437 through 441 Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.862A pdb=" N SER D 457 " --> pdb=" O LYS D 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 35 removed outlier: 3.562A pdb=" N LYS E 35 " --> pdb=" O GLU E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.815A pdb=" N SER E 69 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLN E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N CYS E 71 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR E 72 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 99 removed outlier: 3.643A pdb=" N ASN E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) Proline residue: E 89 - end of helix removed outlier: 3.540A pdb=" N ILE E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N TYR E 97 " --> pdb=" O ALA E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 146 removed outlier: 3.940A pdb=" N LYS E 139 " --> pdb=" O TYR E 135 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASN E 140 " --> pdb=" O GLU E 136 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN E 143 " --> pdb=" O LYS E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 153 Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 191 through 212 removed outlier: 4.003A pdb=" N PHE E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 236 removed outlier: 3.595A pdb=" N GLY E 236 " --> pdb=" O GLN E 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 233 through 236' Processing helix chain 'E' and resid 238 through 247 removed outlier: 3.780A pdb=" N LEU E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 358 through 363 removed outlier: 5.482A pdb=" N GLU E 361 " --> pdb=" O GLY E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 Processing helix chain 'E' and resid 452 through 468 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.608A pdb=" N LYS G 35 " --> pdb=" O GLU G 31 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 72 Processing helix chain 'G' and resid 74 through 99 removed outlier: 3.562A pdb=" N ASN G 78 " --> pdb=" O SER G 74 " (cutoff:3.500A) Proline residue: G 89 - end of helix removed outlier: 3.654A pdb=" N ILE G 96 " --> pdb=" O GLY G 92 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR G 97 " --> pdb=" O ALA G 93 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.995A pdb=" N LYS G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN G 140 " --> pdb=" O GLU G 136 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN G 143 " --> pdb=" O LYS G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 153 Processing helix chain 'G' and resid 175 through 188 removed outlier: 4.778A pdb=" N VAL G 184 " --> pdb=" O ASN G 180 " (cutoff:3.500A) Proline residue: G 185 - end of helix removed outlier: 4.333A pdb=" N ASP G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 211 removed outlier: 3.927A pdb=" N SER G 198 " --> pdb=" O GLN G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 233 through 236 Processing helix chain 'G' and resid 238 through 246 removed outlier: 3.826A pdb=" N LEU G 242 " --> pdb=" O ASN G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 349 through 356 Processing helix chain 'G' and resid 357 through 358 No H-bonds generated for 'chain 'G' and resid 357 through 358' Processing helix chain 'G' and resid 359 through 363 removed outlier: 3.736A pdb=" N LYS G 362 " --> pdb=" O SER G 359 " (cutoff:3.500A) Processing helix chain 'G' and resid 437 through 441 Processing helix chain 'G' and resid 452 through 468 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 164 removed outlier: 6.765A pdb=" N LYS A 167 " --> pdb=" O GLU A 163 " (cutoff:3.500A) removed outlier: 10.475A pdb=" N THR A 168 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASP A 56 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N TYR A 170 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 275 through 298 current: chain 'A' and resid 332 through 333 Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 270 removed outlier: 6.067A pdb=" N ILE A 266 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG A 279 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 268 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 275 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N ILE A 277 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N LYS A 60 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N ARG A 279 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 9.877A pdb=" N VAL A 58 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 9.593A pdb=" N TYR A 281 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 9.669A pdb=" N ASP A 56 " --> pdb=" O TYR A 281 " (cutoff:3.500A) removed outlier: 9.113A pdb=" N THR A 54 " --> pdb=" O PRO A 283 " (cutoff:3.500A) removed outlier: 10.688A pdb=" N LEU A 285 " --> pdb=" O PRO A 52 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLU A 287 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 9.599A pdb=" N SER A 50 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N GLN A 289 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N ILE A 48 " --> pdb=" O GLN A 289 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 291 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 46 " --> pdb=" O ALA A 291 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A 42 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N LEU A 297 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N LYS A 40 " --> pdb=" O LEU A 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 60 current: chain 'A' and resid 322 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.654A pdb=" N LEU G 383 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.268A pdb=" N MET A 226 " --> pdb=" O GLY A 264 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 303 removed outlier: 6.082A pdb=" N ARG A 365 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'A' and resid 393 through 394 removed outlier: 3.506A pdb=" N VAL A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 164 removed outlier: 6.619A pdb=" N LYS B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 10.473A pdb=" N THR B 168 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASP B 56 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TYR B 170 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 275 through 298 current: chain 'B' and resid 332 through 333 Processing sheet with id=AB1, first strand: chain 'B' and resid 226 through 227 removed outlier: 4.337A pdb=" N MET B 226 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 263 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 277 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N VAL B 269 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR B 275 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N ILE B 277 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N LYS B 60 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 9.224A pdb=" N ARG B 279 " --> pdb=" O VAL B 58 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N VAL B 58 " --> pdb=" O ARG B 279 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N TYR B 281 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 9.562A pdb=" N ASP B 56 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N THR B 54 " --> pdb=" O PRO B 283 " (cutoff:3.500A) removed outlier: 10.625A pdb=" N LEU B 285 " --> pdb=" O PRO B 52 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N GLU B 287 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N SER B 50 " --> pdb=" O GLU B 287 " (cutoff:3.500A) removed outlier: 9.517A pdb=" N GLN B 289 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ILE B 48 " --> pdb=" O GLN B 289 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA B 291 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR B 46 " --> pdb=" O ALA B 291 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL B 42 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N LEU B 297 " --> pdb=" O LYS B 40 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYS B 40 " --> pdb=" O LEU B 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 60 current: chain 'B' and resid 322 through 326 Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 103 removed outlier: 3.546A pdb=" N HIS B 102 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N VAL B 113 " --> pdb=" O ILE E 426 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER E 428 " --> pdb=" O VAL B 113 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET B 115 " --> pdb=" O SER E 428 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 124 Processing sheet with id=AB4, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AB5, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AB6, first strand: chain 'B' and resid 393 through 394 removed outlier: 6.671A pdb=" N ILE B 426 " --> pdb=" O MET C 115 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 158 through 162 removed outlier: 17.003A pdb=" N THR C 168 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N THR C 54 " --> pdb=" O THR C 168 " (cutoff:3.500A) removed outlier: 11.309A pdb=" N TYR C 170 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ASP C 56 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N PHE C 172 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 58 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C 46 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N SER C 50 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLU C 287 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N LEU C 285 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR C 54 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N ASP C 56 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N TYR C 281 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL C 58 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG C 279 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS C 60 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ILE C 277 " --> pdb=" O LYS C 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 275 through 298 current: chain 'C' and resid 332 through 333 Processing sheet with id=AB8, first strand: chain 'C' and resid 226 through 227 removed outlier: 4.256A pdb=" N MET C 226 " --> pdb=" O GLY C 264 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 263 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL C 269 " --> pdb=" O TYR C 275 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 9.754A pdb=" N ILE C 277 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 9.452A pdb=" N LYS C 60 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N ARG C 279 " --> pdb=" O VAL C 58 " (cutoff:3.500A) removed outlier: 9.692A pdb=" N VAL C 58 " --> pdb=" O ARG C 279 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N TYR C 281 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 9.881A pdb=" N ASP C 56 " --> pdb=" O TYR C 281 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N THR C 54 " --> pdb=" O PRO C 283 " (cutoff:3.500A) removed outlier: 10.719A pdb=" N LEU C 285 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLU C 287 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N SER C 50 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N GLN C 289 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 10.749A pdb=" N ILE C 48 " --> pdb=" O GLN C 289 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA C 291 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR C 46 " --> pdb=" O ALA C 291 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 42 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU C 297 " --> pdb=" O LYS C 40 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS C 40 " --> pdb=" O LEU C 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 60 current: chain 'C' and resid 322 through 326 Processing sheet with id=AB9, first strand: chain 'C' and resid 301 through 302 removed outlier: 6.070A pdb=" N ARG C 365 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 410 through 412 Processing sheet with id=AC2, first strand: chain 'C' and resid 399 through 401 removed outlier: 4.452A pdb=" N CYS C 392 " --> pdb=" O ILE C 401 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN C 393 " --> pdb=" O VAL C 421 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 426 " --> pdb=" O MET E 115 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 158 through 164 removed outlier: 6.292A pdb=" N LYS D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N THR D 168 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASP D 56 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR D 170 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 275 through 298 current: chain 'D' and resid 332 through 333 Processing sheet with id=AC4, first strand: chain 'D' and resid 226 through 227 removed outlier: 4.231A pdb=" N MET D 226 " --> pdb=" O GLY D 264 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR D 263 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE D 277 " --> pdb=" O ILE D 267 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL D 269 " --> pdb=" O TYR D 275 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR D 275 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 9.897A pdb=" N ILE D 277 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 9.488A pdb=" N LYS D 60 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N ARG D 279 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL D 58 " --> pdb=" O ARG D 279 " (cutoff:3.500A) removed outlier: 9.623A pdb=" N TYR D 281 " --> pdb=" O ASP D 56 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N ASP D 56 " --> pdb=" O TYR D 281 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N THR D 54 " --> pdb=" O PRO D 283 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N LEU D 285 " --> pdb=" O PRO D 52 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N GLU D 287 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 9.886A pdb=" N SER D 50 " --> pdb=" O GLU D 287 " (cutoff:3.500A) removed outlier: 10.020A pdb=" N GLN D 289 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N ILE D 48 " --> pdb=" O GLN D 289 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA D 291 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL D 42 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LEU D 297 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N LYS D 40 " --> pdb=" O LEU D 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 38 through 60 current: chain 'D' and resid 322 through 326 Processing sheet with id=AC5, first strand: chain 'D' and resid 301 through 303 Processing sheet with id=AC6, first strand: chain 'D' and resid 410 through 412 Processing sheet with id=AC7, first strand: chain 'D' and resid 399 through 401 removed outlier: 4.513A pdb=" N CYS D 392 " --> pdb=" O ILE D 401 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN D 393 " --> pdb=" O VAL D 421 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL D 425 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE D 426 " --> pdb=" O MET G 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.441A pdb=" N TYR E 170 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 275 through 298 current: chain 'E' and resid 332 through 333 Processing sheet with id=AC9, first strand: chain 'E' and resid 266 through 270 removed outlier: 6.094A pdb=" N ILE E 266 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARG E 279 " --> pdb=" O ILE E 266 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR E 268 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.845A pdb=" N ILE E 277 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N LYS E 60 " --> pdb=" O ILE E 277 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N ARG E 279 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 9.983A pdb=" N VAL E 58 " --> pdb=" O ARG E 279 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N TYR E 281 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 9.818A pdb=" N ASP E 56 " --> pdb=" O TYR E 281 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N THR E 54 " --> pdb=" O PRO E 283 " (cutoff:3.500A) removed outlier: 10.702A pdb=" N LEU E 285 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 8.910A pdb=" N GLU E 287 " --> pdb=" O SER E 50 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N SER E 50 " --> pdb=" O GLU E 287 " (cutoff:3.500A) removed outlier: 9.713A pdb=" N GLN E 289 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N ILE E 48 " --> pdb=" O GLN E 289 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA E 291 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR E 46 " --> pdb=" O ALA E 291 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL E 42 " --> pdb=" O GLU E 295 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 297 " --> pdb=" O LYS E 40 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N LYS E 40 " --> pdb=" O LEU E 297 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 38 through 60 current: chain 'E' and resid 322 through 326 Processing sheet with id=AD1, first strand: chain 'E' and resid 226 through 227 removed outlier: 4.132A pdb=" N MET E 226 " --> pdb=" O GLY E 264 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 301 through 303 Processing sheet with id=AD3, first strand: chain 'G' and resid 158 through 162 removed outlier: 17.062A pdb=" N THR G 168 " --> pdb=" O PRO G 52 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N THR G 54 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N TYR G 170 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ASP G 56 " --> pdb=" O TYR G 170 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N PHE G 172 " --> pdb=" O ASP G 56 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL G 58 " --> pdb=" O PHE G 172 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 275 through 298 current: chain 'G' and resid 332 through 333 Processing sheet with id=AD4, first strand: chain 'G' and resid 226 through 227 removed outlier: 4.060A pdb=" N MET G 226 " --> pdb=" O GLY G 264 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR G 263 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE G 277 " --> pdb=" O ILE G 267 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N VAL G 269 " --> pdb=" O TYR G 275 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N TYR G 275 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE G 277 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE G 59 " --> pdb=" O ILE G 277 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG G 279 " --> pdb=" O ILE G 57 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE G 57 " --> pdb=" O ARG G 279 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N TYR G 281 " --> pdb=" O LYS G 55 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LYS G 55 " --> pdb=" O TYR G 281 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU G 53 " --> pdb=" O PRO G 283 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU G 285 " --> pdb=" O ASN G 51 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N ASN G 51 " --> pdb=" O LEU G 285 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLU G 287 " --> pdb=" O LYS G 49 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N LYS G 49 " --> pdb=" O GLU G 287 " (cutoff:3.500A) removed outlier: 9.914A pdb=" N GLN G 289 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 9.438A pdb=" N LYS G 47 " --> pdb=" O GLN G 289 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N ALA G 291 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N LYS G 45 " --> pdb=" O ALA G 291 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE G 293 " --> pdb=" O THR G 43 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N THR G 43 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N GLU G 295 " --> pdb=" O GLY G 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 38 through 60 current: chain 'G' and resid 322 through 326 Processing sheet with id=AD5, first strand: chain 'G' and resid 301 through 303 removed outlier: 6.021A pdb=" N ARG G 365 " --> pdb=" O VAL G 449 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 392 through 394 removed outlier: 4.619A pdb=" N CYS G 392 " --> pdb=" O ILE G 401 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG G 399 " --> pdb=" O CYS G 394 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2223 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: 4.11 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6162 1.34 - 1.46: 3796 1.46 - 1.58: 10309 1.58 - 1.70: 0 1.70 - 1.83: 192 Bond restraints: 20459 Sorted by residual: bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.34e+01 bond pdb=" N ILE C 326 " pdb=" CA ILE C 326 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N VAL D 113 " pdb=" CA VAL D 113 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.14e-02 7.69e+03 9.95e+00 bond pdb=" CA ASN B 51 " pdb=" CB ASN B 51 " ideal model delta sigma weight residual 1.522 1.543 -0.021 7.00e-03 2.04e+04 9.12e+00 bond pdb=" N VAL B 113 " pdb=" CA VAL B 113 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.20e-02 6.94e+03 8.73e+00 ... (remaining 20454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 25920 1.50 - 3.00: 1507 3.00 - 4.50: 315 4.50 - 6.01: 52 6.01 - 7.51: 9 Bond angle restraints: 27803 Sorted by residual: angle pdb=" N ALA B 111 " pdb=" CA ALA B 111 " pdb=" C ALA B 111 " ideal model delta sigma weight residual 110.35 115.91 -5.56 1.40e+00 5.10e-01 1.58e+01 angle pdb=" OE1 GLN D 162 " pdb=" CD GLN D 162 " pdb=" NE2 GLN D 162 " ideal model delta sigma weight residual 122.60 118.80 3.80 1.00e+00 1.00e+00 1.45e+01 angle pdb=" OE1 GLN D 289 " pdb=" CD GLN D 289 " pdb=" NE2 GLN D 289 " ideal model delta sigma weight residual 122.60 118.84 3.76 1.00e+00 1.00e+00 1.41e+01 angle pdb=" N VAL G 369 " pdb=" CA VAL G 369 " pdb=" C VAL G 369 " ideal model delta sigma weight residual 112.29 108.78 3.51 9.40e-01 1.13e+00 1.40e+01 angle pdb=" N ILE B 328 " pdb=" CA ILE B 328 " pdb=" CB ILE B 328 " ideal model delta sigma weight residual 111.23 105.13 6.10 1.65e+00 3.67e-01 1.37e+01 ... (remaining 27798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 11029 17.97 - 35.94: 1159 35.94 - 53.91: 325 53.91 - 71.89: 68 71.89 - 89.86: 30 Dihedral angle restraints: 12611 sinusoidal: 4930 harmonic: 7681 Sorted by residual: dihedral pdb=" CB CYS B 71 " pdb=" SG CYS B 71 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual -86.00 -158.24 72.24 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CB CYS E 71 " pdb=" SG CYS E 71 " pdb=" SG CYS E 192 " pdb=" CB CYS E 192 " ideal model delta sinusoidal sigma weight residual -86.00 -17.40 -68.60 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS G 71 " pdb=" SG CYS G 71 " pdb=" SG CYS G 192 " pdb=" CB CYS G 192 " ideal model delta sinusoidal sigma weight residual -86.00 -152.23 66.23 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 12608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 2206 0.043 - 0.087: 764 0.087 - 0.130: 339 0.130 - 0.173: 75 0.173 - 0.217: 19 Chirality restraints: 3403 Sorted by residual: chirality pdb=" CA ILE A 262 " pdb=" N ILE A 262 " pdb=" C ILE A 262 " pdb=" CB ILE A 262 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 179 " pdb=" N ILE B 179 " pdb=" C ILE B 179 " pdb=" CB ILE B 179 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE C 36 " pdb=" N ILE C 36 " pdb=" C ILE C 36 " pdb=" CB ILE C 36 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 3400 not shown) Planarity restraints: 3525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 240 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C GLU D 240 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU D 240 " -0.018 2.00e-02 2.50e+03 pdb=" N THR D 241 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 350 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C ASN A 350 " -0.046 2.00e-02 2.50e+03 pdb=" O ASN A 350 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 351 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 96 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ILE B 96 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE B 96 " -0.017 2.00e-02 2.50e+03 pdb=" N TYR B 97 " -0.015 2.00e-02 2.50e+03 ... (remaining 3522 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 275 2.62 - 3.19: 18680 3.19 - 3.76: 31827 3.76 - 4.33: 43626 4.33 - 4.90: 71235 Nonbonded interactions: 165643 Sorted by model distance: nonbonded pdb=" OG SER C 404 " pdb=" OE1 GLU C 406 " model vdw 2.056 3.040 nonbonded pdb=" O ASN B 182 " pdb=" OG1 THR B 186 " model vdw 2.110 3.040 nonbonded pdb=" OD1 ASP G 103 " pdb=" OH TYR G 135 " model vdw 2.151 3.040 nonbonded pdb=" NH2 ARG A 244 " pdb=" OD1 ASP D 200 " model vdw 2.169 3.120 nonbonded pdb=" OD1 ASN G 303 " pdb=" NH1 ARG G 365 " model vdw 2.173 3.120 ... (remaining 165638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 104 or resid 112 through 468)) selection = (chain 'B' and (resid 27 through 104 or resid 112 through 468)) selection = chain 'C' selection = (chain 'D' and (resid 27 through 104 or resid 112 through 468)) selection = chain 'E' selection = chain 'G' } 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: 3.810 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.005 0.073 20495 Z= 0.329 Angle : 0.814 7.507 27875 Z= 0.512 Chirality : 0.055 0.217 3403 Planarity : 0.004 0.060 3525 Dihedral : 16.405 89.857 7545 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.54 % Allowed : 21.78 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2605 helix: 0.58 (0.18), residues: 833 sheet: 0.13 (0.24), residues: 430 loop : -0.92 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 375 TYR 0.025 0.002 TYR A 438 PHE 0.020 0.002 PHE C 253 TRP 0.013 0.002 TRP E 308 HIS 0.005 0.001 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00538 (20459) covalent geometry : angle 0.81093 (27803) SS BOND : bond 0.00305 ( 36) SS BOND : angle 1.60715 ( 72) hydrogen bonds : bond 0.18963 ( 797) hydrogen bonds : angle 7.33828 ( 2223) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 534 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7195 (mttm) cc_final: 0.6624 (tptt) REVERT: A 191 PRO cc_start: 0.6469 (Cg_exo) cc_final: 0.6150 (Cg_endo) REVERT: A 197 LEU cc_start: 0.7989 (mp) cc_final: 0.7486 (mp) REVERT: B 156 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5099 (mp0) REVERT: B 261 SER cc_start: 0.7835 (t) cc_final: 0.7608 (m) REVERT: B 383 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6523 (tt) REVERT: C 178 TYR cc_start: 0.6885 (t80) cc_final: 0.6399 (t80) REVERT: C 226 MET cc_start: 0.8117 (ttm) cc_final: 0.7837 (ttp) REVERT: C 348 MET cc_start: 0.8027 (mtp) cc_final: 0.7580 (mtp) REVERT: C 431 LYS cc_start: 0.7457 (tttm) cc_final: 0.7245 (ttmm) REVERT: C 453 LYS cc_start: 0.7874 (tttm) cc_final: 0.7434 (ttpt) REVERT: D 46 TYR cc_start: 0.7424 (t80) cc_final: 0.7128 (t80) REVERT: D 68 MET cc_start: 0.6408 (ptm) cc_final: 0.6205 (ptt) REVERT: D 205 LYS cc_start: 0.8188 (tttm) cc_final: 0.7970 (ttmt) REVERT: D 463 MET cc_start: 0.7053 (mtp) cc_final: 0.6844 (tpt) REVERT: E 197 LEU cc_start: 0.7869 (mp) cc_final: 0.7151 (mp) REVERT: E 335 LYS cc_start: 0.6314 (tppt) cc_final: 0.5070 (ptmt) REVERT: G 44 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6298 (mtt90) REVERT: G 95 GLU cc_start: 0.6310 (mt-10) cc_final: 0.6097 (pt0) REVERT: G 102 HIS cc_start: 0.4275 (p90) cc_final: 0.3260 (m170) REVERT: G 136 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6461 (mm-30) REVERT: G 220 ASP cc_start: 0.7754 (m-30) cc_final: 0.7398 (m-30) outliers start: 36 outliers final: 6 residues processed: 556 average time/residue: 0.1520 time to fit residues: 130.8398 Evaluate side-chains 334 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 326 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain E residue 355 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 140 ASN A 265 GLN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN B 414 ASN C 51 ASN C 127 GLN C 140 ASN C 372 HIS C 407 GLN D 140 ASN D 290 GLN D 351 ASN E 265 GLN G 180 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.189074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.165764 restraints weight = 27705.534| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.99 r_work: 0.3929 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3794 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20495 Z= 0.193 Angle : 0.686 9.894 27875 Z= 0.358 Chirality : 0.050 0.222 3403 Planarity : 0.004 0.040 3525 Dihedral : 5.890 86.165 2802 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.37 % Allowed : 19.77 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2605 helix: 0.85 (0.18), residues: 848 sheet: -0.20 (0.23), residues: 467 loop : -1.02 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 375 TYR 0.019 0.002 TYR D 135 PHE 0.016 0.002 PHE B 315 TRP 0.009 0.002 TRP G 308 HIS 0.011 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00449 (20459) covalent geometry : angle 0.67948 (27803) SS BOND : bond 0.00404 ( 36) SS BOND : angle 2.01877 ( 72) hydrogen bonds : bond 0.04400 ( 797) hydrogen bonds : angle 5.48803 ( 2223) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 320 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7233 (mttm) cc_final: 0.6819 (tptt) REVERT: A 115 MET cc_start: 0.6424 (tpp) cc_final: 0.6144 (mtp) REVERT: A 148 LYS cc_start: 0.7153 (ttmt) cc_final: 0.6739 (tttm) REVERT: A 161 LEU cc_start: 0.8017 (mt) cc_final: 0.7637 (mt) REVERT: B 145 ASN cc_start: 0.8038 (m110) cc_final: 0.7695 (m-40) REVERT: B 152 GLU cc_start: 0.7838 (tt0) cc_final: 0.7611 (tm-30) REVERT: B 156 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5525 (mp0) REVERT: B 177 ASP cc_start: 0.6841 (t0) cc_final: 0.6464 (p0) REVERT: C 138 MET cc_start: 0.5414 (mtm) cc_final: 0.4969 (tpt) REVERT: C 178 TYR cc_start: 0.6892 (t80) cc_final: 0.6491 (t80) REVERT: C 224 ASN cc_start: 0.6165 (p0) cc_final: 0.5273 (t0) REVERT: D 331 CYS cc_start: 0.6524 (m) cc_final: 0.6193 (m) REVERT: E 229 GLN cc_start: 0.7197 (OUTLIER) cc_final: 0.5942 (mt0) REVERT: E 335 LYS cc_start: 0.6561 (tppt) cc_final: 0.5268 (ptmt) REVERT: G 95 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6361 (pt0) REVERT: G 138 MET cc_start: 0.6757 (tpt) cc_final: 0.5960 (mtp) REVERT: G 226 MET cc_start: 0.8323 (ttm) cc_final: 0.8078 (ttp) outliers start: 102 outliers final: 48 residues processed: 402 average time/residue: 0.1404 time to fit residues: 90.8314 Evaluate side-chains 304 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 254 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 114 CYS Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 104 CYS Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 396 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 214 optimal weight: 0.5980 chunk 188 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 244 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS B 100 ASN B 182 ASN B 303 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN C 407 GLN D 290 GLN E 29 HIS G 217 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.187766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164568 restraints weight = 27562.681| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.98 r_work: 0.3918 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20495 Z= 0.166 Angle : 0.617 9.401 27875 Z= 0.323 Chirality : 0.048 0.208 3403 Planarity : 0.004 0.039 3525 Dihedral : 5.205 54.656 2793 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 4.29 % Allowed : 20.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.16), residues: 2605 helix: 0.99 (0.18), residues: 845 sheet: -0.21 (0.24), residues: 441 loop : -1.08 (0.16), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 365 TYR 0.024 0.002 TYR B 438 PHE 0.022 0.002 PHE D 315 TRP 0.008 0.002 TRP G 308 HIS 0.007 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00392 (20459) covalent geometry : angle 0.61392 (27803) SS BOND : bond 0.00406 ( 36) SS BOND : angle 1.38940 ( 72) hydrogen bonds : bond 0.03987 ( 797) hydrogen bonds : angle 5.25406 ( 2223) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 293 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7292 (mttm) cc_final: 0.6865 (tptt) REVERT: A 115 MET cc_start: 0.6695 (tpp) cc_final: 0.6270 (mtp) REVERT: A 148 LYS cc_start: 0.7269 (ttmt) cc_final: 0.6812 (tttm) REVERT: B 145 ASN cc_start: 0.8046 (m110) cc_final: 0.7734 (m-40) REVERT: B 152 GLU cc_start: 0.7892 (tt0) cc_final: 0.7626 (tm-30) REVERT: B 156 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5395 (mp0) REVERT: B 180 ASN cc_start: 0.6978 (m-40) cc_final: 0.6218 (t0) REVERT: B 192 CYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6627 (t) REVERT: C 59 ILE cc_start: 0.6985 (OUTLIER) cc_final: 0.6593 (mt) REVERT: C 201 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6506 (mp) REVERT: C 226 MET cc_start: 0.8235 (ttm) cc_final: 0.7968 (ttp) REVERT: C 304 ASP cc_start: 0.7754 (m-30) cc_final: 0.7540 (m-30) REVERT: D 142 ASP cc_start: 0.6437 (m-30) cc_final: 0.6161 (m-30) REVERT: D 143 ASN cc_start: 0.7744 (t0) cc_final: 0.7431 (t0) REVERT: D 331 CYS cc_start: 0.6547 (m) cc_final: 0.6295 (m) REVERT: E 229 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.5894 (mt0) REVERT: G 95 GLU cc_start: 0.6691 (mt-10) cc_final: 0.6423 (pt0) REVERT: G 226 MET cc_start: 0.8269 (ttm) cc_final: 0.8019 (ttp) REVERT: G 319 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6477 (ttm110) REVERT: G 412 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6723 (pt) outliers start: 100 outliers final: 58 residues processed: 378 average time/residue: 0.1296 time to fit residues: 80.4145 Evaluate side-chains 313 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 248 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 387 CYS Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 127 GLN A 302 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 194 GLN ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN D 351 ASN E 127 GLN E 176 GLN E 180 ASN E 303 ASN G 180 ASN G 372 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.185376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161585 restraints weight = 27936.283| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.04 r_work: 0.3882 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20495 Z= 0.188 Angle : 0.645 10.473 27875 Z= 0.334 Chirality : 0.049 0.207 3403 Planarity : 0.004 0.044 3525 Dihedral : 5.263 52.424 2793 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.63 % Allowed : 21.78 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.16), residues: 2605 helix: 0.96 (0.18), residues: 845 sheet: -0.66 (0.23), residues: 463 loop : -1.11 (0.16), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 375 TYR 0.025 0.002 TYR D 438 PHE 0.027 0.002 PHE C 253 TRP 0.008 0.002 TRP G 308 HIS 0.004 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00450 (20459) covalent geometry : angle 0.64079 (27803) SS BOND : bond 0.00349 ( 36) SS BOND : angle 1.60647 ( 72) hydrogen bonds : bond 0.03958 ( 797) hydrogen bonds : angle 5.21292 ( 2223) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 271 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7058 (t) cc_final: 0.6304 (p) REVERT: A 55 LYS cc_start: 0.7296 (mttm) cc_final: 0.6821 (tptt) REVERT: A 114 CYS cc_start: 0.5206 (t) cc_final: 0.4582 (m) REVERT: A 115 MET cc_start: 0.6687 (tpp) cc_final: 0.6222 (mtp) REVERT: A 148 LYS cc_start: 0.7296 (ttmt) cc_final: 0.6784 (tttm) REVERT: B 46 TYR cc_start: 0.7439 (t80) cc_final: 0.7179 (t80) REVERT: B 152 GLU cc_start: 0.7944 (tt0) cc_final: 0.7663 (tm-30) REVERT: B 156 GLU cc_start: 0.5614 (OUTLIER) cc_final: 0.5305 (mp0) REVERT: B 333 ILE cc_start: 0.6787 (mm) cc_final: 0.6537 (mm) REVERT: C 59 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6611 (mt) REVERT: C 138 MET cc_start: 0.4803 (mtp) cc_final: 0.4581 (tpt) REVERT: C 226 MET cc_start: 0.8186 (ttm) cc_final: 0.7915 (ttp) REVERT: E 115 MET cc_start: 0.6618 (tpp) cc_final: 0.6361 (mtp) REVERT: E 229 GLN cc_start: 0.7138 (OUTLIER) cc_final: 0.5929 (mt0) REVERT: E 327 GLU cc_start: 0.8085 (mp0) cc_final: 0.7856 (mp0) REVERT: G 95 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6523 (pt0) REVERT: G 138 MET cc_start: 0.6612 (tpt) cc_final: 0.5834 (mtp) REVERT: G 226 MET cc_start: 0.8262 (ttm) cc_final: 0.8003 (ttp) REVERT: G 319 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6500 (ttm110) REVERT: G 412 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6691 (pt) outliers start: 108 outliers final: 71 residues processed: 361 average time/residue: 0.1290 time to fit residues: 76.6990 Evaluate side-chains 318 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 320 ASN Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 246 optimal weight: 1.9990 chunk 222 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 221 optimal weight: 2.9990 chunk 256 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN D 290 GLN E 342 GLN G 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.187475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164180 restraints weight = 27638.076| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.98 r_work: 0.3915 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20495 Z= 0.133 Angle : 0.596 12.733 27875 Z= 0.308 Chirality : 0.047 0.245 3403 Planarity : 0.004 0.070 3525 Dihedral : 5.019 54.373 2792 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.90 % Allowed : 22.51 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.16), residues: 2605 helix: 1.08 (0.18), residues: 847 sheet: -0.64 (0.24), residues: 442 loop : -1.08 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 TYR 0.028 0.001 TYR D 438 PHE 0.018 0.001 PHE G 253 TRP 0.007 0.001 TRP G 308 HIS 0.003 0.001 HIS B 372 Details of bonding type rmsd covalent geometry : bond 0.00319 (20459) covalent geometry : angle 0.59177 (27803) SS BOND : bond 0.00382 ( 36) SS BOND : angle 1.48665 ( 72) hydrogen bonds : bond 0.03638 ( 797) hydrogen bonds : angle 4.99890 ( 2223) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 256 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7021 (t) cc_final: 0.6300 (p) REVERT: A 55 LYS cc_start: 0.7217 (mttm) cc_final: 0.6725 (tptt) REVERT: A 115 MET cc_start: 0.6908 (tpp) cc_final: 0.6488 (mtp) REVERT: A 148 LYS cc_start: 0.7282 (ttmt) cc_final: 0.6772 (tttm) REVERT: B 46 TYR cc_start: 0.7434 (t80) cc_final: 0.7213 (t80) REVERT: B 72 THR cc_start: 0.5834 (t) cc_final: 0.5352 (m) REVERT: B 152 GLU cc_start: 0.7880 (tt0) cc_final: 0.7567 (tm-30) REVERT: B 333 ILE cc_start: 0.6811 (mm) cc_final: 0.6518 (mm) REVERT: C 45 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7220 (mptt) REVERT: C 102 HIS cc_start: 0.4081 (p90) cc_final: 0.1920 (m-70) REVERT: C 226 MET cc_start: 0.8102 (ttm) cc_final: 0.7841 (ttp) REVERT: C 263 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7447 (m) REVERT: C 355 CYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6429 (t) REVERT: E 115 MET cc_start: 0.6670 (tpp) cc_final: 0.6407 (mtp) REVERT: E 229 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.5865 (mt0) REVERT: E 433 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7801 (mp) REVERT: G 95 GLU cc_start: 0.6705 (mt-10) cc_final: 0.6345 (pt0) REVERT: G 138 MET cc_start: 0.6490 (tpt) cc_final: 0.5754 (mtp) REVERT: G 226 MET cc_start: 0.8180 (ttm) cc_final: 0.7929 (ttp) REVERT: G 412 ILE cc_start: 0.7060 (OUTLIER) cc_final: 0.6744 (pt) outliers start: 91 outliers final: 60 residues processed: 334 average time/residue: 0.1317 time to fit residues: 71.9106 Evaluate side-chains 308 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 242 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 186 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 154 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 102 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN D 290 GLN E 342 GLN G 407 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.186611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.162868 restraints weight = 27667.748| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.04 r_work: 0.3901 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20495 Z= 0.149 Angle : 0.601 10.894 27875 Z= 0.310 Chirality : 0.047 0.235 3403 Planarity : 0.004 0.058 3525 Dihedral : 4.849 54.391 2789 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.07 % Allowed : 22.47 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2605 helix: 1.20 (0.19), residues: 827 sheet: -0.69 (0.24), residues: 436 loop : -1.17 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 375 TYR 0.026 0.001 TYR D 438 PHE 0.019 0.002 PHE C 253 TRP 0.007 0.002 TRP G 308 HIS 0.002 0.001 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00361 (20459) covalent geometry : angle 0.59672 (27803) SS BOND : bond 0.00533 ( 36) SS BOND : angle 1.59842 ( 72) hydrogen bonds : bond 0.03608 ( 797) hydrogen bonds : angle 4.95531 ( 2223) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 251 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7067 (t) cc_final: 0.6362 (p) REVERT: A 55 LYS cc_start: 0.7221 (mttm) cc_final: 0.6734 (tptt) REVERT: A 115 MET cc_start: 0.6990 (tpp) cc_final: 0.6553 (mtp) REVERT: A 148 LYS cc_start: 0.7335 (ttmt) cc_final: 0.6821 (tttm) REVERT: A 352 MET cc_start: 0.7326 (tpp) cc_final: 0.7089 (tpp) REVERT: B 72 THR cc_start: 0.5759 (t) cc_final: 0.5263 (m) REVERT: B 152 GLU cc_start: 0.7970 (tt0) cc_final: 0.7650 (tm-30) REVERT: B 333 ILE cc_start: 0.6876 (mm) cc_final: 0.6581 (mm) REVERT: C 102 HIS cc_start: 0.4053 (p90) cc_final: 0.1934 (m-70) REVERT: C 138 MET cc_start: 0.6631 (tpt) cc_final: 0.5975 (mtp) REVERT: C 226 MET cc_start: 0.8129 (ttm) cc_final: 0.7873 (ttp) REVERT: C 355 CYS cc_start: 0.6981 (OUTLIER) cc_final: 0.6423 (t) REVERT: C 453 LYS cc_start: 0.7901 (tttm) cc_final: 0.7349 (ttpt) REVERT: E 115 MET cc_start: 0.6742 (tpp) cc_final: 0.6450 (mtp) REVERT: E 229 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.5870 (mt0) REVERT: G 95 GLU cc_start: 0.6857 (mt-10) cc_final: 0.6525 (pt0) REVERT: G 138 MET cc_start: 0.6434 (tpt) cc_final: 0.5786 (mtp) REVERT: G 412 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6727 (pt) outliers start: 95 outliers final: 75 residues processed: 331 average time/residue: 0.1187 time to fit residues: 65.0843 Evaluate side-chains 316 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 238 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 107 ASP Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 96 ILE Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 288 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 104 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 0.4980 chunk 27 optimal weight: 0.9980 chunk 93 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 249 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS C 176 GLN C 407 GLN ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 407 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.188463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.164865 restraints weight = 27579.458| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.03 r_work: 0.3925 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3791 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20495 Z= 0.120 Angle : 0.577 10.279 27875 Z= 0.298 Chirality : 0.047 0.199 3403 Planarity : 0.004 0.060 3525 Dihedral : 4.718 56.245 2789 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.43 % Allowed : 22.90 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.16), residues: 2605 helix: 1.29 (0.19), residues: 827 sheet: -0.49 (0.23), residues: 472 loop : -1.11 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 375 TYR 0.025 0.001 TYR D 438 PHE 0.019 0.001 PHE C 253 TRP 0.007 0.001 TRP G 308 HIS 0.002 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00285 (20459) covalent geometry : angle 0.57309 (27803) SS BOND : bond 0.00308 ( 36) SS BOND : angle 1.42255 ( 72) hydrogen bonds : bond 0.03405 ( 797) hydrogen bonds : angle 4.83215 ( 2223) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 255 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.6962 (t) cc_final: 0.6309 (p) REVERT: A 55 LYS cc_start: 0.7127 (mttm) cc_final: 0.6672 (tptt) REVERT: A 115 MET cc_start: 0.6806 (tpp) cc_final: 0.6416 (mtp) REVERT: A 148 LYS cc_start: 0.7317 (ttmt) cc_final: 0.6826 (tttm) REVERT: A 162 GLN cc_start: 0.6390 (pm20) cc_final: 0.5962 (mm-40) REVERT: A 352 MET cc_start: 0.7308 (tpp) cc_final: 0.7093 (tpp) REVERT: B 72 THR cc_start: 0.5603 (t) cc_final: 0.5145 (m) REVERT: B 152 GLU cc_start: 0.7972 (tt0) cc_final: 0.7645 (tm-30) REVERT: B 333 ILE cc_start: 0.6831 (mm) cc_final: 0.6564 (mm) REVERT: C 45 LYS cc_start: 0.7644 (OUTLIER) cc_final: 0.7248 (mptt) REVERT: C 102 HIS cc_start: 0.4021 (p90) cc_final: 0.1761 (m90) REVERT: C 138 MET cc_start: 0.6561 (tpt) cc_final: 0.5996 (mtp) REVERT: C 226 MET cc_start: 0.8091 (ttm) cc_final: 0.7847 (ttp) REVERT: C 263 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7440 (m) REVERT: C 453 LYS cc_start: 0.7946 (tttm) cc_final: 0.7350 (ttpt) REVERT: E 115 MET cc_start: 0.6700 (tpp) cc_final: 0.6427 (mtp) REVERT: E 145 ASN cc_start: 0.8078 (m-40) cc_final: 0.7701 (m-40) REVERT: E 162 GLN cc_start: 0.6569 (pm20) cc_final: 0.6015 (mt0) REVERT: G 76 MET cc_start: 0.6613 (mmt) cc_final: 0.6312 (tpp) REVERT: G 95 GLU cc_start: 0.6707 (mt-10) cc_final: 0.6484 (pt0) REVERT: G 226 MET cc_start: 0.8208 (ttm) cc_final: 0.7977 (ttp) REVERT: G 412 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6795 (pt) outliers start: 80 outliers final: 65 residues processed: 318 average time/residue: 0.1165 time to fit residues: 60.7973 Evaluate side-chains 303 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 235 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 167 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 257 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 193 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 407 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN G 303 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.187143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.163506 restraints weight = 27744.090| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 2.03 r_work: 0.3908 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20495 Z= 0.139 Angle : 0.589 10.569 27875 Z= 0.302 Chirality : 0.047 0.199 3403 Planarity : 0.004 0.056 3525 Dihedral : 4.719 55.957 2789 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.86 % Allowed : 22.68 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.16), residues: 2605 helix: 1.29 (0.19), residues: 828 sheet: -0.48 (0.24), residues: 466 loop : -1.18 (0.16), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 TYR 0.023 0.001 TYR D 438 PHE 0.019 0.002 PHE E 212 TRP 0.009 0.001 TRP G 308 HIS 0.003 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00335 (20459) covalent geometry : angle 0.58542 (27803) SS BOND : bond 0.00309 ( 36) SS BOND : angle 1.38366 ( 72) hydrogen bonds : bond 0.03455 ( 797) hydrogen bonds : angle 4.83950 ( 2223) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 241 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7000 (t) cc_final: 0.6347 (p) REVERT: A 55 LYS cc_start: 0.7111 (mttm) cc_final: 0.6643 (tptt) REVERT: A 115 MET cc_start: 0.6875 (tpp) cc_final: 0.6497 (mtp) REVERT: A 148 LYS cc_start: 0.7332 (ttmt) cc_final: 0.6831 (tttm) REVERT: A 162 GLN cc_start: 0.6386 (pm20) cc_final: 0.5937 (mm-40) REVERT: A 352 MET cc_start: 0.7334 (tpp) cc_final: 0.7104 (tpp) REVERT: B 72 THR cc_start: 0.5689 (t) cc_final: 0.5153 (m) REVERT: B 152 GLU cc_start: 0.7980 (tt0) cc_final: 0.7654 (tm-30) REVERT: C 59 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6520 (mt) REVERT: C 102 HIS cc_start: 0.4063 (p90) cc_final: 0.1928 (m-70) REVERT: C 138 MET cc_start: 0.6627 (tpt) cc_final: 0.6032 (mtp) REVERT: C 226 MET cc_start: 0.8096 (ttm) cc_final: 0.7846 (ttp) REVERT: C 263 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7407 (m) REVERT: C 453 LYS cc_start: 0.7949 (tttm) cc_final: 0.7359 (ttpt) REVERT: E 115 MET cc_start: 0.6801 (tpp) cc_final: 0.6488 (mtp) REVERT: E 162 GLN cc_start: 0.6578 (pm20) cc_final: 0.5924 (mt0) REVERT: E 229 GLN cc_start: 0.7037 (OUTLIER) cc_final: 0.5872 (mt0) REVERT: G 68 MET cc_start: 0.6083 (ppp) cc_final: 0.4816 (ptt) REVERT: G 95 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6515 (pt0) REVERT: G 226 MET cc_start: 0.8254 (ttm) cc_final: 0.7983 (ttp) REVERT: G 412 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6783 (pt) outliers start: 90 outliers final: 76 residues processed: 317 average time/residue: 0.1276 time to fit residues: 66.7684 Evaluate side-chains 320 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 240 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 165 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 162 optimal weight: 0.6980 chunk 228 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS C 407 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.187512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.163832 restraints weight = 27585.569| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.02 r_work: 0.3913 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20495 Z= 0.131 Angle : 0.585 10.362 27875 Z= 0.300 Chirality : 0.047 0.224 3403 Planarity : 0.004 0.055 3525 Dihedral : 4.711 56.246 2789 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.77 % Allowed : 22.68 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.16), residues: 2605 helix: 1.33 (0.19), residues: 828 sheet: -0.62 (0.23), residues: 487 loop : -1.15 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 375 TYR 0.022 0.001 TYR D 438 PHE 0.020 0.001 PHE C 253 TRP 0.009 0.001 TRP G 308 HIS 0.003 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00316 (20459) covalent geometry : angle 0.58067 (27803) SS BOND : bond 0.00331 ( 36) SS BOND : angle 1.47348 ( 72) hydrogen bonds : bond 0.03424 ( 797) hydrogen bonds : angle 4.77564 ( 2223) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 250 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7023 (t) cc_final: 0.6408 (p) REVERT: A 55 LYS cc_start: 0.7179 (mttm) cc_final: 0.6694 (tptt) REVERT: A 115 MET cc_start: 0.6838 (tpp) cc_final: 0.6548 (mtp) REVERT: A 162 GLN cc_start: 0.6261 (pm20) cc_final: 0.5808 (mm-40) REVERT: A 352 MET cc_start: 0.7301 (tpp) cc_final: 0.7085 (tpp) REVERT: B 72 THR cc_start: 0.5609 (t) cc_final: 0.5137 (m) REVERT: B 152 GLU cc_start: 0.8036 (tt0) cc_final: 0.7698 (tm-30) REVERT: C 59 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6632 (mt) REVERT: C 102 HIS cc_start: 0.4194 (p90) cc_final: 0.1979 (m-70) REVERT: C 138 MET cc_start: 0.6582 (tpt) cc_final: 0.5990 (mtp) REVERT: C 226 MET cc_start: 0.8062 (ttm) cc_final: 0.7805 (ttp) REVERT: C 263 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.7441 (m) REVERT: C 453 LYS cc_start: 0.7981 (tttm) cc_final: 0.7389 (ttpt) REVERT: E 115 MET cc_start: 0.6829 (tpp) cc_final: 0.6420 (mtp) REVERT: E 162 GLN cc_start: 0.6507 (pm20) cc_final: 0.5758 (mt0) REVERT: E 229 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.5830 (mt0) REVERT: G 68 MET cc_start: 0.6118 (ppp) cc_final: 0.4779 (ptt) REVERT: G 95 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6575 (pt0) REVERT: G 226 MET cc_start: 0.8233 (ttm) cc_final: 0.7959 (ttp) REVERT: G 319 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6365 (ttm110) REVERT: G 412 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6791 (pt) outliers start: 88 outliers final: 77 residues processed: 323 average time/residue: 0.1261 time to fit residues: 67.3420 Evaluate side-chains 319 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 237 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 92 optimal weight: 0.6980 chunk 235 optimal weight: 0.9980 chunk 247 optimal weight: 0.1980 chunk 106 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 174 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS D 140 ASN E 342 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.164366 restraints weight = 27782.732| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 2.04 r_work: 0.3920 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20495 Z= 0.125 Angle : 0.596 11.268 27875 Z= 0.305 Chirality : 0.047 0.220 3403 Planarity : 0.004 0.055 3525 Dihedral : 4.707 56.386 2789 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.34 % Allowed : 23.46 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2605 helix: 1.34 (0.19), residues: 828 sheet: -0.61 (0.23), residues: 488 loop : -1.12 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 375 TYR 0.022 0.001 TYR D 438 PHE 0.020 0.001 PHE C 253 TRP 0.009 0.001 TRP G 308 HIS 0.003 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00300 (20459) covalent geometry : angle 0.58763 (27803) SS BOND : bond 0.00366 ( 36) SS BOND : angle 1.98832 ( 72) hydrogen bonds : bond 0.03375 ( 797) hydrogen bonds : angle 4.73031 ( 2223) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5210 Ramachandran restraints generated. 2605 Oldfield, 0 Emsley, 2605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7019 (t) cc_final: 0.6411 (p) REVERT: A 55 LYS cc_start: 0.7181 (mttm) cc_final: 0.6683 (tptt) REVERT: A 115 MET cc_start: 0.6906 (tpp) cc_final: 0.6639 (mtp) REVERT: A 162 GLN cc_start: 0.6256 (pm20) cc_final: 0.5806 (mm-40) REVERT: A 352 MET cc_start: 0.7302 (tpp) cc_final: 0.7079 (tpp) REVERT: B 72 THR cc_start: 0.5618 (t) cc_final: 0.5156 (m) REVERT: B 115 MET cc_start: 0.7006 (tpp) cc_final: 0.6686 (mtt) REVERT: B 152 GLU cc_start: 0.8017 (tt0) cc_final: 0.7669 (tm-30) REVERT: C 102 HIS cc_start: 0.4215 (p90) cc_final: 0.1981 (m-70) REVERT: C 138 MET cc_start: 0.6551 (tpt) cc_final: 0.6007 (mtp) REVERT: C 226 MET cc_start: 0.8079 (ttm) cc_final: 0.7835 (ttp) REVERT: C 263 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7445 (m) REVERT: C 453 LYS cc_start: 0.7983 (tttm) cc_final: 0.7383 (ttpt) REVERT: E 115 MET cc_start: 0.6905 (tpp) cc_final: 0.6557 (mtp) REVERT: E 148 LYS cc_start: 0.7692 (tttm) cc_final: 0.6995 (mmmm) REVERT: E 162 GLN cc_start: 0.6480 (pm20) cc_final: 0.5740 (mt0) REVERT: E 196 GLU cc_start: 0.8068 (tp30) cc_final: 0.7859 (tp30) REVERT: E 229 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.5670 (mp10) REVERT: G 68 MET cc_start: 0.6086 (ppp) cc_final: 0.4745 (ptt) REVERT: G 76 MET cc_start: 0.6521 (mmt) cc_final: 0.6266 (tpp) REVERT: G 95 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6576 (pt0) REVERT: G 226 MET cc_start: 0.8216 (ttm) cc_final: 0.7938 (ttp) REVERT: G 319 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.6329 (ttm110) REVERT: G 412 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6827 (pt) outliers start: 78 outliers final: 71 residues processed: 314 average time/residue: 0.1264 time to fit residues: 65.0275 Evaluate side-chains 317 residues out of total 2332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 242 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 355 CYS Chi-restraints excluded: chain A residue 401 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 417 CYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 102 HIS Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 330 PHE Chi-restraints excluded: chain D residue 355 CYS Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 373 VAL Chi-restraints excluded: chain D residue 392 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 401 ILE Chi-restraints excluded: chain E residue 454 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 176 GLN Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 241 THR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 352 MET Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 394 CYS Chi-restraints excluded: chain G residue 412 ILE Chi-restraints excluded: chain G residue 440 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 35 optimal weight: 0.9990 chunk 230 optimal weight: 0.0010 chunk 29 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.188125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.164454 restraints weight = 27769.943| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 2.03 r_work: 0.3924 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 20495 Z= 0.195 Angle : 0.797 59.200 27875 Z= 0.445 Chirality : 0.047 0.313 3403 Planarity : 0.004 0.062 3525 Dihedral : 4.708 56.386 2789 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.26 % Allowed : 23.50 % Favored : 73.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.16), residues: 2605 helix: 1.34 (0.19), residues: 828 sheet: -0.61 (0.23), residues: 488 loop : -1.13 (0.16), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 375 TYR 0.022 0.001 TYR D 438 PHE 0.016 0.001 PHE C 253 TRP 0.009 0.001 TRP G 308 HIS 0.002 0.000 HIS D 29 Details of bonding type rmsd covalent geometry : bond 0.00411 (20459) covalent geometry : angle 0.79130 (27803) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.97345 ( 72) hydrogen bonds : bond 0.03463 ( 797) hydrogen bonds : angle 4.75852 ( 2223) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5239.11 seconds wall clock time: 90 minutes 53.00 seconds (5453.00 seconds total)