Starting phenix.real_space_refine on Mon Mar 18 06:54:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_27590_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_27590.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_27590.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_27590_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8do4_27590/03_2024/8do4_27590_neut.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 Residue "A GLU 77": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 95": "OE1" <-> "OE2" Residue "C GLU 136": "OE1" <-> "OE2" Residue "C GLU 327": "OE1" <-> "OE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "E TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "G GLU 295": "OE1" <-> "OE2" Residue "G PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 9.60, per 1000 atoms: 0.48 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 - 3.50 Amino acid : False - 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: 7.56 Conformation dependent library (CDL) restraints added in 3.6 seconds 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: 2.45 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: 7.06 Time building geometry restraints manager: 8.22 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: 93.39 - 101.51: 57 101.51 - 109.62: 2163 109.62 - 117.73: 13586 117.73 - 125.85: 11850 125.85 - 133.96: 147 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 2.440 nonbonded pdb=" O ASN B 182 " pdb=" OG1 THR B 186 " model vdw 2.110 2.440 nonbonded pdb=" OD1 ASP G 103 " pdb=" OH TYR G 135 " model vdw 2.151 2.440 nonbonded pdb=" NH2 ARG A 244 " pdb=" OD1 ASP D 200 " model vdw 2.169 2.520 nonbonded pdb=" OD1 ASN G 303 " pdb=" NH1 ARG G 365 " model vdw 2.173 2.520 ... (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 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: 5.090 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: 13.620 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 51.110 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.790 ------------------------------------------------------------------------------- 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 20459 Z= 0.349 Angle : 0.811 7.507 27803 Z= 0.511 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 : 12.09 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (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 TRP 0.013 0.002 TRP E 308 HIS 0.005 0.001 HIS D 29 PHE 0.020 0.002 PHE C 253 TYR 0.025 0.002 TYR A 438 ARG 0.005 0.001 ARG D 375 *********************** 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 fitting. rotamer outliers: 36 poor density : 534 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7195 (mttm) cc_final: 0.6647 (tptt) REVERT: A 191 PRO cc_start: 0.6469 (Cg_exo) cc_final: 0.6149 (Cg_endo) REVERT: A 197 LEU cc_start: 0.7989 (mp) cc_final: 0.7486 (mp) REVERT: A 279 ARG cc_start: 0.6859 (ttm170) cc_final: 0.6648 (ttt180) REVERT: B 145 ASN cc_start: 0.7999 (m110) cc_final: 0.7630 (m-40) REVERT: B 156 GLU cc_start: 0.5667 (OUTLIER) cc_final: 0.5098 (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: 0.7836 (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 205 LYS cc_start: 0.8188 (tttm) cc_final: 0.7969 (ttmt) REVERT: D 463 MET cc_start: 0.7053 (mtp) cc_final: 0.6845 (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: 0.5069 (ptmt) REVERT: G 44 ARG cc_start: 0.6594 (mtt90) cc_final: 0.6297 (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: 0.3259 (m170) REVERT: G 136 GLU cc_start: 0.6732 (mt-10) cc_final: 0.6460 (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: 0.3029 time to fit residues: 257.9776 Evaluate side-chains 334 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 326 time to evaluate : 2.362 ------------------------------------------------------------------------------- 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 219 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 105 optimal weight: 0.4980 chunk 203 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 151 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 265 GLN B 182 ASN B 229 GLN B 290 GLN B 320 ASN B 414 ASN C 51 ASN C 372 HIS C 407 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 140 ASN D 290 GLN E 265 GLN G 180 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 20459 Z= 0.233 Angle : 0.623 9.472 27803 Z= 0.324 Chirality : 0.048 0.230 3403 Planarity : 0.004 0.032 3525 Dihedral : 5.732 85.131 2802 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.82 % Allowed : 20.88 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.16), residues: 2605 helix: 1.04 (0.19), residues: 848 sheet: -0.14 (0.24), residues: 472 loop : -0.91 (0.16), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 308 HIS 0.010 0.001 HIS B 372 PHE 0.015 0.002 PHE G 253 TYR 0.018 0.001 TYR C 438 ARG 0.006 0.001 ARG B 375 *********************** 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 417 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 328 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.7295 (mttm) cc_final: 0.6705 (tptt) REVERT: A 115 MET cc_start: 0.6431 (tpp) cc_final: 0.6132 (mtp) REVERT: A 161 LEU cc_start: 0.7953 (mt) cc_final: 0.7675 (mt) REVERT: A 341 ASN cc_start: 0.6778 (p0) cc_final: 0.6540 (p0) REVERT: B 145 ASN cc_start: 0.8154 (m110) cc_final: 0.7896 (m-40) REVERT: B 156 GLU cc_start: 0.5991 (OUTLIER) cc_final: 0.5181 (mp0) REVERT: C 43 THR cc_start: 0.7899 (m) cc_final: 0.7674 (p) REVERT: C 138 MET cc_start: 0.5225 (mtm) cc_final: 0.5013 (tpt) REVERT: C 178 TYR cc_start: 0.6781 (t80) cc_final: 0.6414 (t80) REVERT: C 226 MET cc_start: 0.7932 (ttm) cc_final: 0.7688 (ttp) REVERT: D 79 TYR cc_start: 0.6339 (t80) cc_final: 0.6127 (t80) REVERT: D 205 LYS cc_start: 0.8321 (tttm) cc_final: 0.8068 (ttmt) REVERT: E 229 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6066 (mp-120) REVERT: E 335 LYS cc_start: 0.6464 (tppt) cc_final: 0.5270 (ptmt) REVERT: G 95 GLU cc_start: 0.6404 (mt-10) cc_final: 0.6171 (pt0) REVERT: G 138 MET cc_start: 0.6535 (tpt) cc_final: 0.5807 (mtp) REVERT: G 220 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: G 226 MET cc_start: 0.8074 (ttm) cc_final: 0.7789 (ttp) outliers start: 89 outliers final: 46 residues processed: 398 average time/residue: 0.2679 time to fit residues: 172.2967 Evaluate side-chains 308 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 259 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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 156 GLU 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 32 LYS 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 176 GLN 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 404 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain C residue 51 ASN Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 36 ILE 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 305 ASN Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 355 CYS 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 278 VAL Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 101 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.1980 chunk 196 optimal weight: 0.6980 chunk 160 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 189 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 B 100 ASN ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN C 51 ASN C 407 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN E 29 HIS E 78 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6733 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20459 Z= 0.176 Angle : 0.555 8.617 27803 Z= 0.290 Chirality : 0.046 0.199 3403 Planarity : 0.004 0.032 3525 Dihedral : 5.416 84.488 2796 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.31 % Rotamer: Outliers : 3.82 % Allowed : 21.66 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2605 helix: 1.31 (0.19), residues: 832 sheet: -0.15 (0.24), residues: 452 loop : -0.89 (0.16), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 308 HIS 0.007 0.001 HIS B 372 PHE 0.016 0.001 PHE C 253 TYR 0.020 0.001 TYR B 438 ARG 0.006 0.000 ARG D 375 *********************** 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 383 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 294 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7080 (t) cc_final: 0.6364 (p) REVERT: A 55 LYS cc_start: 0.7250 (mttm) cc_final: 0.6679 (tptt) REVERT: A 115 MET cc_start: 0.6596 (tpp) cc_final: 0.6226 (mtp) REVERT: A 148 LYS cc_start: 0.7507 (ttmt) cc_final: 0.7177 (mttm) REVERT: A 161 LEU cc_start: 0.8073 (mt) cc_final: 0.7810 (mt) REVERT: B 156 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5370 (mp0) REVERT: B 388 ILE cc_start: 0.5848 (OUTLIER) cc_final: 0.4954 (tp) REVERT: C 178 TYR cc_start: 0.6823 (t80) cc_final: 0.6514 (t80) REVERT: C 226 MET cc_start: 0.7913 (ttm) cc_final: 0.7673 (ttp) REVERT: D 79 TYR cc_start: 0.6255 (t80) cc_final: 0.5865 (t80) REVERT: D 205 LYS cc_start: 0.8377 (tttm) cc_final: 0.8117 (ttmt) REVERT: E 115 MET cc_start: 0.6431 (tpp) cc_final: 0.6140 (mtp) REVERT: E 156 GLU cc_start: 0.7303 (tt0) cc_final: 0.7063 (tt0) REVERT: E 229 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6048 (mp-120) REVERT: G 95 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6228 (pt0) REVERT: G 138 MET cc_start: 0.6389 (tpt) cc_final: 0.5751 (mtp) REVERT: G 220 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: G 226 MET cc_start: 0.8037 (ttm) cc_final: 0.7779 (ttp) REVERT: G 279 ARG cc_start: 0.5725 (ttm170) cc_final: 0.5501 (ttm170) REVERT: G 412 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6606 (pt) outliers start: 89 outliers final: 46 residues processed: 368 average time/residue: 0.2641 time to fit residues: 157.0533 Evaluate side-chains 305 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 254 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 181 THR 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 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 176 GLN Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 355 CYS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 392 CYS Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 143 ASN Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain D residue 42 VAL 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 305 ASN 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 132 VAL Chi-restraints excluded: chain E residue 229 GLN 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 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 101 THR 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 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 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 233 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 224 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS B 182 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 290 GLN E 180 ASN E 303 ASN G 176 GLN G 180 ASN G 217 ASN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20459 Z= 0.339 Angle : 0.670 9.527 27803 Z= 0.344 Chirality : 0.049 0.175 3403 Planarity : 0.004 0.036 3525 Dihedral : 5.471 62.258 2796 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.76 % Allowed : 22.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2605 helix: 0.99 (0.18), residues: 850 sheet: -0.47 (0.23), residues: 489 loop : -1.09 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 308 HIS 0.005 0.001 HIS B 372 PHE 0.020 0.002 PHE G 253 TYR 0.018 0.002 TYR C 135 ARG 0.004 0.001 ARG B 82 *********************** 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 391 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 280 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7173 (t) cc_final: 0.6454 (p) REVERT: A 55 LYS cc_start: 0.7296 (mttm) cc_final: 0.6679 (tptt) REVERT: A 114 CYS cc_start: 0.4149 (t) cc_final: 0.3752 (m) REVERT: A 148 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7171 (mmmt) REVERT: B 46 TYR cc_start: 0.7604 (t80) cc_final: 0.7249 (t80) REVERT: B 156 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5111 (mp0) REVERT: B 333 ILE cc_start: 0.6878 (mm) cc_final: 0.6627 (mm) REVERT: C 226 MET cc_start: 0.7908 (ttm) cc_final: 0.7662 (ttp) REVERT: D 68 MET cc_start: 0.6262 (ptt) cc_final: 0.5936 (ptt) REVERT: D 79 TYR cc_start: 0.6778 (t80) cc_final: 0.6075 (t80) REVERT: D 205 LYS cc_start: 0.8431 (tttm) cc_final: 0.8022 (ttmm) REVERT: D 331 CYS cc_start: 0.6422 (m) cc_final: 0.5966 (m) REVERT: E 156 GLU cc_start: 0.7326 (tt0) cc_final: 0.7101 (tt0) REVERT: E 229 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.6101 (mt0) REVERT: G 95 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6345 (pt0) REVERT: G 102 HIS cc_start: 0.4764 (p90) cc_final: 0.3669 (m170) REVERT: G 412 ILE cc_start: 0.6943 (OUTLIER) cc_final: 0.6662 (pt) outliers start: 111 outliers final: 74 residues processed: 369 average time/residue: 0.2687 time to fit residues: 160.8090 Evaluate side-chains 325 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 248 time to evaluate : 2.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 369 VAL Chi-restraints excluded: chain A residue 404 SER 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 305 ASN 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 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 320 ASN Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 416 THR 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 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 305 ASN 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 346 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 261 SER Chi-restraints excluded: chain E residue 266 ILE 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 322 LEU Chi-restraints excluded: chain E residue 390 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 416 THR Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 40 LYS Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 181 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 306 SER Chi-restraints excluded: chain G residue 320 ASN Chi-restraints excluded: chain G residue 355 CYS Chi-restraints excluded: chain G residue 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 187 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 214 optimal weight: 0.1980 chunk 173 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 chunk 225 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 302 ASN C 407 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 290 GLN ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20459 Z= 0.193 Angle : 0.572 11.477 27803 Z= 0.295 Chirality : 0.047 0.208 3403 Planarity : 0.004 0.069 3525 Dihedral : 4.986 55.647 2792 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 4.25 % Allowed : 22.34 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.16), residues: 2605 helix: 1.19 (0.18), residues: 834 sheet: -0.54 (0.23), residues: 463 loop : -1.00 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 308 HIS 0.005 0.001 HIS G 102 PHE 0.019 0.002 PHE A 212 TYR 0.025 0.001 TYR D 438 ARG 0.003 0.000 ARG D 375 *********************** 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 366 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 267 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7089 (t) cc_final: 0.6405 (p) REVERT: A 55 LYS cc_start: 0.7305 (mttm) cc_final: 0.6678 (tptt) REVERT: A 115 MET cc_start: 0.6887 (tpp) cc_final: 0.6437 (mtp) REVERT: A 148 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7167 (mmmt) REVERT: A 412 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6787 (mt) REVERT: B 76 MET cc_start: 0.6465 (tpt) cc_final: 0.5576 (mmm) REVERT: B 156 GLU cc_start: 0.6111 (OUTLIER) cc_final: 0.5207 (mp0) REVERT: B 333 ILE cc_start: 0.6929 (mm) cc_final: 0.6653 (mm) REVERT: C 138 MET cc_start: 0.5212 (mtp) cc_final: 0.4908 (tpt) REVERT: C 226 MET cc_start: 0.7854 (ttm) cc_final: 0.7610 (ttp) REVERT: C 355 CYS cc_start: 0.7036 (OUTLIER) cc_final: 0.6478 (t) REVERT: D 68 MET cc_start: 0.6380 (ptt) cc_final: 0.6111 (ptt) REVERT: D 79 TYR cc_start: 0.6837 (t80) cc_final: 0.6047 (t80) REVERT: D 107 ASP cc_start: 0.3036 (OUTLIER) cc_final: 0.2764 (m-30) REVERT: D 199 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6858 (mt) REVERT: D 205 LYS cc_start: 0.8439 (tttm) cc_final: 0.8032 (ttmm) REVERT: D 331 CYS cc_start: 0.6164 (m) cc_final: 0.5747 (m) REVERT: E 156 GLU cc_start: 0.7303 (tt0) cc_final: 0.7035 (tt0) REVERT: E 229 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.5995 (mt0) REVERT: E 411 MET cc_start: 0.7328 (ttp) cc_final: 0.7105 (ttp) REVERT: G 95 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6342 (pt0) REVERT: G 138 MET cc_start: 0.6378 (tpt) cc_final: 0.5773 (mtp) REVERT: G 226 MET cc_start: 0.8019 (ttm) cc_final: 0.7752 (ttp) REVERT: G 319 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6542 (ttm110) REVERT: G 412 ILE cc_start: 0.6949 (OUTLIER) cc_final: 0.6643 (pt) outliers start: 99 outliers final: 67 residues processed: 341 average time/residue: 0.2746 time to fit residues: 152.0937 Evaluate side-chains 323 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 248 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR 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 404 SER Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 56 ASP 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 284 ILE Chi-restraints excluded: chain B residue 305 ASN 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 C residue 181 THR Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 355 CYS 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 58 VAL 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 198 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 305 ASN 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 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL 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 304 ASP 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 101 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 232 SER 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 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 0.9990 chunk 226 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 132 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** G 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 372 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 20459 Z= 0.224 Angle : 0.578 9.240 27803 Z= 0.297 Chirality : 0.047 0.185 3403 Planarity : 0.004 0.052 3525 Dihedral : 4.924 55.725 2792 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.37 % Allowed : 22.68 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2605 helix: 1.23 (0.18), residues: 842 sheet: -0.38 (0.23), residues: 487 loop : -1.00 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 308 HIS 0.002 0.001 HIS D 29 PHE 0.018 0.002 PHE C 253 TYR 0.027 0.001 TYR D 438 ARG 0.003 0.000 ARG D 375 *********************** 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 360 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 258 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7131 (t) cc_final: 0.6490 (p) REVERT: A 55 LYS cc_start: 0.7454 (mttm) cc_final: 0.6797 (tptt) REVERT: A 115 MET cc_start: 0.7008 (tpp) cc_final: 0.6578 (mtp) REVERT: A 148 LYS cc_start: 0.7564 (ttmt) cc_final: 0.7205 (mmmt) REVERT: A 412 ILE cc_start: 0.7020 (OUTLIER) cc_final: 0.6800 (mt) REVERT: B 156 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5264 (mp0) REVERT: B 180 ASN cc_start: 0.6892 (m-40) cc_final: 0.6124 (t0) REVERT: B 333 ILE cc_start: 0.6927 (mm) cc_final: 0.6713 (mm) REVERT: C 226 MET cc_start: 0.7866 (ttm) cc_final: 0.7624 (ttp) REVERT: C 355 CYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6510 (t) REVERT: C 453 LYS cc_start: 0.7642 (tttm) cc_final: 0.7184 (ttpt) REVERT: D 68 MET cc_start: 0.6475 (ptt) cc_final: 0.6195 (ptt) REVERT: D 79 TYR cc_start: 0.6689 (t80) cc_final: 0.5929 (t80) REVERT: D 107 ASP cc_start: 0.2961 (OUTLIER) cc_final: 0.2718 (m-30) REVERT: D 199 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6869 (mt) REVERT: D 205 LYS cc_start: 0.8398 (tttm) cc_final: 0.8016 (ttmm) REVERT: E 102 HIS cc_start: 0.4726 (OUTLIER) cc_final: 0.4000 (p90) REVERT: E 156 GLU cc_start: 0.7341 (tt0) cc_final: 0.7069 (tt0) REVERT: E 229 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.5967 (mt0) REVERT: G 95 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6344 (pt0) REVERT: G 102 HIS cc_start: 0.3931 (p90) cc_final: 0.3706 (m170) REVERT: G 138 MET cc_start: 0.6369 (tpt) cc_final: 0.5756 (mtp) REVERT: G 226 MET cc_start: 0.8027 (ttm) cc_final: 0.7753 (ttp) REVERT: G 319 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6514 (ttm110) REVERT: G 412 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6759 (pt) outliers start: 102 outliers final: 74 residues processed: 339 average time/residue: 0.2838 time to fit residues: 156.0198 Evaluate side-chains 321 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 238 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 404 SER Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain A residue 433 LEU 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 305 ASN 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 104 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 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 320 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 416 THR 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 58 VAL 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 198 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 ASN 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 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL 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 304 ASP Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 220 ASP Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 232 SER Chi-restraints excluded: chain G residue 266 ILE Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 319 ARG Chi-restraints excluded: chain G residue 320 ASN 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 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 183 optimal weight: 0.7980 chunk 142 optimal weight: 0.1980 chunk 211 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 250 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN ** G 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20459 Z= 0.197 Angle : 0.562 8.413 27803 Z= 0.288 Chirality : 0.046 0.210 3403 Planarity : 0.004 0.056 3525 Dihedral : 4.828 57.191 2792 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.20 % Allowed : 22.98 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.16), residues: 2605 helix: 1.25 (0.18), residues: 847 sheet: -0.39 (0.23), residues: 487 loop : -0.99 (0.16), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 308 HIS 0.004 0.001 HIS G 29 PHE 0.019 0.002 PHE C 253 TYR 0.026 0.001 TYR D 438 ARG 0.003 0.000 ARG D 319 *********************** 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 359 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 261 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7119 (t) cc_final: 0.6514 (p) REVERT: A 55 LYS cc_start: 0.7306 (mttm) cc_final: 0.6710 (tptt) REVERT: A 115 MET cc_start: 0.6984 (tpp) cc_final: 0.6558 (mtp) REVERT: A 148 LYS cc_start: 0.7555 (ttmt) cc_final: 0.7213 (mmmt) REVERT: A 162 GLN cc_start: 0.6389 (pm20) cc_final: 0.5919 (mm-40) REVERT: B 76 MET cc_start: 0.6521 (tpt) cc_final: 0.5633 (mmm) REVERT: B 156 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5253 (mp0) REVERT: B 180 ASN cc_start: 0.6933 (m-40) cc_final: 0.6280 (t0) REVERT: B 333 ILE cc_start: 0.6940 (mm) cc_final: 0.6722 (mm) REVERT: C 59 ILE cc_start: 0.6732 (OUTLIER) cc_final: 0.6525 (mt) REVERT: C 226 MET cc_start: 0.7841 (ttm) cc_final: 0.7599 (ttp) REVERT: C 355 CYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6484 (t) REVERT: C 453 LYS cc_start: 0.7660 (tttm) cc_final: 0.7173 (ttpt) REVERT: D 68 MET cc_start: 0.6446 (ptt) cc_final: 0.6142 (ptt) REVERT: D 79 TYR cc_start: 0.6750 (t80) cc_final: 0.5939 (t80) REVERT: D 199 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6878 (mt) REVERT: D 205 LYS cc_start: 0.8407 (tttm) cc_final: 0.7976 (ttmm) REVERT: D 331 CYS cc_start: 0.5857 (m) cc_final: 0.5297 (m) REVERT: E 102 HIS cc_start: 0.4806 (OUTLIER) cc_final: 0.4091 (p90) REVERT: E 156 GLU cc_start: 0.7327 (tt0) cc_final: 0.7054 (tt0) REVERT: E 229 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.5888 (mt0) REVERT: G 95 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6414 (pt0) REVERT: G 102 HIS cc_start: 0.3984 (p90) cc_final: 0.3779 (m-70) REVERT: G 138 MET cc_start: 0.6232 (tpt) cc_final: 0.5756 (mtp) REVERT: G 199 LEU cc_start: 0.7515 (tt) cc_final: 0.7311 (tt) REVERT: G 226 MET cc_start: 0.8011 (ttm) cc_final: 0.7746 (ttp) REVERT: G 319 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6485 (ttm110) REVERT: G 412 ILE cc_start: 0.7038 (OUTLIER) cc_final: 0.6741 (pt) outliers start: 98 outliers final: 78 residues processed: 340 average time/residue: 0.2633 time to fit residues: 145.3448 Evaluate side-chains 330 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 244 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 369 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 433 LEU 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 156 GLU Chi-restraints excluded: chain B residue 192 CYS Chi-restraints excluded: chain B residue 305 ASN 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 104 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 232 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 407 GLN Chi-restraints excluded: chain C residue 416 THR 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 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 ASN 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 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL 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 304 ASP Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 THR 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 232 SER 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 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 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 196 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN D 140 ASN E 127 GLN ** G 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 20459 Z= 0.313 Angle : 0.636 8.589 27803 Z= 0.323 Chirality : 0.049 0.209 3403 Planarity : 0.004 0.055 3525 Dihedral : 5.056 55.573 2792 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 4.25 % Allowed : 22.98 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2605 helix: 0.98 (0.18), residues: 867 sheet: -0.57 (0.23), residues: 513 loop : -1.10 (0.17), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 308 HIS 0.004 0.001 HIS A 29 PHE 0.019 0.002 PHE A 301 TYR 0.023 0.002 TYR D 438 ARG 0.003 0.000 ARG C 365 *********************** 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 344 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 245 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7275 (t) cc_final: 0.6692 (p) REVERT: A 55 LYS cc_start: 0.7347 (mttm) cc_final: 0.6725 (tptt) REVERT: A 115 MET cc_start: 0.7148 (tpp) cc_final: 0.6641 (mtp) REVERT: A 148 LYS cc_start: 0.7588 (ttmt) cc_final: 0.7264 (mmmt) REVERT: A 162 GLN cc_start: 0.6440 (pm20) cc_final: 0.5749 (mm-40) REVERT: B 76 MET cc_start: 0.6536 (tpt) cc_final: 0.5644 (mmm) REVERT: B 156 GLU cc_start: 0.6223 (OUTLIER) cc_final: 0.5137 (mp0) REVERT: C 59 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6554 (mt) REVERT: C 102 HIS cc_start: 0.4102 (p90) cc_final: 0.2175 (m-70) REVERT: C 138 MET cc_start: 0.6649 (tpt) cc_final: 0.6181 (mtp) REVERT: C 226 MET cc_start: 0.7897 (ttm) cc_final: 0.7653 (ttp) REVERT: C 355 CYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6543 (t) REVERT: C 453 LYS cc_start: 0.7732 (tttm) cc_final: 0.7135 (ttpt) REVERT: D 205 LYS cc_start: 0.8354 (tttm) cc_final: 0.7966 (ttmm) REVERT: E 102 HIS cc_start: 0.5041 (OUTLIER) cc_final: 0.4452 (p90) REVERT: E 156 GLU cc_start: 0.7356 (tt0) cc_final: 0.7082 (tt0) REVERT: E 229 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.5975 (mt0) REVERT: G 95 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6562 (pt0) REVERT: G 102 HIS cc_start: 0.3902 (p90) cc_final: 0.3614 (m-70) REVERT: G 138 MET cc_start: 0.6341 (tpt) cc_final: 0.5812 (mtp) REVERT: G 226 MET cc_start: 0.8073 (ttm) cc_final: 0.7807 (ttp) REVERT: G 319 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6529 (ttm110) REVERT: G 412 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6776 (pt) outliers start: 99 outliers final: 80 residues processed: 323 average time/residue: 0.2646 time to fit residues: 140.1095 Evaluate side-chains 327 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 240 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 369 VAL Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain B residue 42 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 305 ASN 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 104 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 232 SER 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 320 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 416 THR 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 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 ASN 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 D residue 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL 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 304 ASP Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 168 THR Chi-restraints excluded: chain G residue 181 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 232 SER 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 320 ASN 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 396 THR Chi-restraints excluded: chain G residue 412 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 101 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 0.3980 chunk 220 optimal weight: 0.7980 chunk 232 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 407 GLN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 127 GLN ** G 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20459 Z= 0.183 Angle : 0.555 8.339 27803 Z= 0.284 Chirality : 0.046 0.204 3403 Planarity : 0.004 0.054 3525 Dihedral : 4.816 58.186 2792 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.60 % Allowed : 23.24 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.16), residues: 2605 helix: 1.20 (0.18), residues: 843 sheet: -0.52 (0.23), residues: 513 loop : -0.97 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 308 HIS 0.003 0.000 HIS D 29 PHE 0.021 0.001 PHE C 253 TYR 0.023 0.001 TYR D 438 ARG 0.003 0.000 ARG D 375 *********************** 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 340 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 256 time to evaluate : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7161 (t) cc_final: 0.6686 (p) REVERT: A 55 LYS cc_start: 0.7299 (mttm) cc_final: 0.6671 (tptt) REVERT: A 115 MET cc_start: 0.6864 (tpp) cc_final: 0.6490 (mtp) REVERT: A 148 LYS cc_start: 0.7525 (ttmt) cc_final: 0.7230 (mmmt) REVERT: A 162 GLN cc_start: 0.6414 (pm20) cc_final: 0.5730 (mm-40) REVERT: B 76 MET cc_start: 0.6541 (tpt) cc_final: 0.5763 (mmm) REVERT: C 138 MET cc_start: 0.6637 (tpt) cc_final: 0.6168 (mtp) REVERT: C 226 MET cc_start: 0.7813 (ttm) cc_final: 0.7574 (ttp) REVERT: C 355 CYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6544 (t) REVERT: C 375 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6794 (mtm-85) REVERT: C 453 LYS cc_start: 0.7741 (tttm) cc_final: 0.7135 (ttpt) REVERT: D 76 MET cc_start: 0.6184 (tpt) cc_final: 0.5722 (mmm) REVERT: D 79 TYR cc_start: 0.6784 (t80) cc_final: 0.5925 (t80) REVERT: D 142 ASP cc_start: 0.6574 (m-30) cc_final: 0.6319 (m-30) REVERT: D 205 LYS cc_start: 0.8384 (tttm) cc_final: 0.7974 (ttmm) REVERT: E 102 HIS cc_start: 0.5024 (OUTLIER) cc_final: 0.4440 (p90) REVERT: E 156 GLU cc_start: 0.7321 (tt0) cc_final: 0.7048 (tt0) REVERT: E 229 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.5913 (mt0) REVERT: G 95 GLU cc_start: 0.6703 (mt-10) cc_final: 0.6498 (pt0) REVERT: G 102 HIS cc_start: 0.4314 (p90) cc_final: 0.3657 (m170) REVERT: G 138 MET cc_start: 0.6160 (tpt) cc_final: 0.5743 (mtp) REVERT: G 199 LEU cc_start: 0.7561 (tt) cc_final: 0.7330 (tt) REVERT: G 226 MET cc_start: 0.8001 (ttm) cc_final: 0.7745 (ttp) REVERT: G 412 ILE cc_start: 0.6977 (OUTLIER) cc_final: 0.6743 (pt) outliers start: 84 outliers final: 73 residues processed: 324 average time/residue: 0.2695 time to fit residues: 141.3450 Evaluate side-chains 327 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 249 time to evaluate : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 404 SER 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 305 ASN 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 B residue 413 ASP 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 104 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 232 SER Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 306 SER Chi-restraints excluded: chain C residue 320 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 416 THR 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 102 HIS Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 250 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 305 ASN 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 D residue 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 355 CYS Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 232 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 117 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 238 optimal weight: 0.8980 chunk 206 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 ASN E 127 GLN ** G 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20459 Z= 0.233 Angle : 0.591 12.873 27803 Z= 0.301 Chirality : 0.047 0.206 3403 Planarity : 0.004 0.055 3525 Dihedral : 4.776 57.682 2789 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.56 % Allowed : 23.37 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2605 helix: 1.17 (0.19), residues: 849 sheet: -0.55 (0.23), residues: 512 loop : -1.03 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 308 HIS 0.003 0.000 HIS D 29 PHE 0.021 0.002 PHE C 253 TYR 0.024 0.001 TYR D 438 ARG 0.002 0.000 ARG D 375 ********************** 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 330 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 247 time to evaluate : 2.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 SER cc_start: 0.7210 (t) cc_final: 0.6732 (p) REVERT: A 55 LYS cc_start: 0.7278 (mttm) cc_final: 0.6668 (tptt) REVERT: A 115 MET cc_start: 0.7058 (tpp) cc_final: 0.6623 (mtp) REVERT: A 148 LYS cc_start: 0.7570 (ttmt) cc_final: 0.7250 (mttm) REVERT: A 162 GLN cc_start: 0.6402 (pm20) cc_final: 0.5656 (mm-40) REVERT: B 76 MET cc_start: 0.6525 (tpt) cc_final: 0.5667 (mmm) REVERT: B 115 MET cc_start: 0.7160 (tpp) cc_final: 0.6893 (mtt) REVERT: C 138 MET cc_start: 0.6571 (tpt) cc_final: 0.6146 (mtp) REVERT: C 226 MET cc_start: 0.7832 (ttm) cc_final: 0.7596 (ttp) REVERT: C 355 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6590 (t) REVERT: C 375 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6787 (mtm-85) REVERT: C 453 LYS cc_start: 0.7772 (tttm) cc_final: 0.7187 (ttpt) REVERT: D 142 ASP cc_start: 0.6436 (m-30) cc_final: 0.6190 (m-30) REVERT: D 205 LYS cc_start: 0.8344 (tttm) cc_final: 0.7944 (ttmm) REVERT: E 102 HIS cc_start: 0.5088 (OUTLIER) cc_final: 0.4520 (p90) REVERT: E 156 GLU cc_start: 0.7325 (tt0) cc_final: 0.7043 (tt0) REVERT: E 229 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.5853 (mt0) REVERT: G 102 HIS cc_start: 0.3968 (p90) cc_final: 0.3370 (m170) REVERT: G 138 MET cc_start: 0.6207 (tpt) cc_final: 0.5771 (mtp) REVERT: G 199 LEU cc_start: 0.7626 (tt) cc_final: 0.7402 (tt) REVERT: G 226 MET cc_start: 0.7997 (ttm) cc_final: 0.7745 (ttp) REVERT: G 412 ILE cc_start: 0.7010 (OUTLIER) cc_final: 0.6801 (pt) outliers start: 83 outliers final: 72 residues processed: 316 average time/residue: 0.2622 time to fit residues: 135.5948 Evaluate side-chains 318 residues out of total 2332 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 241 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 204 SER 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 404 SER 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 305 ASN 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 B residue 411 MET Chi-restraints excluded: chain B residue 413 ASP 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 104 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 232 SER 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 320 ASN Chi-restraints excluded: chain C residue 355 CYS Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 392 CYS Chi-restraints excluded: chain C residue 416 THR 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 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 284 ILE Chi-restraints excluded: chain D residue 305 ASN 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 D residue 461 SER Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 67 ASN Chi-restraints excluded: chain E residue 102 HIS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 229 GLN Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 304 ASP Chi-restraints excluded: chain E residue 392 CYS Chi-restraints excluded: chain E residue 404 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 227 THR Chi-restraints excluded: chain G residue 232 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 206 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 212 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 51 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.187301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.163782 restraints weight = 28125.876| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 2.02 r_work: 0.3921 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3785 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20459 Z= 0.205 Angle : 0.591 16.518 27803 Z= 0.298 Chirality : 0.046 0.208 3403 Planarity : 0.004 0.054 3525 Dihedral : 4.713 58.286 2789 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.64 % Allowed : 23.58 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2605 helix: 1.28 (0.19), residues: 829 sheet: -0.57 (0.24), residues: 494 loop : -1.03 (0.16), residues: 1282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 308 HIS 0.005 0.001 HIS B 102 PHE 0.022 0.002 PHE C 253 TYR 0.028 0.001 TYR D 438 ARG 0.002 0.000 ARG D 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4504.05 seconds wall clock time: 82 minutes 11.86 seconds (4931.86 seconds total)