Starting phenix.real_space_refine on Sat Mar 16 17:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ysz_10911/03_2024/6ysz_10911.pdb" } resolution = 3.6 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= 0.007 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 60 5.16 5 C 9348 2.51 5 N 2742 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 105": "NH1" <-> "NH2" Residue "A ARG 110": "NH1" <-> "NH2" Residue "A ARG 130": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 145": "OE1" <-> "OE2" Residue "A GLU 152": "OE1" <-> "OE2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "A ARG 310": "NH1" <-> "NH2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" Residue "B GLU 85": "OE1" <-> "OE2" Residue "B ARG 105": "NH1" <-> "NH2" Residue "B ARG 110": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 142": "NH1" <-> "NH2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 310": "NH1" <-> "NH2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C ARG 105": "NH1" <-> "NH2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 139": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ARG 105": "NH1" <-> "NH2" Residue "D ARG 110": "NH1" <-> "NH2" Residue "D ARG 130": "NH1" <-> "NH2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 139": "NH1" <-> "NH2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D ARG 310": "NH1" <-> "NH2" Residue "D GLU 320": "OE1" <-> "OE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" Residue "E GLU 85": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 130": "NH1" <-> "NH2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 139": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 145": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E ARG 279": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "E ARG 310": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E GLU 335": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F GLU 85": "OE1" <-> "OE2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F ARG 139": "NH1" <-> "NH2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F ARG 279": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F ARG 310": "NH1" <-> "NH2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F GLU 335": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "B" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "C" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "D" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "E" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain: "F" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2532 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Time building chain proxies: 7.52, per 1000 atoms: 0.49 Number of scatterers: 15192 At special positions: 0 Unit cell: (101.15, 97.75, 143.65, 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 60 16.00 O 3042 8.00 N 2742 7.00 C 9348 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 5.06 Conformation dependent library (CDL) restraints added in 2.5 seconds 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3576 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 6 sheets defined 81.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 59 through 78 removed outlier: 3.519A pdb=" N ARG A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP A 65 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN A 88 " --> pdb=" O ARG A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET A 101 " --> pdb=" O ASP A 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG A 110 " --> pdb=" O VAL A 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU A 126 " --> pdb=" O GLN A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 154 Processing helix chain 'A' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 200 " --> pdb=" O MET A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 205 Processing helix chain 'A' and resid 216 through 231 Processing helix chain 'A' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE A 260 " --> pdb=" O GLY A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 282' Processing helix chain 'A' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA A 325 " --> pdb=" O ASP A 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP B 65 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU B 78 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 88 removed outlier: 3.722A pdb=" N ASN B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET B 101 " --> pdb=" O ASP B 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 110 " --> pdb=" O VAL B 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU B 126 " --> pdb=" O GLN B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 Processing helix chain 'B' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 200 " --> pdb=" O MET B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 205 Processing helix chain 'B' and resid 216 through 231 Processing helix chain 'B' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE B 260 " --> pdb=" O GLY B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 282' Processing helix chain 'B' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN B 298 " --> pdb=" O ALA B 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA B 325 " --> pdb=" O ASP B 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'C' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 65 " --> pdb=" O GLN C 61 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN C 88 " --> pdb=" O ARG C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET C 101 " --> pdb=" O ASP C 97 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 154 Processing helix chain 'C' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN C 164 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG C 174 " --> pdb=" O ASP C 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 200 " --> pdb=" O MET C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 216 through 231 Processing helix chain 'C' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE C 260 " --> pdb=" O GLY C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 282' Processing helix chain 'C' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN C 298 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA C 325 " --> pdb=" O ASP C 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 340 No H-bonds generated for 'chain 'C' and resid 338 through 340' Processing helix chain 'C' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'D' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP D 65 " --> pdb=" O GLN D 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN D 88 " --> pdb=" O ARG D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET D 101 " --> pdb=" O ASP D 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU D 126 " --> pdb=" O GLN D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 154 Processing helix chain 'D' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN D 164 " --> pdb=" O ASP D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG D 174 " --> pdb=" O ASP D 170 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL D 200 " --> pdb=" O MET D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 205 Processing helix chain 'D' and resid 216 through 231 Processing helix chain 'D' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.709A pdb=" N PHE D 260 " --> pdb=" O GLY D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 282' Processing helix chain 'D' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN D 298 " --> pdb=" O ALA D 294 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.640A pdb=" N ASN D 306 " --> pdb=" O ASP D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA D 325 " --> pdb=" O ASP D 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 340 No H-bonds generated for 'chain 'D' and resid 338 through 340' Processing helix chain 'D' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA D 371 " --> pdb=" O THR D 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'E' and resid 60 through 78 removed outlier: 3.519A pdb=" N ARG E 64 " --> pdb=" O GLU E 60 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN E 88 " --> pdb=" O ARG E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 126 removed outlier: 3.503A pdb=" N MET E 101 " --> pdb=" O ASP E 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG E 110 " --> pdb=" O VAL E 106 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA E 112 " --> pdb=" O THR E 108 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 154 Processing helix chain 'E' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN E 164 " --> pdb=" O ASP E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG E 174 " --> pdb=" O ASP E 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG E 199 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL E 200 " --> pdb=" O MET E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 205 Processing helix chain 'E' and resid 216 through 231 Processing helix chain 'E' and resid 238 through 253 removed outlier: 4.346A pdb=" N GLN E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE E 260 " --> pdb=" O GLY E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.638A pdb=" N ILE E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 282' Processing helix chain 'E' and resid 283 through 302 removed outlier: 4.530A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE E 299 " --> pdb=" O GLN E 295 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASP E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN E 306 " --> pdb=" O ASP E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA E 325 " --> pdb=" O ASP E 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 340 No H-bonds generated for 'chain 'E' and resid 338 through 340' Processing helix chain 'E' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA E 371 " --> pdb=" O THR E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'F' and resid 60 through 78 removed outlier: 3.520A pdb=" N ARG F 64 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP F 65 " --> pdb=" O GLN F 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 88 removed outlier: 3.723A pdb=" N ASN F 88 " --> pdb=" O ARG F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 126 removed outlier: 3.504A pdb=" N MET F 101 " --> pdb=" O ASP F 97 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA F 112 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU F 126 " --> pdb=" O GLN F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 154 Processing helix chain 'F' and resid 160 through 168 removed outlier: 3.562A pdb=" N GLN F 164 " --> pdb=" O ASP F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 201 removed outlier: 3.795A pdb=" N ARG F 174 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG F 199 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL F 200 " --> pdb=" O MET F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 205 Processing helix chain 'F' and resid 216 through 231 Processing helix chain 'F' and resid 238 through 253 removed outlier: 4.345A pdb=" N GLN F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.708A pdb=" N PHE F 260 " --> pdb=" O GLY F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.639A pdb=" N ILE F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 283 through 302 removed outlier: 4.529A pdb=" N GLN F 298 " --> pdb=" O ALA F 294 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N PHE F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 318 removed outlier: 3.641A pdb=" N ASN F 306 " --> pdb=" O ASP F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 321 through 337 removed outlier: 3.522A pdb=" N ALA F 325 " --> pdb=" O ASP F 321 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 340 No H-bonds generated for 'chain 'F' and resid 338 through 340' Processing helix chain 'F' and resid 348 through 371 removed outlier: 3.816A pdb=" N ALA F 371 " --> pdb=" O THR F 367 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing sheet with id=AA1, first strand: chain 'A' and resid 268 through 270 Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 270 Processing sheet with id=AA3, first strand: chain 'C' and resid 268 through 270 Processing sheet with id=AA4, first strand: chain 'D' and resid 268 through 270 Processing sheet with id=AA5, first strand: chain 'E' and resid 268 through 270 Processing sheet with id=AA6, first strand: chain 'F' and resid 268 through 270 1021 hydrogen bonds defined for protein. 3045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 5.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5418 1.34 - 1.46: 1718 1.46 - 1.57: 8158 1.57 - 1.69: 0 1.69 - 1.80: 120 Bond restraints: 15414 Sorted by residual: bond pdb=" N GLN C 298 " pdb=" CA GLN C 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.88e+00 bond pdb=" N GLN F 298 " pdb=" CA GLN F 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.87e+00 bond pdb=" N GLN D 298 " pdb=" CA GLN D 298 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.27e-02 6.20e+03 5.83e+00 bond pdb=" N GLN A 298 " pdb=" CA GLN A 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.70e+00 bond pdb=" N GLN B 298 " pdb=" CA GLN B 298 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.27e-02 6.20e+03 5.69e+00 ... (remaining 15409 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.79: 312 106.79 - 113.59: 8349 113.59 - 120.39: 6577 120.39 - 127.19: 5437 127.19 - 133.99: 103 Bond angle restraints: 20778 Sorted by residual: angle pdb=" N THR B 276 " pdb=" CA THR B 276 " pdb=" C THR B 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.78e+00 angle pdb=" N THR E 276 " pdb=" CA THR E 276 " pdb=" C THR E 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR C 276 " pdb=" CA THR C 276 " pdb=" C THR C 276 " ideal model delta sigma weight residual 108.34 111.49 -3.15 1.31e+00 5.83e-01 5.77e+00 angle pdb=" N THR F 276 " pdb=" CA THR F 276 " pdb=" C THR F 276 " ideal model delta sigma weight residual 108.34 111.48 -3.14 1.31e+00 5.83e-01 5.73e+00 angle pdb=" N THR A 276 " pdb=" CA THR A 276 " pdb=" C THR A 276 " ideal model delta sigma weight residual 108.34 111.47 -3.13 1.31e+00 5.83e-01 5.70e+00 ... (remaining 20773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.18: 8054 15.18 - 30.35: 1084 30.35 - 45.53: 294 45.53 - 60.70: 60 60.70 - 75.88: 36 Dihedral angle restraints: 9528 sinusoidal: 4002 harmonic: 5526 Sorted by residual: dihedral pdb=" CA GLU B 126 " pdb=" C GLU B 126 " pdb=" N GLY B 127 " pdb=" CA GLY B 127 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA GLU D 126 " pdb=" C GLU D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual -180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA GLU A 126 " pdb=" C GLU A 126 " pdb=" N GLY A 127 " pdb=" CA GLY A 127 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 9525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1267 0.027 - 0.054: 642 0.054 - 0.081: 193 0.081 - 0.109: 80 0.109 - 0.136: 26 Chirality restraints: 2208 Sorted by residual: chirality pdb=" CB ILE B 171 " pdb=" CA ILE B 171 " pdb=" CG1 ILE B 171 " pdb=" CG2 ILE B 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CB ILE D 171 " pdb=" CA ILE D 171 " pdb=" CG1 ILE D 171 " pdb=" CG2 ILE D 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CB ILE E 171 " pdb=" CA ILE E 171 " pdb=" CG1 ILE E 171 " pdb=" CG2 ILE E 171 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2205 not shown) Planarity restraints: 2826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 346 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 347 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 346 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO A 347 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.025 5.00e-02 4.00e+02 ... (remaining 2823 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4750 2.82 - 3.34: 15895 3.34 - 3.86: 25778 3.86 - 4.38: 27270 4.38 - 4.90: 46431 Nonbonded interactions: 120124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 191 " pdb=" OE1 GLN B 239 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN D 191 " pdb=" OE1 GLN D 239 " model vdw 2.295 2.520 nonbonded pdb=" NE2 GLN E 191 " pdb=" OE1 GLN E 239 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN A 191 " pdb=" OE1 GLN A 239 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN C 191 " pdb=" OE1 GLN C 239 " model vdw 2.296 2.520 ... (remaining 120119 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.670 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: 3.600 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 38.680 Find NCS groups from input model: 0.970 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15414 Z= 0.273 Angle : 0.562 4.755 20778 Z= 0.338 Chirality : 0.038 0.136 2208 Planarity : 0.003 0.046 2826 Dihedral : 15.540 75.878 5952 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.38 % Allowed : 8.27 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.18), residues: 1884 helix: -0.42 (0.13), residues: 1422 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS C 182 PHE 0.009 0.001 PHE D 185 TYR 0.009 0.001 TYR A 163 ARG 0.009 0.000 ARG C 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 433 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 LYS cc_start: 0.8595 (tppp) cc_final: 0.8106 (tppp) REVERT: A 135 MET cc_start: 0.7875 (tmm) cc_final: 0.7361 (tmm) REVERT: A 152 GLU cc_start: 0.8045 (tp30) cc_final: 0.7645 (tp30) REVERT: A 159 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7310 (tm-30) REVERT: A 243 LEU cc_start: 0.7512 (tp) cc_final: 0.7223 (tp) REVERT: B 82 GLN cc_start: 0.8844 (mt0) cc_final: 0.8581 (mt0) REVERT: B 85 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7810 (tm-30) REVERT: B 121 MET cc_start: 0.7679 (tpt) cc_final: 0.7337 (tmm) REVERT: B 125 LYS cc_start: 0.8451 (tppp) cc_final: 0.7887 (ttmm) REVERT: B 144 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7430 (mm-40) REVERT: B 145 GLU cc_start: 0.8034 (tp30) cc_final: 0.7305 (tp30) REVERT: B 196 MET cc_start: 0.8228 (tpp) cc_final: 0.7960 (tmm) REVERT: B 211 MET cc_start: 0.8295 (tpp) cc_final: 0.7928 (tpt) REVERT: B 286 GLN cc_start: 0.8324 (mm110) cc_final: 0.8122 (mm-40) REVERT: B 335 GLU cc_start: 0.8219 (tp30) cc_final: 0.7801 (tm-30) REVERT: B 344 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8301 (mm110) REVERT: C 68 ASP cc_start: 0.8048 (t70) cc_final: 0.7686 (t70) REVERT: C 94 TYR cc_start: 0.8595 (m-80) cc_final: 0.7711 (m-80) REVERT: C 121 MET cc_start: 0.7725 (tpt) cc_final: 0.7465 (tpp) REVERT: C 125 LYS cc_start: 0.8482 (tppp) cc_final: 0.8000 (tppp) REVERT: C 159 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7203 (tm-30) REVERT: C 211 MET cc_start: 0.8277 (tpp) cc_final: 0.8016 (ttp) REVERT: C 252 SER cc_start: 0.8446 (p) cc_final: 0.8083 (p) REVERT: C 291 MET cc_start: 0.8506 (tpt) cc_final: 0.8246 (tpp) REVERT: C 300 GLU cc_start: 0.8619 (tp30) cc_final: 0.8193 (mm-30) REVERT: D 95 GLN cc_start: 0.8848 (tp-100) cc_final: 0.8570 (tp-100) REVERT: D 125 LYS cc_start: 0.8579 (tppp) cc_final: 0.8071 (tppp) REVERT: D 135 MET cc_start: 0.7809 (tmm) cc_final: 0.7279 (tmm) REVERT: D 152 GLU cc_start: 0.7999 (tp30) cc_final: 0.7549 (tp30) REVERT: D 159 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7347 (tm-30) REVERT: D 196 MET cc_start: 0.8206 (tpp) cc_final: 0.7929 (tmm) REVERT: D 243 LEU cc_start: 0.7517 (tp) cc_final: 0.7267 (tp) REVERT: D 335 GLU cc_start: 0.8309 (tp30) cc_final: 0.7729 (tm-30) REVERT: E 82 GLN cc_start: 0.8852 (mt0) cc_final: 0.8651 (mt0) REVERT: E 95 GLN cc_start: 0.8975 (tp-100) cc_final: 0.8748 (tp40) REVERT: E 125 LYS cc_start: 0.8446 (tppp) cc_final: 0.7959 (ttmm) REVERT: E 144 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7455 (mm-40) REVERT: E 145 GLU cc_start: 0.7975 (tp30) cc_final: 0.7158 (tp30) REVERT: E 196 MET cc_start: 0.8219 (tpp) cc_final: 0.7910 (tmm) REVERT: E 211 MET cc_start: 0.8304 (tpp) cc_final: 0.7808 (tpt) REVERT: E 335 GLU cc_start: 0.8249 (tp30) cc_final: 0.7801 (tm-30) REVERT: F 82 GLN cc_start: 0.8903 (mt0) cc_final: 0.8546 (mt0) REVERT: F 94 TYR cc_start: 0.8618 (m-80) cc_final: 0.7820 (m-80) REVERT: F 117 ASP cc_start: 0.7725 (t0) cc_final: 0.7216 (t0) REVERT: F 125 LYS cc_start: 0.8505 (tppp) cc_final: 0.8043 (tppp) REVERT: F 159 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7194 (tm-30) REVERT: F 211 MET cc_start: 0.8258 (tpp) cc_final: 0.7890 (tpp) REVERT: F 252 SER cc_start: 0.8474 (p) cc_final: 0.8164 (p) REVERT: F 261 LEU cc_start: 0.7924 (mm) cc_final: 0.7667 (mm) REVERT: F 291 MET cc_start: 0.8501 (tpt) cc_final: 0.8252 (tpp) REVERT: F 300 GLU cc_start: 0.8651 (tp30) cc_final: 0.8236 (mm-30) outliers start: 6 outliers final: 2 residues processed: 437 average time/residue: 0.2798 time to fit residues: 174.9449 Evaluate side-chains 360 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 358 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLN Chi-restraints excluded: chain D residue 298 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 7.9990 chunk 140 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 ASN ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 319 GLN A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN B 203 ASN B 286 GLN ** B 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 GLN B 344 GLN ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 203 ASN ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 203 ASN ** E 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN E 344 GLN ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 203 ASN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 319 GLN F 344 GLN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15414 Z= 0.154 Angle : 0.504 9.938 20778 Z= 0.250 Chirality : 0.036 0.140 2208 Planarity : 0.004 0.043 2826 Dihedral : 3.869 32.548 2100 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.63 % Allowed : 15.41 % Favored : 80.95 % 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: 0.35 (0.19), residues: 1884 helix: 0.84 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.56 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.002 0.001 HIS A 182 PHE 0.009 0.001 PHE E 185 TYR 0.010 0.001 TYR C 114 ARG 0.006 0.000 ARG B 142 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 1.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7795 (tm-30) REVERT: A 125 LYS cc_start: 0.8551 (tppp) cc_final: 0.8150 (tppp) REVERT: A 135 MET cc_start: 0.7736 (tmm) cc_final: 0.7282 (tmm) REVERT: A 159 GLU cc_start: 0.7536 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 335 GLU cc_start: 0.8369 (tp30) cc_final: 0.7770 (tm-30) REVERT: B 82 GLN cc_start: 0.8724 (mt0) cc_final: 0.8413 (mt0) REVERT: B 85 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7843 (tm-30) REVERT: B 125 LYS cc_start: 0.8430 (tppp) cc_final: 0.7969 (ttpt) REVERT: B 145 GLU cc_start: 0.7985 (tp30) cc_final: 0.7334 (tp30) REVERT: B 196 MET cc_start: 0.8079 (tpp) cc_final: 0.7858 (tmm) REVERT: B 201 GLU cc_start: 0.8633 (tp30) cc_final: 0.8197 (tp30) REVERT: B 211 MET cc_start: 0.8305 (tpp) cc_final: 0.8076 (tpt) REVERT: B 286 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7858 (mm-40) REVERT: B 335 GLU cc_start: 0.8176 (tp30) cc_final: 0.7795 (tm-30) REVERT: B 344 GLN cc_start: 0.8612 (mm110) cc_final: 0.8326 (mm110) REVERT: B 345 MET cc_start: 0.8648 (tpt) cc_final: 0.8368 (tpt) REVERT: C 85 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7633 (tm-30) REVERT: C 117 ASP cc_start: 0.7555 (t0) cc_final: 0.6978 (t0) REVERT: C 125 LYS cc_start: 0.8409 (tppp) cc_final: 0.7885 (ttpt) REVERT: C 135 MET cc_start: 0.7897 (tmm) cc_final: 0.7575 (tmm) REVERT: C 152 GLU cc_start: 0.7903 (tp30) cc_final: 0.7412 (tp30) REVERT: C 159 GLU cc_start: 0.7525 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 211 MET cc_start: 0.8328 (tpp) cc_final: 0.8049 (ttp) REVERT: C 222 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7525 (tm-30) REVERT: C 223 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7420 (tppt) REVERT: C 261 LEU cc_start: 0.7837 (mm) cc_final: 0.7576 (mm) REVERT: C 300 GLU cc_start: 0.8613 (tp30) cc_final: 0.8155 (mm-30) REVERT: C 344 GLN cc_start: 0.8563 (mm110) cc_final: 0.8319 (mm110) REVERT: C 345 MET cc_start: 0.8929 (tpt) cc_final: 0.8080 (tpt) REVERT: D 85 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7739 (tm-30) REVERT: D 101 MET cc_start: 0.8022 (mmp) cc_final: 0.7373 (mmm) REVERT: D 120 VAL cc_start: 0.7818 (t) cc_final: 0.7571 (p) REVERT: D 125 LYS cc_start: 0.8539 (tppp) cc_final: 0.8068 (tppp) REVERT: D 135 MET cc_start: 0.7716 (tmm) cc_final: 0.7266 (tmm) REVERT: D 335 GLU cc_start: 0.8196 (tp30) cc_final: 0.7740 (tm-30) REVERT: E 82 GLN cc_start: 0.8769 (mt0) cc_final: 0.8472 (mt0) REVERT: E 85 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7788 (tm-30) REVERT: E 101 MET cc_start: 0.7825 (mmp) cc_final: 0.7110 (mmm) REVERT: E 125 LYS cc_start: 0.8449 (tppp) cc_final: 0.7966 (ttpt) REVERT: E 145 GLU cc_start: 0.7920 (tp30) cc_final: 0.6988 (tp30) REVERT: E 196 MET cc_start: 0.8036 (tpp) cc_final: 0.7793 (tmm) REVERT: E 201 GLU cc_start: 0.8611 (tp30) cc_final: 0.8199 (tp30) REVERT: E 211 MET cc_start: 0.8285 (tpp) cc_final: 0.8043 (tpt) REVERT: E 335 GLU cc_start: 0.8218 (tp30) cc_final: 0.7830 (tm-30) REVERT: E 344 GLN cc_start: 0.8610 (mm110) cc_final: 0.8324 (mm110) REVERT: E 345 MET cc_start: 0.8636 (tpt) cc_final: 0.8309 (tpt) REVERT: F 82 GLN cc_start: 0.8868 (mt0) cc_final: 0.8558 (mt0) REVERT: F 85 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7658 (tm-30) REVERT: F 117 ASP cc_start: 0.7567 (t0) cc_final: 0.7294 (t0) REVERT: F 125 LYS cc_start: 0.8437 (tppp) cc_final: 0.7935 (ttpt) REVERT: F 135 MET cc_start: 0.7876 (tmm) cc_final: 0.7578 (tmm) REVERT: F 159 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7083 (tm-30) REVERT: F 206 LEU cc_start: 0.7872 (mp) cc_final: 0.7551 (mp) REVERT: F 223 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7465 (mppt) REVERT: F 300 GLU cc_start: 0.8616 (tp30) cc_final: 0.8161 (mm-30) REVERT: F 344 GLN cc_start: 0.8571 (mm110) cc_final: 0.8318 (mm110) outliers start: 58 outliers final: 47 residues processed: 378 average time/residue: 0.2460 time to fit residues: 138.7894 Evaluate side-chains 370 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 323 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 160 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 269 VAL Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 169 optimal weight: 0.1980 chunk 182 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 144 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15414 Z= 0.214 Angle : 0.482 7.505 20778 Z= 0.246 Chirality : 0.036 0.132 2208 Planarity : 0.003 0.038 2826 Dihedral : 3.629 16.457 2094 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.82 % Allowed : 19.80 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.20), residues: 1884 helix: 1.32 (0.14), residues: 1434 sheet: None (None), residues: 0 loop : -1.36 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 366 HIS 0.003 0.001 HIS D 182 PHE 0.010 0.001 PHE A 185 TYR 0.012 0.001 TYR B 278 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 334 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 94 TYR cc_start: 0.8209 (m-80) cc_final: 0.7810 (m-80) REVERT: A 135 MET cc_start: 0.7827 (tmm) cc_final: 0.7395 (tmm) REVERT: A 211 MET cc_start: 0.8392 (tpp) cc_final: 0.7935 (ttp) REVERT: A 335 GLU cc_start: 0.8348 (tp30) cc_final: 0.7788 (tm-30) REVERT: B 82 GLN cc_start: 0.8764 (mt0) cc_final: 0.8463 (mt0) REVERT: B 85 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7825 (tm-30) REVERT: B 125 LYS cc_start: 0.8439 (tppp) cc_final: 0.7973 (ttpt) REVERT: B 156 ILE cc_start: 0.8146 (mm) cc_final: 0.7729 (tp) REVERT: B 157 ASP cc_start: 0.8010 (t0) cc_final: 0.7765 (t0) REVERT: B 159 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7182 (tm-30) REVERT: B 201 GLU cc_start: 0.8604 (tp30) cc_final: 0.8146 (tp30) REVERT: B 211 MET cc_start: 0.8297 (tpp) cc_final: 0.8016 (tpt) REVERT: B 286 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7919 (mm-40) REVERT: B 335 GLU cc_start: 0.8133 (tp30) cc_final: 0.7791 (tm-30) REVERT: B 344 GLN cc_start: 0.8660 (mm110) cc_final: 0.8400 (mm-40) REVERT: B 345 MET cc_start: 0.8766 (tpt) cc_final: 0.8265 (tpp) REVERT: C 85 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7591 (tm-30) REVERT: C 125 LYS cc_start: 0.8495 (tppp) cc_final: 0.7965 (ttpt) REVERT: C 159 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7075 (tm-30) REVERT: C 211 MET cc_start: 0.8307 (tpp) cc_final: 0.7861 (mtp) REVERT: C 222 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7713 (tm-30) REVERT: C 223 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7585 (mppt) REVERT: C 300 GLU cc_start: 0.8580 (tp30) cc_final: 0.8133 (mm-30) REVERT: C 344 GLN cc_start: 0.8567 (mm110) cc_final: 0.8309 (mm110) REVERT: C 345 MET cc_start: 0.8984 (tpt) cc_final: 0.8117 (tpt) REVERT: D 85 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7766 (tm-30) REVERT: D 101 MET cc_start: 0.8041 (mmp) cc_final: 0.7402 (mmm) REVERT: D 120 VAL cc_start: 0.7847 (t) cc_final: 0.7605 (p) REVERT: D 135 MET cc_start: 0.7780 (tmm) cc_final: 0.7352 (tmm) REVERT: D 335 GLU cc_start: 0.8280 (tp30) cc_final: 0.7741 (tm-30) REVERT: E 82 GLN cc_start: 0.8808 (mt0) cc_final: 0.8495 (mt0) REVERT: E 85 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7778 (tm-30) REVERT: E 125 LYS cc_start: 0.8453 (tppp) cc_final: 0.7987 (ttpt) REVERT: E 145 GLU cc_start: 0.7942 (tp30) cc_final: 0.7086 (tp30) REVERT: E 201 GLU cc_start: 0.8603 (tp30) cc_final: 0.8176 (tp30) REVERT: E 211 MET cc_start: 0.8273 (tpp) cc_final: 0.7985 (tpt) REVERT: E 300 GLU cc_start: 0.8488 (tp30) cc_final: 0.8280 (mm-30) REVERT: E 335 GLU cc_start: 0.8303 (tp30) cc_final: 0.7808 (tm-30) REVERT: E 344 GLN cc_start: 0.8679 (mm110) cc_final: 0.8363 (mm110) REVERT: F 85 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7621 (tm-30) REVERT: F 125 LYS cc_start: 0.8491 (tppp) cc_final: 0.7943 (ttpt) REVERT: F 159 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7093 (tm-30) REVERT: F 223 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7533 (mppt) REVERT: F 300 GLU cc_start: 0.8584 (tp30) cc_final: 0.8141 (mm-30) REVERT: F 335 GLU cc_start: 0.8427 (tp30) cc_final: 0.7955 (tm-30) REVERT: F 344 GLN cc_start: 0.8521 (mm110) cc_final: 0.8281 (mm110) REVERT: F 345 MET cc_start: 0.9046 (tpt) cc_final: 0.8840 (tpt) outliers start: 61 outliers final: 54 residues processed: 359 average time/residue: 0.2436 time to fit residues: 132.2427 Evaluate side-chains 378 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 324 time to evaluate : 1.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 226 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 226 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 280 GLU Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 169 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 ASN ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN E 314 ASN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15414 Z= 0.154 Angle : 0.454 6.876 20778 Z= 0.228 Chirality : 0.035 0.138 2208 Planarity : 0.003 0.035 2826 Dihedral : 3.433 15.348 2094 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.64 % Allowed : 20.68 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.20), residues: 1884 helix: 1.47 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 366 HIS 0.002 0.001 HIS D 182 PHE 0.009 0.001 PHE F 185 TYR 0.012 0.001 TYR F 94 ARG 0.004 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 338 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7809 (tm-30) REVERT: A 125 LYS cc_start: 0.8581 (tppp) cc_final: 0.8132 (tppp) REVERT: A 135 MET cc_start: 0.7808 (tmm) cc_final: 0.7429 (tmm) REVERT: A 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7442 (tp30) REVERT: A 211 MET cc_start: 0.8382 (tpp) cc_final: 0.7930 (ttp) REVERT: A 300 GLU cc_start: 0.8490 (tp30) cc_final: 0.8286 (mm-30) REVERT: A 335 GLU cc_start: 0.8360 (tp30) cc_final: 0.7757 (tm-30) REVERT: B 82 GLN cc_start: 0.8780 (mt0) cc_final: 0.8461 (mt0) REVERT: B 85 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 125 LYS cc_start: 0.8442 (tppp) cc_final: 0.7983 (ttpt) REVERT: B 157 ASP cc_start: 0.7998 (t0) cc_final: 0.7700 (t0) REVERT: B 211 MET cc_start: 0.8201 (tpp) cc_final: 0.7915 (tpt) REVERT: B 335 GLU cc_start: 0.8117 (tp30) cc_final: 0.7788 (tm-30) REVERT: B 344 GLN cc_start: 0.8648 (mm110) cc_final: 0.8391 (mm-40) REVERT: B 345 MET cc_start: 0.8791 (tpt) cc_final: 0.8311 (tpp) REVERT: C 85 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7568 (tm-30) REVERT: C 125 LYS cc_start: 0.8476 (tppp) cc_final: 0.7947 (ttpt) REVERT: C 152 GLU cc_start: 0.7862 (tp30) cc_final: 0.7373 (tp30) REVERT: C 211 MET cc_start: 0.8227 (tpp) cc_final: 0.7840 (ttp) REVERT: C 223 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7605 (mppt) REVERT: C 280 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7281 (mm-30) REVERT: C 300 GLU cc_start: 0.8524 (tp30) cc_final: 0.7946 (tm-30) REVERT: C 335 GLU cc_start: 0.8498 (tp30) cc_final: 0.8048 (tm-30) REVERT: C 344 GLN cc_start: 0.8560 (mm110) cc_final: 0.8279 (mm110) REVERT: D 94 TYR cc_start: 0.8254 (m-80) cc_final: 0.7738 (m-80) REVERT: D 95 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8473 (tp40) REVERT: D 125 LYS cc_start: 0.8584 (tppp) cc_final: 0.8129 (tppp) REVERT: D 135 MET cc_start: 0.7778 (tmm) cc_final: 0.7395 (tmm) REVERT: D 152 GLU cc_start: 0.7854 (tp30) cc_final: 0.7390 (tp30) REVERT: D 335 GLU cc_start: 0.8260 (tp30) cc_final: 0.7730 (tm-30) REVERT: E 82 GLN cc_start: 0.8776 (mt0) cc_final: 0.8451 (mt0) REVERT: E 85 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7791 (tm-30) REVERT: E 101 MET cc_start: 0.7822 (mmp) cc_final: 0.7094 (mmm) REVERT: E 125 LYS cc_start: 0.8461 (tppp) cc_final: 0.7982 (ttpt) REVERT: E 145 GLU cc_start: 0.7832 (tp30) cc_final: 0.6960 (tp30) REVERT: E 201 GLU cc_start: 0.8571 (tp30) cc_final: 0.8104 (tp30) REVERT: E 335 GLU cc_start: 0.8169 (tp30) cc_final: 0.7807 (tm-30) REVERT: E 344 GLN cc_start: 0.8642 (mm110) cc_final: 0.8395 (mm-40) REVERT: E 345 MET cc_start: 0.8796 (tpt) cc_final: 0.8297 (tpt) REVERT: F 85 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7580 (tm-30) REVERT: F 125 LYS cc_start: 0.8460 (tppp) cc_final: 0.7911 (ttpt) REVERT: F 152 GLU cc_start: 0.7853 (tp30) cc_final: 0.7347 (tp30) REVERT: F 223 LYS cc_start: 0.7976 (mmmm) cc_final: 0.7715 (tppt) REVERT: F 300 GLU cc_start: 0.8556 (tp30) cc_final: 0.7872 (tm-30) REVERT: F 335 GLU cc_start: 0.8440 (tp30) cc_final: 0.7951 (tm-30) REVERT: F 344 GLN cc_start: 0.8527 (mm110) cc_final: 0.8260 (mm110) outliers start: 74 outliers final: 55 residues processed: 373 average time/residue: 0.2406 time to fit residues: 135.2839 Evaluate side-chains 384 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 329 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 45 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 314 ASN ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15414 Z= 0.140 Angle : 0.439 5.989 20778 Z= 0.222 Chirality : 0.035 0.128 2208 Planarity : 0.003 0.034 2826 Dihedral : 3.340 14.685 2094 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.64 % Allowed : 21.74 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1884 helix: 1.71 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.21 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 366 HIS 0.002 0.001 HIS D 182 PHE 0.012 0.001 PHE F 129 TYR 0.013 0.001 TYR F 94 ARG 0.007 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 332 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 TYR cc_start: 0.8164 (m-80) cc_final: 0.7747 (m-80) REVERT: A 125 LYS cc_start: 0.8564 (tppp) cc_final: 0.8121 (tppp) REVERT: A 135 MET cc_start: 0.7780 (tmm) cc_final: 0.7379 (tmm) REVERT: A 152 GLU cc_start: 0.7870 (tp30) cc_final: 0.7382 (tp30) REVERT: A 211 MET cc_start: 0.8399 (tpp) cc_final: 0.7978 (ttm) REVERT: A 300 GLU cc_start: 0.8493 (tp30) cc_final: 0.8283 (mm-30) REVERT: A 335 GLU cc_start: 0.8358 (tp30) cc_final: 0.7787 (tm-30) REVERT: B 82 GLN cc_start: 0.8770 (mt0) cc_final: 0.8511 (mt0) REVERT: B 125 LYS cc_start: 0.8439 (tppp) cc_final: 0.8028 (ttpt) REVERT: B 157 ASP cc_start: 0.7980 (t0) cc_final: 0.7622 (t0) REVERT: B 211 MET cc_start: 0.8189 (tpp) cc_final: 0.7894 (tpt) REVERT: B 234 ILE cc_start: 0.7997 (mm) cc_final: 0.7591 (tp) REVERT: B 335 GLU cc_start: 0.8150 (tp30) cc_final: 0.7794 (tm-30) REVERT: B 345 MET cc_start: 0.8812 (tpt) cc_final: 0.8312 (tpp) REVERT: C 85 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7575 (tm-30) REVERT: C 125 LYS cc_start: 0.8465 (tppp) cc_final: 0.7917 (ttpt) REVERT: C 152 GLU cc_start: 0.7897 (tp30) cc_final: 0.7369 (tp30) REVERT: C 211 MET cc_start: 0.8225 (tpp) cc_final: 0.7856 (ttp) REVERT: C 223 LYS cc_start: 0.7971 (mmmm) cc_final: 0.7575 (mppt) REVERT: C 300 GLU cc_start: 0.8486 (tp30) cc_final: 0.7907 (tm-30) REVERT: C 344 GLN cc_start: 0.8509 (mm110) cc_final: 0.8178 (mm110) REVERT: C 345 MET cc_start: 0.8884 (tpt) cc_final: 0.8681 (tpt) REVERT: D 94 TYR cc_start: 0.8183 (m-80) cc_final: 0.7754 (m-80) REVERT: D 101 MET cc_start: 0.7911 (mmp) cc_final: 0.7343 (mmm) REVERT: D 135 MET cc_start: 0.7759 (tmm) cc_final: 0.7384 (tmm) REVERT: D 152 GLU cc_start: 0.7863 (tp30) cc_final: 0.7349 (tp30) REVERT: D 335 GLU cc_start: 0.8274 (tp30) cc_final: 0.7754 (tm-30) REVERT: E 82 GLN cc_start: 0.8760 (mt0) cc_final: 0.8421 (mt0) REVERT: E 85 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7787 (tm-30) REVERT: E 125 LYS cc_start: 0.8475 (tppp) cc_final: 0.8024 (ttpt) REVERT: E 145 GLU cc_start: 0.7787 (tp30) cc_final: 0.6941 (tp30) REVERT: E 201 GLU cc_start: 0.8515 (tp30) cc_final: 0.8032 (tp30) REVERT: E 234 ILE cc_start: 0.7998 (mm) cc_final: 0.7601 (tp) REVERT: E 335 GLU cc_start: 0.8177 (tp30) cc_final: 0.7787 (tm-30) REVERT: E 345 MET cc_start: 0.8834 (tpt) cc_final: 0.8359 (tpt) REVERT: F 85 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7583 (tm-30) REVERT: F 125 LYS cc_start: 0.8423 (tppp) cc_final: 0.8020 (tppp) REVERT: F 135 MET cc_start: 0.7982 (tmm) cc_final: 0.7086 (tmm) REVERT: F 152 GLU cc_start: 0.7869 (tp30) cc_final: 0.7318 (tp30) REVERT: F 223 LYS cc_start: 0.7953 (mmmm) cc_final: 0.7714 (tppt) REVERT: F 300 GLU cc_start: 0.8492 (tp30) cc_final: 0.7868 (tm-30) REVERT: F 335 GLU cc_start: 0.8443 (tp30) cc_final: 0.8036 (tm-30) REVERT: F 344 GLN cc_start: 0.8504 (mm110) cc_final: 0.8140 (mm-40) outliers start: 74 outliers final: 58 residues processed: 371 average time/residue: 0.2412 time to fit residues: 134.6134 Evaluate side-chains 388 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 330 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 GLN ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15414 Z= 0.182 Angle : 0.458 6.114 20778 Z= 0.232 Chirality : 0.035 0.128 2208 Planarity : 0.003 0.037 2826 Dihedral : 3.370 15.585 2094 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 4.57 % Allowed : 21.68 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.20), residues: 1884 helix: 1.87 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.002 0.001 HIS A 182 PHE 0.015 0.001 PHE F 129 TYR 0.013 0.001 TYR F 94 ARG 0.007 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 330 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7844 (tm-30) REVERT: A 94 TYR cc_start: 0.8212 (m-80) cc_final: 0.7677 (m-80) REVERT: A 135 MET cc_start: 0.7816 (tmm) cc_final: 0.7418 (tmm) REVERT: A 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7378 (tp30) REVERT: A 211 MET cc_start: 0.8407 (tpp) cc_final: 0.7941 (ttm) REVERT: A 335 GLU cc_start: 0.8371 (tp30) cc_final: 0.7820 (tm-30) REVERT: B 82 GLN cc_start: 0.8791 (mt0) cc_final: 0.8548 (mt0) REVERT: B 125 LYS cc_start: 0.8469 (tppp) cc_final: 0.8049 (ttpt) REVERT: B 157 ASP cc_start: 0.8016 (t0) cc_final: 0.7637 (t0) REVERT: B 160 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7411 (t0) REVERT: B 211 MET cc_start: 0.8208 (tpp) cc_final: 0.7904 (tpt) REVERT: B 335 GLU cc_start: 0.8155 (tp30) cc_final: 0.7816 (tm-30) REVERT: B 345 MET cc_start: 0.8867 (tpt) cc_final: 0.8381 (tpt) REVERT: C 85 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7574 (tm-30) REVERT: C 125 LYS cc_start: 0.8429 (tppp) cc_final: 0.7989 (tppp) REVERT: C 211 MET cc_start: 0.8218 (tpp) cc_final: 0.7880 (ttp) REVERT: C 223 LYS cc_start: 0.7979 (mmmm) cc_final: 0.7547 (mppt) REVERT: C 262 MET cc_start: 0.8364 (tpp) cc_final: 0.8032 (tpp) REVERT: C 300 GLU cc_start: 0.8533 (tp30) cc_final: 0.8010 (tm-30) REVERT: C 335 GLU cc_start: 0.8406 (tp30) cc_final: 0.8126 (tm-30) REVERT: C 344 GLN cc_start: 0.8526 (mm110) cc_final: 0.8244 (mm-40) REVERT: D 101 MET cc_start: 0.7956 (mmp) cc_final: 0.7354 (mmm) REVERT: D 135 MET cc_start: 0.7815 (tmm) cc_final: 0.7407 (tmm) REVERT: D 152 GLU cc_start: 0.7875 (tp30) cc_final: 0.7349 (tp30) REVERT: D 335 GLU cc_start: 0.8305 (tp30) cc_final: 0.7781 (tm-30) REVERT: E 82 GLN cc_start: 0.8789 (mt0) cc_final: 0.8458 (mt0) REVERT: E 85 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7784 (tm-30) REVERT: E 125 LYS cc_start: 0.8505 (tppp) cc_final: 0.8125 (ttpt) REVERT: E 145 GLU cc_start: 0.7810 (tp30) cc_final: 0.6985 (tp30) REVERT: E 234 ILE cc_start: 0.7970 (mm) cc_final: 0.7593 (tp) REVERT: E 335 GLU cc_start: 0.8213 (tp30) cc_final: 0.7805 (tm-30) REVERT: E 345 MET cc_start: 0.8850 (tpt) cc_final: 0.8300 (tpt) REVERT: F 85 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7599 (tm-30) REVERT: F 125 LYS cc_start: 0.8388 (tppp) cc_final: 0.7864 (ttpt) REVERT: F 152 GLU cc_start: 0.7919 (tp30) cc_final: 0.7363 (tp30) REVERT: F 223 LYS cc_start: 0.8000 (mmmm) cc_final: 0.7764 (tppt) REVERT: F 300 GLU cc_start: 0.8541 (tp30) cc_final: 0.7908 (tm-30) REVERT: F 335 GLU cc_start: 0.8366 (tp30) cc_final: 0.8115 (tm-30) REVERT: F 344 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8169 (mm-40) REVERT: F 345 MET cc_start: 0.8952 (tpt) cc_final: 0.8166 (tpt) outliers start: 73 outliers final: 64 residues processed: 366 average time/residue: 0.2368 time to fit residues: 131.5359 Evaluate side-chains 390 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 325 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 96 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 179 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15414 Z= 0.232 Angle : 0.479 7.470 20778 Z= 0.245 Chirality : 0.037 0.126 2208 Planarity : 0.003 0.033 2826 Dihedral : 3.471 16.935 2094 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 4.70 % Allowed : 22.93 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.20), residues: 1884 helix: 1.87 (0.14), residues: 1476 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 366 HIS 0.002 0.001 HIS B 182 PHE 0.022 0.002 PHE C 129 TYR 0.014 0.001 TYR F 94 ARG 0.004 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 332 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7924 (tm-30) REVERT: A 94 TYR cc_start: 0.8212 (m-80) cc_final: 0.7804 (m-80) REVERT: A 135 MET cc_start: 0.7867 (tmm) cc_final: 0.7452 (tmm) REVERT: A 152 GLU cc_start: 0.7904 (tp30) cc_final: 0.7432 (tp30) REVERT: A 211 MET cc_start: 0.8390 (tpp) cc_final: 0.7975 (ttm) REVERT: A 335 GLU cc_start: 0.8383 (tp30) cc_final: 0.7863 (tm-30) REVERT: B 82 GLN cc_start: 0.8809 (mt0) cc_final: 0.8497 (mt0) REVERT: B 85 GLU cc_start: 0.8215 (tm-30) cc_final: 0.7820 (tm-30) REVERT: B 125 LYS cc_start: 0.8434 (tppp) cc_final: 0.8008 (ttpt) REVERT: B 157 ASP cc_start: 0.8049 (t0) cc_final: 0.7666 (t0) REVERT: B 160 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7422 (t0) REVERT: B 211 MET cc_start: 0.8259 (tpp) cc_final: 0.7710 (ttp) REVERT: B 335 GLU cc_start: 0.8199 (tp30) cc_final: 0.7857 (tm-30) REVERT: B 345 MET cc_start: 0.8868 (tpt) cc_final: 0.8460 (tpt) REVERT: C 85 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7597 (tm-30) REVERT: C 101 MET cc_start: 0.8066 (mmp) cc_final: 0.7825 (mmp) REVERT: C 125 LYS cc_start: 0.8383 (tppp) cc_final: 0.7954 (tppp) REVERT: C 152 GLU cc_start: 0.7861 (tp30) cc_final: 0.7373 (tp30) REVERT: C 211 MET cc_start: 0.8245 (tpp) cc_final: 0.7928 (mtp) REVERT: C 223 LYS cc_start: 0.8009 (mmmm) cc_final: 0.7794 (tppt) REVERT: C 300 GLU cc_start: 0.8525 (tp30) cc_final: 0.7922 (tm-30) REVERT: C 307 GLU cc_start: 0.7540 (tt0) cc_final: 0.7195 (tt0) REVERT: C 335 GLU cc_start: 0.8406 (tp30) cc_final: 0.8136 (tm-30) REVERT: C 344 GLN cc_start: 0.8617 (mm110) cc_final: 0.8369 (mm-40) REVERT: C 345 MET cc_start: 0.8899 (tpt) cc_final: 0.8034 (tpt) REVERT: D 85 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7836 (tm-30) REVERT: D 94 TYR cc_start: 0.8194 (m-80) cc_final: 0.7756 (m-80) REVERT: D 101 MET cc_start: 0.7983 (mmp) cc_final: 0.7403 (mmm) REVERT: D 135 MET cc_start: 0.7848 (tmm) cc_final: 0.7441 (tmm) REVERT: D 152 GLU cc_start: 0.7894 (tp30) cc_final: 0.7388 (tp30) REVERT: D 211 MET cc_start: 0.8401 (tpp) cc_final: 0.7845 (ttm) REVERT: D 335 GLU cc_start: 0.8298 (tp30) cc_final: 0.7844 (tm-30) REVERT: E 82 GLN cc_start: 0.8821 (mt0) cc_final: 0.8506 (mt0) REVERT: E 85 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7797 (tm-30) REVERT: E 125 LYS cc_start: 0.8526 (tppp) cc_final: 0.8203 (ttpt) REVERT: E 145 GLU cc_start: 0.7852 (tp30) cc_final: 0.7040 (tp30) REVERT: E 335 GLU cc_start: 0.8245 (tp30) cc_final: 0.7839 (tm-30) REVERT: E 345 MET cc_start: 0.8945 (tpt) cc_final: 0.8443 (tpt) REVERT: F 85 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7622 (tm-30) REVERT: F 125 LYS cc_start: 0.8347 (tppp) cc_final: 0.7858 (ttpt) REVERT: F 262 MET cc_start: 0.8393 (tpp) cc_final: 0.8117 (tpp) REVERT: F 335 GLU cc_start: 0.8375 (tp30) cc_final: 0.8121 (tm-30) REVERT: F 345 MET cc_start: 0.8960 (tpt) cc_final: 0.8190 (tpt) outliers start: 75 outliers final: 69 residues processed: 363 average time/residue: 0.2302 time to fit residues: 126.8876 Evaluate side-chains 396 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 326 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 214 ARG Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 7.9990 chunk 71 optimal weight: 0.0470 chunk 107 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.6980 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN C 314 ASN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 319 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 15414 Z= 0.152 Angle : 0.456 7.400 20778 Z= 0.229 Chirality : 0.035 0.130 2208 Planarity : 0.003 0.033 2826 Dihedral : 3.337 16.401 2094 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.39 % Allowed : 22.93 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.20), residues: 1884 helix: 1.96 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.05 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 287 HIS 0.002 0.001 HIS A 182 PHE 0.020 0.001 PHE F 129 TYR 0.014 0.001 TYR E 94 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 321 time to evaluate : 1.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8226 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 135 MET cc_start: 0.7795 (tmm) cc_final: 0.7395 (tmm) REVERT: A 152 GLU cc_start: 0.7867 (tp30) cc_final: 0.7357 (tp30) REVERT: A 211 MET cc_start: 0.8388 (tpp) cc_final: 0.7926 (ttm) REVERT: A 321 ASP cc_start: 0.7286 (OUTLIER) cc_final: 0.6737 (p0) REVERT: A 335 GLU cc_start: 0.8370 (tp30) cc_final: 0.7853 (tm-30) REVERT: B 82 GLN cc_start: 0.8778 (mt0) cc_final: 0.8538 (mt0) REVERT: B 125 LYS cc_start: 0.8394 (tppp) cc_final: 0.7948 (ttpt) REVERT: B 157 ASP cc_start: 0.8009 (t0) cc_final: 0.7603 (t0) REVERT: B 160 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7432 (t0) REVERT: B 211 MET cc_start: 0.8229 (tpp) cc_final: 0.7689 (ttp) REVERT: B 335 GLU cc_start: 0.8210 (tp30) cc_final: 0.7836 (tm-30) REVERT: B 345 MET cc_start: 0.8877 (tpt) cc_final: 0.8453 (tpt) REVERT: C 82 GLN cc_start: 0.8796 (mt0) cc_final: 0.8543 (mt0) REVERT: C 85 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7543 (tm-30) REVERT: C 125 LYS cc_start: 0.8229 (tppp) cc_final: 0.7871 (tppp) REVERT: C 152 GLU cc_start: 0.7815 (tp30) cc_final: 0.7316 (tp30) REVERT: C 211 MET cc_start: 0.8226 (tpp) cc_final: 0.7913 (mtp) REVERT: C 291 MET cc_start: 0.8507 (tpp) cc_final: 0.8279 (tpp) REVERT: C 300 GLU cc_start: 0.8498 (tp30) cc_final: 0.7908 (tm-30) REVERT: C 307 GLU cc_start: 0.7444 (tt0) cc_final: 0.7123 (tt0) REVERT: C 318 ASN cc_start: 0.9041 (t0) cc_final: 0.8316 (t0) REVERT: C 335 GLU cc_start: 0.8391 (tp30) cc_final: 0.8127 (tm-30) REVERT: D 82 GLN cc_start: 0.8806 (mt0) cc_final: 0.8593 (mt0) REVERT: D 94 TYR cc_start: 0.8140 (m-80) cc_final: 0.7607 (m-80) REVERT: D 101 MET cc_start: 0.7904 (mmp) cc_final: 0.7340 (mmm) REVERT: D 125 LYS cc_start: 0.8575 (tppp) cc_final: 0.8071 (tppp) REVERT: D 135 MET cc_start: 0.7772 (tmm) cc_final: 0.7370 (tmm) REVERT: D 152 GLU cc_start: 0.7807 (tp30) cc_final: 0.7295 (tp30) REVERT: D 211 MET cc_start: 0.8392 (tpp) cc_final: 0.7805 (ttm) REVERT: D 318 ASN cc_start: 0.8950 (t0) cc_final: 0.7860 (t0) REVERT: D 321 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6740 (p0) REVERT: D 335 GLU cc_start: 0.8379 (tp30) cc_final: 0.7833 (tm-30) REVERT: E 82 GLN cc_start: 0.8791 (mt0) cc_final: 0.8467 (mt0) REVERT: E 85 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7783 (tm-30) REVERT: E 125 LYS cc_start: 0.8512 (tppp) cc_final: 0.8231 (ttpt) REVERT: E 145 GLU cc_start: 0.7783 (tp30) cc_final: 0.6935 (tp30) REVERT: E 335 GLU cc_start: 0.8235 (tp30) cc_final: 0.7824 (tm-30) REVERT: E 345 MET cc_start: 0.8920 (tpt) cc_final: 0.8479 (tpt) REVERT: F 85 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7588 (tm-30) REVERT: F 125 LYS cc_start: 0.8307 (tppp) cc_final: 0.7827 (ttpt) REVERT: F 152 GLU cc_start: 0.7794 (tp30) cc_final: 0.7343 (tp30) REVERT: F 262 MET cc_start: 0.8389 (tpp) cc_final: 0.8132 (tpp) REVERT: F 335 GLU cc_start: 0.8371 (tp30) cc_final: 0.8114 (tm-30) REVERT: F 345 MET cc_start: 0.8942 (tpt) cc_final: 0.8132 (tpt) outliers start: 70 outliers final: 64 residues processed: 354 average time/residue: 0.2359 time to fit residues: 126.3121 Evaluate side-chains 381 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 314 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 167 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15414 Z= 0.163 Angle : 0.462 8.277 20778 Z= 0.231 Chirality : 0.035 0.137 2208 Planarity : 0.003 0.032 2826 Dihedral : 3.343 16.310 2094 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.51 % Allowed : 23.25 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1884 helix: 2.01 (0.14), residues: 1470 sheet: None (None), residues: 0 loop : -1.00 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 287 HIS 0.002 0.001 HIS D 182 PHE 0.021 0.001 PHE F 129 TYR 0.014 0.001 TYR F 94 ARG 0.003 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 318 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7833 (tm-30) REVERT: A 94 TYR cc_start: 0.8214 (m-80) cc_final: 0.7621 (m-80) REVERT: A 135 MET cc_start: 0.7793 (tmm) cc_final: 0.7382 (tmm) REVERT: A 152 GLU cc_start: 0.7804 (tp30) cc_final: 0.7301 (tp30) REVERT: A 211 MET cc_start: 0.8392 (tpp) cc_final: 0.7929 (ttm) REVERT: A 262 MET cc_start: 0.8353 (tpp) cc_final: 0.8137 (tpp) REVERT: A 318 ASN cc_start: 0.8920 (t0) cc_final: 0.7863 (t0) REVERT: A 321 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6687 (p0) REVERT: A 335 GLU cc_start: 0.8383 (tp30) cc_final: 0.7861 (tm-30) REVERT: B 82 GLN cc_start: 0.8783 (mt0) cc_final: 0.8463 (mt0) REVERT: B 85 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 125 LYS cc_start: 0.8382 (tppp) cc_final: 0.7926 (ttpt) REVERT: B 129 PHE cc_start: 0.8573 (m-10) cc_final: 0.8327 (m-10) REVERT: B 157 ASP cc_start: 0.8012 (t0) cc_final: 0.7625 (t0) REVERT: B 160 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7416 (t0) REVERT: B 211 MET cc_start: 0.8238 (tpp) cc_final: 0.7684 (ttp) REVERT: B 335 GLU cc_start: 0.8154 (tp30) cc_final: 0.7928 (tm-30) REVERT: B 343 GLU cc_start: 0.7503 (mm-30) cc_final: 0.7275 (mm-30) REVERT: B 345 MET cc_start: 0.8827 (tpt) cc_final: 0.8382 (tpp) REVERT: C 85 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7583 (tm-30) REVERT: C 125 LYS cc_start: 0.8210 (tppp) cc_final: 0.7691 (ttpt) REVERT: C 152 GLU cc_start: 0.7871 (tp30) cc_final: 0.7350 (tp30) REVERT: C 211 MET cc_start: 0.8228 (tpp) cc_final: 0.7902 (mtp) REVERT: C 300 GLU cc_start: 0.8489 (tp30) cc_final: 0.8193 (tp30) REVERT: C 307 GLU cc_start: 0.7474 (tt0) cc_final: 0.7125 (tt0) REVERT: C 318 ASN cc_start: 0.9041 (t0) cc_final: 0.8315 (t0) REVERT: C 335 GLU cc_start: 0.8406 (tp30) cc_final: 0.8126 (tm-30) REVERT: D 82 GLN cc_start: 0.8818 (mt0) cc_final: 0.8610 (mt0) REVERT: D 94 TYR cc_start: 0.8123 (m-80) cc_final: 0.7554 (m-80) REVERT: D 101 MET cc_start: 0.7885 (mmp) cc_final: 0.7339 (mmm) REVERT: D 135 MET cc_start: 0.7758 (tmm) cc_final: 0.7375 (tmm) REVERT: D 152 GLU cc_start: 0.7796 (tp30) cc_final: 0.7269 (tp30) REVERT: D 211 MET cc_start: 0.8387 (tpp) cc_final: 0.7776 (ttm) REVERT: D 318 ASN cc_start: 0.8925 (t0) cc_final: 0.7873 (t0) REVERT: D 321 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6730 (p0) REVERT: D 335 GLU cc_start: 0.8397 (tp30) cc_final: 0.7846 (tm-30) REVERT: E 82 GLN cc_start: 0.8807 (mt0) cc_final: 0.8487 (mt0) REVERT: E 85 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 125 LYS cc_start: 0.8516 (tppp) cc_final: 0.8264 (ttpt) REVERT: E 145 GLU cc_start: 0.7773 (tp30) cc_final: 0.6935 (tp30) REVERT: E 335 GLU cc_start: 0.8212 (tp30) cc_final: 0.7920 (tm-30) REVERT: E 345 MET cc_start: 0.8875 (tpt) cc_final: 0.8429 (tpt) REVERT: F 85 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7593 (tm-30) REVERT: F 125 LYS cc_start: 0.8302 (tppp) cc_final: 0.7743 (ttmm) REVERT: F 152 GLU cc_start: 0.7805 (tp30) cc_final: 0.7348 (tp30) REVERT: F 318 ASN cc_start: 0.9022 (t0) cc_final: 0.8277 (t0) REVERT: F 335 GLU cc_start: 0.8381 (tp30) cc_final: 0.8117 (tm-30) REVERT: F 345 MET cc_start: 0.8943 (tpt) cc_final: 0.8168 (tpt) outliers start: 72 outliers final: 62 residues processed: 353 average time/residue: 0.2351 time to fit residues: 125.9652 Evaluate side-chains 378 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 214 ARG Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 321 ASP Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 264 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 321 ASP Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.5980 chunk 176 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 GLN ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15414 Z= 0.143 Angle : 0.471 7.793 20778 Z= 0.233 Chirality : 0.034 0.133 2208 Planarity : 0.003 0.032 2826 Dihedral : 3.276 16.043 2094 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.26 % Allowed : 23.62 % Favored : 72.12 % 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: 2.26 (0.20), residues: 1884 helix: 2.22 (0.14), residues: 1446 sheet: None (None), residues: 0 loop : -1.03 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 287 HIS 0.003 0.001 HIS A 182 PHE 0.023 0.001 PHE F 129 TYR 0.015 0.001 TYR F 94 ARG 0.003 0.000 ARG A 139 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3768 Ramachandran restraints generated. 1884 Oldfield, 0 Emsley, 1884 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 319 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7881 (tm-30) REVERT: A 101 MET cc_start: 0.7863 (mmp) cc_final: 0.7164 (mmm) REVERT: A 135 MET cc_start: 0.7759 (tmm) cc_final: 0.7369 (tmm) REVERT: A 152 GLU cc_start: 0.7790 (tp30) cc_final: 0.7280 (tp30) REVERT: A 211 MET cc_start: 0.8423 (tpp) cc_final: 0.7942 (ttm) REVERT: A 302 ASP cc_start: 0.7427 (m-30) cc_final: 0.7088 (t0) REVERT: A 318 ASN cc_start: 0.8955 (t0) cc_final: 0.7913 (t0) REVERT: A 321 ASP cc_start: 0.7279 (OUTLIER) cc_final: 0.6697 (p0) REVERT: A 335 GLU cc_start: 0.8346 (tp30) cc_final: 0.7838 (tm-30) REVERT: B 82 GLN cc_start: 0.8798 (mt0) cc_final: 0.8548 (mt0) REVERT: B 125 LYS cc_start: 0.8408 (tppp) cc_final: 0.7981 (ttpt) REVERT: B 157 ASP cc_start: 0.7995 (t0) cc_final: 0.7606 (t0) REVERT: B 160 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7401 (t0) REVERT: B 211 MET cc_start: 0.8213 (tpp) cc_final: 0.7673 (ttp) REVERT: B 328 MET cc_start: 0.7507 (ttm) cc_final: 0.7272 (ttp) REVERT: B 335 GLU cc_start: 0.8128 (tp30) cc_final: 0.7889 (tm-30) REVERT: B 345 MET cc_start: 0.8829 (tpt) cc_final: 0.8342 (tpt) REVERT: C 82 GLN cc_start: 0.8791 (mt0) cc_final: 0.8537 (mt0) REVERT: C 85 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7560 (tm-30) REVERT: C 125 LYS cc_start: 0.8194 (tppp) cc_final: 0.7695 (ttpt) REVERT: C 152 GLU cc_start: 0.7850 (tp30) cc_final: 0.7336 (tp30) REVERT: C 211 MET cc_start: 0.8227 (tpp) cc_final: 0.7907 (ttp) REVERT: C 300 GLU cc_start: 0.8473 (tp30) cc_final: 0.8197 (tp30) REVERT: C 318 ASN cc_start: 0.9043 (t0) cc_final: 0.8331 (t0) REVERT: C 335 GLU cc_start: 0.8398 (tp30) cc_final: 0.8117 (tm-30) REVERT: D 82 GLN cc_start: 0.8810 (mt0) cc_final: 0.8594 (mt0) REVERT: D 101 MET cc_start: 0.7832 (mmp) cc_final: 0.7316 (mmm) REVERT: D 125 LYS cc_start: 0.8570 (tppp) cc_final: 0.8089 (tppp) REVERT: D 135 MET cc_start: 0.7728 (tmm) cc_final: 0.7318 (tmm) REVERT: D 152 GLU cc_start: 0.7773 (tp30) cc_final: 0.7214 (tp30) REVERT: D 302 ASP cc_start: 0.7421 (m-30) cc_final: 0.7074 (t0) REVERT: D 307 GLU cc_start: 0.7044 (tt0) cc_final: 0.6829 (tt0) REVERT: D 318 ASN cc_start: 0.8950 (t0) cc_final: 0.7880 (t0) REVERT: D 321 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6701 (p0) REVERT: D 328 MET cc_start: 0.7002 (ttp) cc_final: 0.6717 (ttp) REVERT: D 335 GLU cc_start: 0.8402 (tp30) cc_final: 0.7854 (tm-30) REVERT: E 82 GLN cc_start: 0.8794 (mt0) cc_final: 0.8491 (mt0) REVERT: E 85 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7785 (tm-30) REVERT: E 125 LYS cc_start: 0.8482 (tppp) cc_final: 0.8230 (ttpt) REVERT: E 145 GLU cc_start: 0.7708 (tp30) cc_final: 0.6912 (tp30) REVERT: E 318 ASN cc_start: 0.9101 (t0) cc_final: 0.8022 (t0) REVERT: E 328 MET cc_start: 0.7545 (ttm) cc_final: 0.7303 (ttp) REVERT: E 335 GLU cc_start: 0.8159 (tp30) cc_final: 0.7900 (tm-30) REVERT: E 345 MET cc_start: 0.8883 (tpt) cc_final: 0.8305 (tpt) REVERT: F 85 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7589 (tm-30) REVERT: F 125 LYS cc_start: 0.8274 (tppp) cc_final: 0.7713 (ttmm) REVERT: F 152 GLU cc_start: 0.7766 (tp30) cc_final: 0.7321 (tp30) REVERT: F 291 MET cc_start: 0.8498 (tpp) cc_final: 0.8291 (tpp) REVERT: F 318 ASN cc_start: 0.9040 (t0) cc_final: 0.8309 (t0) REVERT: F 335 GLU cc_start: 0.8378 (tp30) cc_final: 0.8062 (tm-30) REVERT: F 345 MET cc_start: 0.8952 (tpt) cc_final: 0.8143 (tpt) outliers start: 68 outliers final: 62 residues processed: 357 average time/residue: 0.2411 time to fit residues: 129.7413 Evaluate side-chains 380 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 91 THR Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 326 TRP Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 96 ASP Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 326 TRP Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 ASP Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 326 TRP Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain D residue 170 ASP Chi-restraints excluded: chain D residue 200 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 326 TRP Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain D residue 367 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 170 ASP Chi-restraints excluded: chain E residue 225 ILE Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 326 TRP Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 367 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.3980 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 GLN ** C 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 GLN ** E 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102796 restraints weight = 24921.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106237 restraints weight = 13296.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.108536 restraints weight = 8266.745| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15414 Z= 0.151 Angle : 0.477 8.786 20778 Z= 0.236 Chirality : 0.035 0.132 2208 Planarity : 0.003 0.030 2826 Dihedral : 3.263 15.892 2094 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.88 % Allowed : 24.19 % Favored : 71.93 % 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: 2.38 (0.20), residues: 1884 helix: 2.27 (0.13), residues: 1452 sheet: None (None), residues: 0 loop : -0.91 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 287 HIS 0.003 0.001 HIS A 182 PHE 0.022 0.001 PHE F 129 TYR 0.015 0.001 TYR C 94 ARG 0.003 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3020.17 seconds wall clock time: 55 minutes 15.50 seconds (3315.50 seconds total)