Starting phenix.real_space_refine on Tue Aug 6 09:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/08_2024/8wbe_37422_neut.cif" } resolution = 3.0 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= 0.003 sd= 0.148 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 126 5.16 5 C 10161 2.51 5 N 2769 2.21 5 O 3038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16094 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2596 Classifications: {'peptide': 330} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "C" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Chain: "a" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "b" Number of atoms: 2782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2782 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "c" Number of atoms: 2576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2576 Classifications: {'peptide': 327} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 9.32, per 1000 atoms: 0.58 Number of scatterers: 16094 At special positions: 0 Unit cell: (124.1, 125.8, 121.55, 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 126 16.00 O 3038 8.00 N 2769 7.00 C 10161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=30, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 15 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 143 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 223 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 329 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 316 " distance=2.06 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 4 " - pdb=" SG CYS c 15 " distance=2.03 Simple disulfide: pdb=" SG CYS c 55 " - pdb=" SG CYS c 143 " distance=2.03 Simple disulfide: pdb=" SG CYS c 179 " - pdb=" SG CYS c 223 " distance=2.03 Simple disulfide: pdb=" SG CYS c 280 " - pdb=" SG CYS c 329 " distance=2.03 Simple disulfide: pdb=" SG CYS c 313 " - pdb=" SG CYS c 316 " distance=2.02 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: 6.04 Conformation dependent library (CDL) restraints added in 2.9 seconds 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3738 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 25 sheets defined 18.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.581A pdb=" N ASN A 73 " --> pdb=" O LYS A 69 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N GLU A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.524A pdb=" N LEU A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.528A pdb=" N THR A 230 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 removed outlier: 3.718A pdb=" N ALA A 248 " --> pdb=" O LYS A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.685A pdb=" N LEU B 42 " --> pdb=" O SER B 38 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP B 52 " --> pdb=" O ASN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.546A pdb=" N ILE B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.594A pdb=" N TYR B 77 " --> pdb=" O ASN B 73 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 180 through 183 removed outlier: 3.689A pdb=" N LEU B 183 " --> pdb=" O ASP B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 183' Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.634A pdb=" N THR B 230 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 248 removed outlier: 3.600A pdb=" N ALA B 248 " --> pdb=" O LYS B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 271 removed outlier: 3.541A pdb=" N LEU B 270 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'C' and resid 40 through 53 removed outlier: 3.913A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 82 removed outlier: 5.170A pdb=" N ASN C 73 " --> pdb=" O LYS C 69 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLU C 74 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 148 Processing helix chain 'C' and resid 180 through 183 removed outlier: 3.747A pdb=" N LEU C 183 " --> pdb=" O ASP C 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 183' Processing helix chain 'C' and resid 226 through 230 removed outlier: 3.612A pdb=" N THR C 230 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 248 removed outlier: 3.678A pdb=" N ALA C 248 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 271 removed outlier: 3.814A pdb=" N GLY C 271 " --> pdb=" O TRP C 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 53 Processing helix chain 'a' and resid 61 through 82 removed outlier: 3.642A pdb=" N ASN a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE a 66 " --> pdb=" O ARG a 62 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET a 67 " --> pdb=" O LEU a 63 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ASN a 73 " --> pdb=" O LYS a 69 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N GLU a 74 " --> pdb=" O GLN a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.709A pdb=" N LEU a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 removed outlier: 3.821A pdb=" N THR a 230 " --> pdb=" O LYS a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 244 through 248 removed outlier: 3.590A pdb=" N ALA a 248 " --> pdb=" O LYS a 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 271 removed outlier: 3.602A pdb=" N GLY a 271 " --> pdb=" O TRP a 268 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 38 through 51 Processing helix chain 'b' and resid 61 through 72 removed outlier: 3.578A pdb=" N ASN b 65 " --> pdb=" O THR b 61 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE b 66 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N MET b 67 " --> pdb=" O LEU b 63 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 83 removed outlier: 3.853A pdb=" N GLY b 83 " --> pdb=" O LEU b 79 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 148 removed outlier: 3.733A pdb=" N ARG b 148 " --> pdb=" O ASN b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 180 through 183 Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.516A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 53 removed outlier: 3.801A pdb=" N ALA c 43 " --> pdb=" O PRO c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 61 through 82 removed outlier: 3.671A pdb=" N ILE c 66 " --> pdb=" O ARG c 62 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N MET c 67 " --> pdb=" O LEU c 63 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ASN c 73 " --> pdb=" O LYS c 69 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N GLU c 74 " --> pdb=" O GLN c 70 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY c 82 " --> pdb=" O VAL c 78 " (cutoff:3.500A) Processing helix chain 'c' and resid 144 through 148 removed outlier: 3.562A pdb=" N ARG c 148 " --> pdb=" O ASN c 145 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 183 removed outlier: 3.889A pdb=" N LEU c 183 " --> pdb=" O ASP c 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 180 through 183' Processing helix chain 'c' and resid 226 through 230 Processing helix chain 'c' and resid 244 through 248 removed outlier: 3.514A pdb=" N ALA c 248 " --> pdb=" O LYS c 245 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 271 removed outlier: 3.725A pdb=" N LEU c 270 " --> pdb=" O PRO c 267 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY c 271 " --> pdb=" O TRP c 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 267 through 271' Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.227A pdb=" N LYS A 33 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N MET A 169 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN A 35 " --> pdb=" O MET A 169 " (cutoff:3.500A) removed outlier: 8.753A pdb=" N PHE A 171 " --> pdb=" O GLN A 35 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ASN A 166 " --> pdb=" O TYR A 158 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N TYR A 158 " --> pdb=" O ASN A 166 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.821A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 89 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.529A pdb=" N GLU A 274 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE A 277 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N GLU A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU A 203 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N TRP a 201 " --> pdb=" O ALA a 215 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA a 215 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU a 203 " --> pdb=" O GLU a 213 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N GLU a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N PHE a 277 " --> pdb=" O GLU a 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 284 through 287 removed outlier: 5.952A pdb=" N THR A 284 " --> pdb=" O TRP A 311 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 313 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR A 286 " --> pdb=" O CYS A 313 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 13 through 16 Processing sheet with id=AA7, first strand: chain 'B' and resid 34 through 35 removed outlier: 6.515A pdb=" N ASN B 166 " --> pdb=" O TYR B 158 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 158 " --> pdb=" O ASN B 166 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TRP B 168 " --> pdb=" O GLU B 156 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 89 removed outlier: 6.903A pdb=" N GLY B 56 " --> pdb=" O ALA B 149 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.881A pdb=" N GLY B 328 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 274 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 277 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 9.600A pdb=" N GLU B 213 " --> pdb=" O PHE B 277 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLU B 203 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA B 215 " --> pdb=" O TRP B 201 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP B 201 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N SER b 205 " --> pdb=" O ILE b 212 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE b 212 " --> pdb=" O SER b 205 " (cutoff:3.500A) removed outlier: 9.235A pdb=" N GLU b 213 " --> pdb=" O PHE b 277 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE b 277 " --> pdb=" O GLU b 213 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU b 274 " --> pdb=" O LEU b 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 284 through 287 removed outlier: 6.250A pdb=" N THR B 284 " --> pdb=" O TRP B 311 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N CYS B 313 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N THR B 286 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.743A pdb=" N ASN C 166 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N TYR C 158 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 168 " --> pdb=" O GLU C 156 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 89 through 90 removed outlier: 6.221A pdb=" N VAL C 89 " --> pdb=" O ILE C 135 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE C 57 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 210 through 214 removed outlier: 6.942A pdb=" N GLU C 203 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 196 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TRP c 201 " --> pdb=" O ALA c 215 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA c 215 " --> pdb=" O TRP c 201 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU c 203 " --> pdb=" O GLU c 213 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N GLU c 213 " --> pdb=" O PHE c 277 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE c 277 " --> pdb=" O GLU c 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 274 through 277 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 287 removed outlier: 6.155A pdb=" N THR C 286 " --> pdb=" O CYS C 313 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'a' and resid 33 through 35 removed outlier: 6.542A pdb=" N ASN a 166 " --> pdb=" O TYR a 158 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TYR a 158 " --> pdb=" O ASN a 166 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N TRP a 168 " --> pdb=" O GLU a 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.871A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL a 89 " --> pdb=" O ILE a 135 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.163A pdb=" N THR a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N CYS a 313 " --> pdb=" O THR a 284 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 32 through 35 removed outlier: 6.323A pdb=" N LYS b 33 " --> pdb=" O ILE b 167 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N MET b 169 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLN b 35 " --> pdb=" O MET b 169 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N PHE b 171 " --> pdb=" O GLN b 35 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASN b 166 " --> pdb=" O TYR b 158 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TYR b 158 " --> pdb=" O ASN b 166 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N TRP b 168 " --> pdb=" O GLU b 156 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'b' and resid 87 through 90 removed outlier: 7.243A pdb=" N THR b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE b 135 " --> pdb=" O THR b 87 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 284 through 287 removed outlier: 6.521A pdb=" N THR b 284 " --> pdb=" O TRP b 311 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N CYS b 313 " --> pdb=" O THR b 284 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR b 286 " --> pdb=" O CYS b 313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'c' and resid 33 through 35 removed outlier: 7.023A pdb=" N TRP c 168 " --> pdb=" O GLU c 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'c' and resid 89 through 90 removed outlier: 6.478A pdb=" N VAL c 89 " --> pdb=" O ILE c 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 284 through 287 423 hydrogen bonds defined for protein. 1086 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: 4.67 Time building geometry restraints manager: 6.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5216 1.34 - 1.46: 3962 1.46 - 1.58: 7156 1.58 - 1.71: 0 1.71 - 1.83: 180 Bond restraints: 16514 Sorted by residual: bond pdb=" N TRP B 80 " pdb=" CA TRP B 80 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.15e+00 bond pdb=" N ASN B 76 " pdb=" CA ASN B 76 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.25e-02 6.40e+03 6.42e+00 bond pdb=" N LEU B 75 " pdb=" CA LEU B 75 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.32e-02 5.74e+03 6.31e+00 bond pdb=" N VAL B 78 " pdb=" CA VAL B 78 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.17e-02 7.31e+03 6.23e+00 bond pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.80e+00 ... (remaining 16509 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.44: 554 106.44 - 113.40: 8942 113.40 - 120.36: 5624 120.36 - 127.33: 6985 127.33 - 134.29: 297 Bond angle restraints: 22402 Sorted by residual: angle pdb=" N LEU B 75 " pdb=" CA LEU B 75 " pdb=" C LEU B 75 " ideal model delta sigma weight residual 113.20 108.63 4.57 1.21e+00 6.83e-01 1.43e+01 angle pdb=" N THR C 317 " pdb=" CA THR C 317 " pdb=" C THR C 317 " ideal model delta sigma weight residual 109.40 103.40 6.00 1.63e+00 3.76e-01 1.35e+01 angle pdb=" CA THR C 317 " pdb=" C THR C 317 " pdb=" O THR C 317 " ideal model delta sigma weight residual 120.70 117.12 3.58 1.08e+00 8.57e-01 1.10e+01 angle pdb=" CA GLU B 81 " pdb=" C GLU B 81 " pdb=" O GLU B 81 " ideal model delta sigma weight residual 120.51 115.87 4.64 1.43e+00 4.89e-01 1.05e+01 angle pdb=" C THR a 27 " pdb=" N TRP a 28 " pdb=" CA TRP a 28 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 22397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8851 17.38 - 34.75: 783 34.75 - 52.13: 132 52.13 - 69.50: 28 69.50 - 86.88: 13 Dihedral angle restraints: 9807 sinusoidal: 3987 harmonic: 5820 Sorted by residual: dihedral pdb=" CB CYS A 313 " pdb=" SG CYS A 313 " pdb=" SG CYS A 316 " pdb=" CB CYS A 316 " ideal model delta sinusoidal sigma weight residual 93.00 173.67 -80.67 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual -86.00 -141.86 55.86 1 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" CA TYR B 158 " pdb=" C TYR B 158 " pdb=" N GLY B 159 " pdb=" CA GLY B 159 " ideal model delta harmonic sigma weight residual 180.00 152.36 27.64 0 5.00e+00 4.00e-02 3.06e+01 ... (remaining 9804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1613 0.037 - 0.074: 554 0.074 - 0.111: 171 0.111 - 0.148: 45 0.148 - 0.184: 4 Chirality restraints: 2387 Sorted by residual: chirality pdb=" CA THR C 317 " pdb=" N THR C 317 " pdb=" C THR C 317 " pdb=" CB THR C 317 " both_signs ideal model delta sigma weight residual False 2.53 2.71 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA LEU C 321 " pdb=" N LEU C 321 " pdb=" C LEU C 321 " pdb=" CB LEU C 321 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.32e-01 chirality pdb=" CB ILE C 287 " pdb=" CA ILE C 287 " pdb=" CG1 ILE C 287 " pdb=" CG2 ILE C 287 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2384 not shown) Planarity restraints: 2862 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 75 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C LEU B 75 " -0.073 2.00e-02 2.50e+03 pdb=" O LEU B 75 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 76 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 74 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C GLU B 74 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 74 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 75 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 81 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLU B 81 " -0.040 2.00e-02 2.50e+03 pdb=" O GLU B 81 " 0.015 2.00e-02 2.50e+03 pdb=" N GLY B 82 " 0.014 2.00e-02 2.50e+03 ... (remaining 2859 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1094 2.74 - 3.28: 14705 3.28 - 3.82: 24684 3.82 - 4.36: 31902 4.36 - 4.90: 55270 Nonbonded interactions: 127655 Sorted by model distance: nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.196 3.120 nonbonded pdb=" O THR B 262 " pdb=" NH2 ARG B 294 " model vdw 2.198 3.120 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.203 3.040 nonbonded pdb=" O THR c 262 " pdb=" NH2 ARG c 294 " model vdw 2.217 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.226 3.120 ... (remaining 127650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'C' selection = (chain 'a' and (resid 1 through 107 or resid 133 through 352)) selection = (chain 'b' and (resid 1 through 107 or resid 133 through 352)) selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.480 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.002 0.038 16514 Z= 0.152 Angle : 0.540 6.172 22402 Z= 0.308 Chirality : 0.042 0.184 2387 Planarity : 0.003 0.053 2862 Dihedral : 13.421 86.876 5979 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 0.23 % Allowed : 0.23 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.78 (0.18), residues: 2022 helix: 0.97 (0.37), residues: 224 sheet: -2.23 (0.22), residues: 513 loop : -1.10 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 80 HIS 0.003 0.001 HIS A 229 PHE 0.024 0.001 PHE b 20 TYR 0.017 0.001 TYR B 158 ARG 0.002 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 343 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7032 (m-90) cc_final: 0.6587 (p-90) REVERT: A 70 GLN cc_start: 0.7309 (tt0) cc_final: 0.6819 (tt0) REVERT: A 272 LYS cc_start: 0.8809 (mttp) cc_final: 0.8367 (mtpm) REVERT: A 309 THR cc_start: 0.8395 (m) cc_final: 0.8146 (p) REVERT: B 17 SER cc_start: 0.9000 (p) cc_final: 0.8765 (t) REVERT: B 30 GLU cc_start: 0.8491 (pt0) cc_final: 0.7735 (mm-30) REVERT: B 35 GLN cc_start: 0.7239 (mm-40) cc_final: 0.7011 (mm110) REVERT: B 59 SER cc_start: 0.8840 (m) cc_final: 0.8434 (p) REVERT: B 70 GLN cc_start: 0.6983 (mt0) cc_final: 0.6736 (mp10) REVERT: B 166 ASN cc_start: 0.8086 (m-40) cc_final: 0.7784 (m-40) REVERT: B 168 TRP cc_start: 0.7647 (m100) cc_final: 0.7236 (m100) REVERT: B 214 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7971 (mtpp) REVERT: B 274 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7631 (tp30) REVERT: B 340 GLU cc_start: 0.5594 (tm-30) cc_final: 0.5182 (tm-30) REVERT: C 12 GLU cc_start: 0.7039 (tt0) cc_final: 0.6637 (tt0) REVERT: C 14 LYS cc_start: 0.8682 (tptm) cc_final: 0.8342 (tptp) REVERT: C 23 ASP cc_start: 0.8182 (t0) cc_final: 0.7809 (t70) REVERT: C 35 GLN cc_start: 0.7382 (tp40) cc_final: 0.7138 (tp40) REVERT: C 74 GLU cc_start: 0.6436 (mt-10) cc_final: 0.6067 (mp0) REVERT: C 177 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6957 (tt0) REVERT: C 274 GLU cc_start: 0.7513 (tp30) cc_final: 0.7217 (tp30) REVERT: a 55 CYS cc_start: 0.6994 (t) cc_final: 0.6739 (p) REVERT: a 74 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6192 (mp0) REVERT: a 214 LYS cc_start: 0.8342 (mtmt) cc_final: 0.7862 (mtpp) REVERT: a 240 GLN cc_start: 0.8768 (mm110) cc_final: 0.8370 (mm110) REVERT: a 314 ARG cc_start: 0.6720 (ttm170) cc_final: 0.6409 (ttm170) REVERT: a 344 ASN cc_start: 0.7197 (t0) cc_final: 0.6960 (m110) REVERT: b 14 LYS cc_start: 0.8325 (tptt) cc_final: 0.8074 (tptp) REVERT: b 92 ASP cc_start: 0.6581 (p0) cc_final: 0.6126 (p0) REVERT: b 99 LYS cc_start: 0.8149 (ttpp) cc_final: 0.7704 (tttp) REVERT: b 324 LEU cc_start: 0.8554 (mp) cc_final: 0.8343 (mt) REVERT: c 99 LYS cc_start: 0.7025 (ttmt) cc_final: 0.6630 (ttpp) REVERT: c 168 TRP cc_start: 0.6784 (m100) cc_final: 0.6472 (m100) outliers start: 4 outliers final: 3 residues processed: 347 average time/residue: 1.2621 time to fit residues: 483.8673 Evaluate side-chains 244 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 218 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 183 optimal weight: 0.1980 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 48 ASN b 48 ASN b 76 ASN b 84 HIS c 166 ASN c 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16514 Z= 0.321 Angle : 0.584 7.888 22402 Z= 0.310 Chirality : 0.044 0.138 2387 Planarity : 0.004 0.037 2862 Dihedral : 4.981 44.495 2172 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.63 % Allowed : 9.72 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.59 (0.18), residues: 2022 helix: 1.34 (0.37), residues: 225 sheet: -1.81 (0.22), residues: 539 loop : -1.15 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 330 HIS 0.007 0.001 HIS a 50 PHE 0.029 0.002 PHE b 20 TYR 0.016 0.002 TYR c 256 ARG 0.006 0.001 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7165 (m-90) cc_final: 0.6620 (p-90) REVERT: A 70 GLN cc_start: 0.7401 (tt0) cc_final: 0.6944 (tt0) REVERT: A 102 ARG cc_start: 0.7826 (mmm-85) cc_final: 0.7293 (mmt90) REVERT: A 203 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 214 LYS cc_start: 0.8654 (mtmt) cc_final: 0.8440 (mtmm) REVERT: A 309 THR cc_start: 0.8470 (m) cc_final: 0.8153 (p) REVERT: A 314 ARG cc_start: 0.6925 (ttp-170) cc_final: 0.6669 (ttm-80) REVERT: B 31 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7097 (mm-40) REVERT: B 59 SER cc_start: 0.8891 (m) cc_final: 0.8627 (p) REVERT: B 70 GLN cc_start: 0.7133 (mt0) cc_final: 0.6817 (mp10) REVERT: B 76 ASN cc_start: 0.5943 (m-40) cc_final: 0.5528 (m110) REVERT: B 89 VAL cc_start: 0.6816 (t) cc_final: 0.6299 (m) REVERT: B 142 GLU cc_start: 0.6167 (pt0) cc_final: 0.5639 (tm-30) REVERT: B 154 GLU cc_start: 0.7656 (pt0) cc_final: 0.7008 (pt0) REVERT: B 166 ASN cc_start: 0.8215 (m-40) cc_final: 0.7878 (m-40) REVERT: B 168 TRP cc_start: 0.7727 (m100) cc_final: 0.7351 (m100) REVERT: B 214 LYS cc_start: 0.8461 (mtmt) cc_final: 0.8160 (mtpp) REVERT: B 274 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7500 (tp30) REVERT: C 12 GLU cc_start: 0.7146 (tt0) cc_final: 0.6736 (tt0) REVERT: C 14 LYS cc_start: 0.8329 (tptm) cc_final: 0.8070 (tptp) REVERT: C 23 ASP cc_start: 0.8197 (t0) cc_final: 0.7944 (t0) REVERT: C 74 GLU cc_start: 0.6521 (mt-10) cc_final: 0.6078 (mp0) REVERT: C 101 LYS cc_start: 0.6908 (mptt) cc_final: 0.6613 (mppt) REVERT: C 177 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6848 (tt0) REVERT: C 214 LYS cc_start: 0.7512 (ptmm) cc_final: 0.7079 (pptt) REVERT: C 274 GLU cc_start: 0.7162 (tp30) cc_final: 0.6921 (tp30) REVERT: a 30 GLU cc_start: 0.7883 (tt0) cc_final: 0.7376 (tt0) REVERT: a 74 GLU cc_start: 0.6597 (mt-10) cc_final: 0.6267 (mp0) REVERT: a 214 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8116 (mtpp) REVERT: a 240 GLN cc_start: 0.8798 (mm110) cc_final: 0.8407 (mm110) REVERT: a 287 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (mm) REVERT: a 314 ARG cc_start: 0.6790 (ttm170) cc_final: 0.6494 (ttm170) REVERT: b 147 ARG cc_start: 0.6351 (ptm160) cc_final: 0.6007 (ptm160) REVERT: b 157 ASP cc_start: 0.8093 (p0) cc_final: 0.7732 (t0) REVERT: c 41 ARG cc_start: 0.7386 (ttt90) cc_final: 0.7076 (tpt90) REVERT: c 99 LYS cc_start: 0.6891 (ttmt) cc_final: 0.6568 (ttpp) REVERT: c 146 GLU cc_start: 0.5639 (pt0) cc_final: 0.5341 (mp0) REVERT: c 154 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6607 (mt-10) REVERT: c 168 TRP cc_start: 0.6770 (m100) cc_final: 0.6452 (m100) REVERT: c 197 ASP cc_start: 0.8374 (p0) cc_final: 0.7964 (p0) REVERT: c 318 MET cc_start: 0.7521 (mpp) cc_final: 0.7249 (mpm) REVERT: c 340 GLU cc_start: 0.4790 (tp30) cc_final: 0.4453 (tp30) outliers start: 46 outliers final: 21 residues processed: 284 average time/residue: 1.2714 time to fit residues: 398.5728 Evaluate side-chains 261 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 237 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 124 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 145 ASN C 254 HIS a 48 ASN a 65 ASN b 48 ASN b 293 HIS c 166 ASN c 310 GLN c 349 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16514 Z= 0.463 Angle : 0.649 7.021 22402 Z= 0.342 Chirality : 0.047 0.202 2387 Planarity : 0.004 0.040 2862 Dihedral : 5.239 39.314 2168 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 3.89 % Allowed : 13.72 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.69 (0.18), residues: 2022 helix: 1.29 (0.36), residues: 222 sheet: -1.99 (0.23), residues: 499 loop : -1.21 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 330 HIS 0.008 0.002 HIS A 84 PHE 0.025 0.002 PHE b 20 TYR 0.020 0.002 TYR A 256 ARG 0.006 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 243 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7128 (m-90) cc_final: 0.6631 (p-90) REVERT: A 70 GLN cc_start: 0.7320 (tt0) cc_final: 0.6898 (tt0) REVERT: A 102 ARG cc_start: 0.7882 (mmm-85) cc_final: 0.7378 (mmt90) REVERT: A 309 THR cc_start: 0.8495 (m) cc_final: 0.8057 (p) REVERT: A 345 MET cc_start: 0.8357 (mtm) cc_final: 0.8133 (mtm) REVERT: B 31 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7264 (mm-40) REVERT: B 59 SER cc_start: 0.8897 (m) cc_final: 0.8654 (p) REVERT: B 70 GLN cc_start: 0.7125 (mt0) cc_final: 0.6721 (mp10) REVERT: B 76 ASN cc_start: 0.6117 (m-40) cc_final: 0.5913 (m110) REVERT: B 89 VAL cc_start: 0.6893 (t) cc_final: 0.6336 (m) REVERT: B 142 GLU cc_start: 0.6396 (pt0) cc_final: 0.5787 (tm-30) REVERT: B 154 GLU cc_start: 0.7746 (pt0) cc_final: 0.7098 (pt0) REVERT: B 168 TRP cc_start: 0.7741 (m100) cc_final: 0.7475 (m100) REVERT: B 274 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7571 (tp30) REVERT: C 14 LYS cc_start: 0.8375 (tptm) cc_final: 0.8104 (tptp) REVERT: C 62 ARG cc_start: 0.6987 (ppt170) cc_final: 0.6678 (ttp80) REVERT: C 74 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6064 (mp0) REVERT: C 101 LYS cc_start: 0.7036 (mptt) cc_final: 0.6712 (mppt) REVERT: C 177 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6606 (tt0) REVERT: C 214 LYS cc_start: 0.7523 (ptmm) cc_final: 0.7075 (pptt) REVERT: C 258 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6425 (tm-30) REVERT: C 274 GLU cc_start: 0.7306 (tp30) cc_final: 0.7056 (tp30) REVERT: a 30 GLU cc_start: 0.7905 (tt0) cc_final: 0.7348 (tt0) REVERT: a 74 GLU cc_start: 0.6586 (mt-10) cc_final: 0.6323 (mp0) REVERT: a 101 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7740 (mttt) REVERT: a 214 LYS cc_start: 0.8620 (mtmt) cc_final: 0.7552 (mmmt) REVERT: a 287 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7744 (mm) REVERT: a 314 ARG cc_start: 0.6664 (ttm170) cc_final: 0.6345 (ttm170) REVERT: b 157 ASP cc_start: 0.8180 (p0) cc_final: 0.7764 (t0) REVERT: b 180 ASP cc_start: 0.8466 (t0) cc_final: 0.8246 (t0) REVERT: c 148 ARG cc_start: 0.4755 (OUTLIER) cc_final: 0.3481 (tpp80) REVERT: c 154 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: c 168 TRP cc_start: 0.6789 (m100) cc_final: 0.6569 (m100) REVERT: c 276 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: c 318 MET cc_start: 0.7512 (mpp) cc_final: 0.7231 (mpm) REVERT: c 340 GLU cc_start: 0.4773 (tp30) cc_final: 0.4433 (tp30) outliers start: 68 outliers final: 31 residues processed: 279 average time/residue: 1.3001 time to fit residues: 400.0235 Evaluate side-chains 248 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 210 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 293 HIS Chi-restraints excluded: chain b residue 307 LEU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 98 SER Chi-restraints excluded: chain c residue 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 SER Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 174 optimal weight: 40.0000 chunk 52 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 ASN B 207 ASN a 48 ASN b 48 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16514 Z= 0.213 Angle : 0.531 7.592 22402 Z= 0.281 Chirality : 0.043 0.133 2387 Planarity : 0.003 0.031 2862 Dihedral : 4.825 39.548 2168 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.43 % Allowed : 15.67 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.47 (0.19), residues: 2022 helix: 1.53 (0.36), residues: 222 sheet: -1.81 (0.23), residues: 493 loop : -1.08 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.007 0.001 HIS b 293 PHE 0.014 0.001 PHE b 20 TYR 0.017 0.001 TYR c 256 ARG 0.003 0.000 ARG b 336 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 233 time to evaluate : 1.840 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7168 (m-90) cc_final: 0.6923 (m100) REVERT: A 70 GLN cc_start: 0.7302 (tt0) cc_final: 0.6894 (tt0) REVERT: A 272 LYS cc_start: 0.8779 (mttp) cc_final: 0.8303 (mtpm) REVERT: A 345 MET cc_start: 0.8291 (mtm) cc_final: 0.8072 (mtm) REVERT: B 31 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7247 (mm-40) REVERT: B 59 SER cc_start: 0.8851 (m) cc_final: 0.8649 (p) REVERT: B 70 GLN cc_start: 0.7091 (mt0) cc_final: 0.6720 (mp10) REVERT: B 89 VAL cc_start: 0.6920 (t) cc_final: 0.6384 (m) REVERT: B 142 GLU cc_start: 0.6489 (pt0) cc_final: 0.5853 (tm-30) REVERT: B 147 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7415 (mtp85) REVERT: B 154 GLU cc_start: 0.7644 (pt0) cc_final: 0.7280 (pt0) REVERT: B 168 TRP cc_start: 0.7700 (m100) cc_final: 0.7368 (m100) REVERT: B 213 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7872 (pt0) REVERT: B 274 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7428 (tp30) REVERT: C 14 LYS cc_start: 0.8255 (tptm) cc_final: 0.7975 (tptp) REVERT: C 23 ASP cc_start: 0.8178 (t0) cc_final: 0.7866 (t0) REVERT: C 62 ARG cc_start: 0.6868 (ppt170) cc_final: 0.6607 (ttp80) REVERT: C 74 GLU cc_start: 0.6421 (mt-10) cc_final: 0.5962 (mp0) REVERT: C 101 LYS cc_start: 0.6918 (mptt) cc_final: 0.6585 (mppt) REVERT: C 177 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6616 (tt0) REVERT: C 214 LYS cc_start: 0.7536 (ptmm) cc_final: 0.7105 (pptt) REVERT: C 274 GLU cc_start: 0.7229 (tp30) cc_final: 0.7021 (tp30) REVERT: a 30 GLU cc_start: 0.7904 (tt0) cc_final: 0.7349 (tt0) REVERT: a 47 LEU cc_start: 0.7381 (tp) cc_final: 0.7168 (tp) REVERT: a 74 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6154 (mp0) REVERT: a 214 LYS cc_start: 0.8580 (mtmt) cc_final: 0.7504 (mmmt) REVERT: a 287 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7900 (mm) REVERT: a 314 ARG cc_start: 0.6740 (ttm170) cc_final: 0.6259 (ttm170) REVERT: b 157 ASP cc_start: 0.8106 (p0) cc_final: 0.7755 (t0) REVERT: b 180 ASP cc_start: 0.8425 (t0) cc_final: 0.8203 (t0) REVERT: b 238 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7534 (mt-10) REVERT: c 154 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: c 168 TRP cc_start: 0.6811 (m100) cc_final: 0.6576 (m100) REVERT: c 197 ASP cc_start: 0.8221 (p0) cc_final: 0.7874 (p0) REVERT: c 276 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: c 318 MET cc_start: 0.7473 (mpp) cc_final: 0.7174 (mpm) REVERT: c 340 GLU cc_start: 0.4788 (tp30) cc_final: 0.4479 (tp30) outliers start: 60 outliers final: 32 residues processed: 270 average time/residue: 1.1890 time to fit residues: 357.2794 Evaluate side-chains 262 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 224 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 344 ASN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 10.0000 chunk 110 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 134 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 175 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN b 48 ASN b 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 16514 Z= 0.398 Angle : 0.612 8.036 22402 Z= 0.321 Chirality : 0.046 0.149 2387 Planarity : 0.004 0.036 2862 Dihedral : 5.107 42.439 2168 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.82 % Favored : 93.13 % Rotamer: Outliers : 3.83 % Allowed : 16.75 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.62 (0.18), residues: 2022 helix: 1.40 (0.36), residues: 223 sheet: -1.90 (0.23), residues: 497 loop : -1.19 (0.17), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 330 HIS 0.004 0.001 HIS A 254 PHE 0.014 0.002 PHE b 20 TYR 0.017 0.002 TYR c 256 ARG 0.006 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 226 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7152 (m-90) cc_final: 0.6635 (p-90) REVERT: A 70 GLN cc_start: 0.7337 (tt0) cc_final: 0.6905 (tt0) REVERT: A 272 LYS cc_start: 0.8820 (mttp) cc_final: 0.8311 (mtpm) REVERT: A 283 THR cc_start: 0.8105 (p) cc_final: 0.7793 (p) REVERT: B 31 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7274 (mm-40) REVERT: B 60 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8614 (p) REVERT: B 70 GLN cc_start: 0.7183 (mt0) cc_final: 0.6784 (mp10) REVERT: B 142 GLU cc_start: 0.6531 (pt0) cc_final: 0.5876 (tm-30) REVERT: B 147 ARG cc_start: 0.7711 (mtp85) cc_final: 0.7355 (mtp85) REVERT: B 213 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7836 (pt0) REVERT: B 274 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7483 (tp30) REVERT: C 14 LYS cc_start: 0.8349 (tptm) cc_final: 0.8047 (tptp) REVERT: C 62 ARG cc_start: 0.7031 (ppt170) cc_final: 0.6674 (ttp80) REVERT: C 74 GLU cc_start: 0.6486 (mt-10) cc_final: 0.6009 (mp0) REVERT: C 101 LYS cc_start: 0.7003 (mptt) cc_final: 0.6648 (mppt) REVERT: C 177 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6520 (tt0) REVERT: C 214 LYS cc_start: 0.7509 (ptmm) cc_final: 0.7091 (pptt) REVERT: a 74 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6249 (mp0) REVERT: a 287 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7773 (mm) REVERT: a 314 ARG cc_start: 0.6651 (ttm170) cc_final: 0.6158 (ttm170) REVERT: b 96 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8139 (t) REVERT: b 147 ARG cc_start: 0.6324 (mtm110) cc_final: 0.6115 (mtm110) REVERT: b 157 ASP cc_start: 0.8152 (p0) cc_final: 0.7803 (t0) REVERT: b 238 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: c 154 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: c 168 TRP cc_start: 0.6811 (m100) cc_final: 0.6603 (m100) REVERT: c 219 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7860 (pt0) REVERT: c 228 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.7867 (t) REVERT: c 276 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: c 318 MET cc_start: 0.7443 (mpp) cc_final: 0.7176 (mpm) REVERT: c 340 GLU cc_start: 0.4820 (tp30) cc_final: 0.4498 (tp30) outliers start: 67 outliers final: 38 residues processed: 265 average time/residue: 1.2345 time to fit residues: 362.4983 Evaluate side-chains 265 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 217 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 324 LEU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 7.9990 chunk 175 optimal weight: 20.0000 chunk 38 optimal weight: 0.7980 chunk 114 optimal weight: 9.9990 chunk 48 optimal weight: 0.0030 chunk 195 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 ASN B 208 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16514 Z= 0.181 Angle : 0.516 7.885 22402 Z= 0.273 Chirality : 0.042 0.131 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.706 42.024 2168 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 3.09 % Allowed : 18.30 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.36 (0.19), residues: 2022 helix: 1.63 (0.37), residues: 223 sheet: -1.77 (0.24), residues: 467 loop : -1.03 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.004 0.001 HIS b 293 PHE 0.013 0.001 PHE a 277 TYR 0.018 0.001 TYR c 256 ARG 0.004 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 235 time to evaluate : 1.938 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7150 (m-90) cc_final: 0.6619 (p-90) REVERT: A 70 GLN cc_start: 0.7313 (tt0) cc_final: 0.6893 (tt0) REVERT: A 81 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6676 (tt0) REVERT: A 272 LYS cc_start: 0.8766 (mttp) cc_final: 0.8285 (mtpm) REVERT: A 283 THR cc_start: 0.8055 (p) cc_final: 0.7733 (p) REVERT: B 31 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7245 (mm-40) REVERT: B 70 GLN cc_start: 0.7165 (mt0) cc_final: 0.6822 (mp10) REVERT: B 89 VAL cc_start: 0.6879 (t) cc_final: 0.6338 (m) REVERT: B 142 GLU cc_start: 0.6578 (pt0) cc_final: 0.5914 (tm-30) REVERT: B 147 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7413 (mtp85) REVERT: B 168 TRP cc_start: 0.7761 (m100) cc_final: 0.7454 (m100) REVERT: B 213 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: B 274 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7388 (tp30) REVERT: C 14 LYS cc_start: 0.8273 (tptm) cc_final: 0.7910 (tptp) REVERT: C 62 ARG cc_start: 0.6949 (ppt170) cc_final: 0.6388 (ttp-110) REVERT: C 74 GLU cc_start: 0.6455 (mt-10) cc_final: 0.5918 (mp0) REVERT: C 101 LYS cc_start: 0.6910 (mptt) cc_final: 0.6570 (mppt) REVERT: C 177 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6560 (tt0) REVERT: C 214 LYS cc_start: 0.7508 (ptmm) cc_final: 0.7112 (pptt) REVERT: C 258 GLN cc_start: 0.7220 (OUTLIER) cc_final: 0.6343 (tm-30) REVERT: a 74 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6119 (mp0) REVERT: a 214 LYS cc_start: 0.8553 (mtmt) cc_final: 0.7500 (mmmt) REVERT: a 287 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7905 (mm) REVERT: a 314 ARG cc_start: 0.6756 (ttm170) cc_final: 0.6293 (ttm170) REVERT: b 147 ARG cc_start: 0.6447 (mtm110) cc_final: 0.6136 (mtm110) REVERT: b 157 ASP cc_start: 0.8100 (p0) cc_final: 0.7778 (t0) REVERT: c 154 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6707 (mt-10) REVERT: c 197 ASP cc_start: 0.8193 (p0) cc_final: 0.7734 (p0) REVERT: c 276 ASP cc_start: 0.7999 (m-30) cc_final: 0.7268 (m-30) REVERT: c 318 MET cc_start: 0.7426 (mpp) cc_final: 0.7143 (mpm) REVERT: c 340 GLU cc_start: 0.4884 (tp30) cc_final: 0.4629 (tp30) outliers start: 54 outliers final: 31 residues processed: 268 average time/residue: 1.1960 time to fit residues: 356.1235 Evaluate side-chains 253 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 216 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 302 THR Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 142 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 35 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16514 Z= 0.237 Angle : 0.540 7.159 22402 Z= 0.284 Chirality : 0.043 0.162 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.699 41.545 2168 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.87 % Rotamer: Outliers : 3.49 % Allowed : 19.33 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.40 (0.19), residues: 2022 helix: 1.59 (0.37), residues: 224 sheet: -1.98 (0.23), residues: 497 loop : -0.94 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.012 0.001 PHE B 160 TYR 0.018 0.001 TYR c 256 ARG 0.007 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 219 time to evaluate : 2.237 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7139 (m-90) cc_final: 0.6597 (p-90) REVERT: A 70 GLN cc_start: 0.7301 (tt0) cc_final: 0.6905 (tt0) REVERT: A 272 LYS cc_start: 0.8788 (mttp) cc_final: 0.8293 (mtpm) REVERT: A 283 THR cc_start: 0.8005 (p) cc_final: 0.7686 (p) REVERT: B 31 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: B 70 GLN cc_start: 0.7157 (mt0) cc_final: 0.6788 (mp10) REVERT: B 89 VAL cc_start: 0.6887 (t) cc_final: 0.6350 (m) REVERT: B 142 GLU cc_start: 0.6597 (pt0) cc_final: 0.5974 (tm-30) REVERT: B 147 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7431 (mtp85) REVERT: B 154 GLU cc_start: 0.7677 (pt0) cc_final: 0.7323 (pt0) REVERT: B 157 ASP cc_start: 0.7505 (p0) cc_final: 0.7236 (t0) REVERT: B 168 TRP cc_start: 0.7784 (m100) cc_final: 0.7551 (m100) REVERT: B 213 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7869 (pt0) REVERT: B 274 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7417 (tp30) REVERT: C 14 LYS cc_start: 0.8279 (tptm) cc_final: 0.7917 (tptp) REVERT: C 62 ARG cc_start: 0.6941 (ppt170) cc_final: 0.6355 (ttp-110) REVERT: C 74 GLU cc_start: 0.6443 (mt-10) cc_final: 0.5900 (mp0) REVERT: C 101 LYS cc_start: 0.6936 (mptt) cc_final: 0.6513 (mppt) REVERT: C 177 GLU cc_start: 0.7313 (mt-10) cc_final: 0.6577 (tt0) REVERT: C 214 LYS cc_start: 0.7515 (ptmm) cc_final: 0.7103 (pptt) REVERT: C 240 GLN cc_start: 0.7151 (mm-40) cc_final: 0.6917 (mm110) REVERT: C 258 GLN cc_start: 0.7229 (OUTLIER) cc_final: 0.6316 (tm-30) REVERT: a 47 LEU cc_start: 0.7339 (tp) cc_final: 0.7101 (tp) REVERT: a 74 GLU cc_start: 0.6517 (mt-10) cc_final: 0.6121 (mp0) REVERT: a 214 LYS cc_start: 0.8537 (mtmt) cc_final: 0.7499 (mmmt) REVERT: a 287 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7946 (mm) REVERT: a 314 ARG cc_start: 0.6758 (ttm170) cc_final: 0.6296 (ttm170) REVERT: b 147 ARG cc_start: 0.6435 (mtm110) cc_final: 0.6108 (mtm110) REVERT: b 157 ASP cc_start: 0.8091 (p0) cc_final: 0.7814 (t0) REVERT: b 238 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: c 154 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6633 (mt-10) REVERT: c 228 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.7911 (t) REVERT: c 276 ASP cc_start: 0.7990 (m-30) cc_final: 0.7244 (m-30) REVERT: c 318 MET cc_start: 0.7404 (mpp) cc_final: 0.7142 (mpm) REVERT: c 340 GLU cc_start: 0.4903 (tp30) cc_final: 0.4610 (tp30) outliers start: 61 outliers final: 40 residues processed: 256 average time/residue: 1.2777 time to fit residues: 362.6887 Evaluate side-chains 260 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16514 Z= 0.365 Angle : 0.603 7.885 22402 Z= 0.316 Chirality : 0.045 0.152 2387 Planarity : 0.004 0.043 2862 Dihedral : 4.981 43.195 2168 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.78 % Favored : 93.18 % Rotamer: Outliers : 3.54 % Allowed : 19.95 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.56 (0.18), residues: 2022 helix: 1.50 (0.36), residues: 224 sheet: -2.01 (0.23), residues: 481 loop : -1.11 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.012 0.002 PHE c 277 TYR 0.018 0.002 TYR c 256 ARG 0.015 0.001 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 218 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7125 (m-90) cc_final: 0.6903 (m100) REVERT: A 70 GLN cc_start: 0.7327 (tt0) cc_final: 0.6906 (tt0) REVERT: A 272 LYS cc_start: 0.8814 (mttp) cc_final: 0.8194 (mtpm) REVERT: A 283 THR cc_start: 0.8019 (p) cc_final: 0.7738 (p) REVERT: A 309 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 31 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: B 70 GLN cc_start: 0.7285 (mt0) cc_final: 0.6863 (mp10) REVERT: B 142 GLU cc_start: 0.6654 (pt0) cc_final: 0.6039 (tm-30) REVERT: B 147 ARG cc_start: 0.7758 (mtp85) cc_final: 0.7359 (mtp85) REVERT: B 157 ASP cc_start: 0.7548 (p0) cc_final: 0.7272 (t0) REVERT: B 274 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7372 (tp30) REVERT: C 14 LYS cc_start: 0.8355 (tptm) cc_final: 0.7983 (tptp) REVERT: C 62 ARG cc_start: 0.7022 (ppt170) cc_final: 0.6411 (ttp-110) REVERT: C 74 GLU cc_start: 0.6483 (mt-10) cc_final: 0.5938 (mp0) REVERT: C 101 LYS cc_start: 0.6992 (mptt) cc_final: 0.6647 (mppt) REVERT: C 177 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6557 (tt0) REVERT: C 190 ASP cc_start: 0.7726 (t0) cc_final: 0.7367 (t70) REVERT: C 214 LYS cc_start: 0.7496 (ptmm) cc_final: 0.7093 (pptt) REVERT: C 258 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: a 74 GLU cc_start: 0.6549 (mt-10) cc_final: 0.6178 (mp0) REVERT: a 101 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7800 (mttt) REVERT: a 276 ASP cc_start: 0.8336 (p0) cc_final: 0.8043 (p0) REVERT: a 314 ARG cc_start: 0.6654 (ttm170) cc_final: 0.6180 (ttm170) REVERT: b 50 HIS cc_start: 0.6904 (t-90) cc_final: 0.6660 (t-90) REVERT: b 157 ASP cc_start: 0.8117 (p0) cc_final: 0.7817 (t0) REVERT: b 238 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: c 156 GLU cc_start: 0.7834 (pt0) cc_final: 0.7283 (tt0) REVERT: c 276 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: c 318 MET cc_start: 0.7374 (mpp) cc_final: 0.7083 (mpm) outliers start: 62 outliers final: 44 residues processed: 256 average time/residue: 1.2731 time to fit residues: 361.5115 Evaluate side-chains 262 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 70 GLN Chi-restraints excluded: chain a residue 101 LYS Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain b residue 348 SER Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 61 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 181 optimal weight: 20.0000 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 48 ASN b 293 HIS c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16514 Z= 0.164 Angle : 0.518 7.815 22402 Z= 0.272 Chirality : 0.042 0.144 2387 Planarity : 0.003 0.052 2862 Dihedral : 4.575 41.858 2168 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 2.57 % Allowed : 21.10 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.28 (0.19), residues: 2022 helix: 1.64 (0.37), residues: 224 sheet: -1.77 (0.24), residues: 478 loop : -0.92 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 PHE 0.013 0.001 PHE a 277 TYR 0.019 0.001 TYR c 256 ARG 0.014 0.000 ARG C 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7125 (m-90) cc_final: 0.6587 (p-90) REVERT: A 70 GLN cc_start: 0.7274 (tt0) cc_final: 0.6899 (tt0) REVERT: A 283 THR cc_start: 0.7957 (p) cc_final: 0.7641 (p) REVERT: B 31 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7301 (mm-40) REVERT: B 70 GLN cc_start: 0.7138 (mt0) cc_final: 0.6765 (mp10) REVERT: B 89 VAL cc_start: 0.6899 (t) cc_final: 0.6373 (m) REVERT: B 142 GLU cc_start: 0.6593 (pt0) cc_final: 0.5985 (pp20) REVERT: B 147 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7529 (mtp85) REVERT: B 154 GLU cc_start: 0.7678 (pt0) cc_final: 0.7336 (pt0) REVERT: B 168 TRP cc_start: 0.7845 (m100) cc_final: 0.7477 (m100) REVERT: B 213 GLU cc_start: 0.8235 (tt0) cc_final: 0.7939 (pt0) REVERT: B 274 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7310 (tp30) REVERT: C 14 LYS cc_start: 0.8239 (tptm) cc_final: 0.7875 (tptp) REVERT: C 62 ARG cc_start: 0.6902 (ppt170) cc_final: 0.6313 (ttp-110) REVERT: C 74 GLU cc_start: 0.6458 (mt-10) cc_final: 0.5896 (mp0) REVERT: C 101 LYS cc_start: 0.6847 (mptt) cc_final: 0.6472 (mppt) REVERT: C 177 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6568 (tt0) REVERT: C 214 LYS cc_start: 0.7523 (ptmm) cc_final: 0.7109 (pptt) REVERT: C 258 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.6295 (tm-30) REVERT: C 314 ARG cc_start: 0.5013 (ttm170) cc_final: 0.4552 (ttm170) REVERT: a 74 GLU cc_start: 0.6470 (mt-10) cc_final: 0.6079 (mp0) REVERT: a 214 LYS cc_start: 0.8508 (mtmt) cc_final: 0.7475 (mmmt) REVERT: a 314 ARG cc_start: 0.6751 (ttm170) cc_final: 0.6293 (ttm170) REVERT: b 50 HIS cc_start: 0.6888 (t-90) cc_final: 0.6637 (t-90) REVERT: b 157 ASP cc_start: 0.8083 (p0) cc_final: 0.7818 (t0) REVERT: b 238 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7442 (mt-10) REVERT: c 156 GLU cc_start: 0.7775 (pt0) cc_final: 0.7332 (tt0) REVERT: c 197 ASP cc_start: 0.8098 (p0) cc_final: 0.7654 (p0) REVERT: c 228 THR cc_start: 0.8376 (OUTLIER) cc_final: 0.7938 (t) REVERT: c 276 ASP cc_start: 0.8034 (m-30) cc_final: 0.7287 (m-30) REVERT: c 318 MET cc_start: 0.7405 (mpp) cc_final: 0.7132 (mpm) outliers start: 45 outliers final: 33 residues processed: 244 average time/residue: 1.2440 time to fit residues: 336.4768 Evaluate side-chains 248 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 211 time to evaluate : 1.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 133 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 160 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN a 35 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16514 Z= 0.264 Angle : 0.559 7.780 22402 Z= 0.292 Chirality : 0.043 0.139 2387 Planarity : 0.003 0.044 2862 Dihedral : 4.704 41.456 2168 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer: Outliers : 2.69 % Allowed : 21.15 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.36 (0.19), residues: 2022 helix: 1.66 (0.36), residues: 224 sheet: -1.82 (0.23), residues: 517 loop : -0.95 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 168 HIS 0.009 0.001 HIS b 293 PHE 0.014 0.001 PHE c 277 TYR 0.018 0.001 TYR c 256 ARG 0.016 0.000 ARG C 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4044 Ramachandran restraints generated. 2022 Oldfield, 0 Emsley, 2022 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 218 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7139 (m-90) cc_final: 0.6598 (p-90) REVERT: A 70 GLN cc_start: 0.7300 (tt0) cc_final: 0.6908 (tt0) REVERT: A 283 THR cc_start: 0.7966 (p) cc_final: 0.7647 (p) REVERT: B 31 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7291 (mm-40) REVERT: B 70 GLN cc_start: 0.7169 (mt0) cc_final: 0.6822 (mp10) REVERT: B 89 VAL cc_start: 0.6777 (t) cc_final: 0.6253 (m) REVERT: B 142 GLU cc_start: 0.6590 (pt0) cc_final: 0.5988 (tm-30) REVERT: B 146 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: B 147 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7424 (mtp85) REVERT: B 154 GLU cc_start: 0.7672 (pt0) cc_final: 0.7324 (pt0) REVERT: B 168 TRP cc_start: 0.7889 (m100) cc_final: 0.7574 (m100) REVERT: B 213 GLU cc_start: 0.8256 (tt0) cc_final: 0.7921 (pt0) REVERT: B 274 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7347 (tp30) REVERT: C 14 LYS cc_start: 0.8275 (tptm) cc_final: 0.7912 (tptp) REVERT: C 62 ARG cc_start: 0.6986 (ppt170) cc_final: 0.6374 (ttp-110) REVERT: C 74 GLU cc_start: 0.6471 (mt-10) cc_final: 0.5907 (mp0) REVERT: C 101 LYS cc_start: 0.6911 (mptt) cc_final: 0.6496 (mppt) REVERT: C 177 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6567 (tt0) REVERT: C 197 ASP cc_start: 0.7933 (p0) cc_final: 0.7684 (p0) REVERT: C 214 LYS cc_start: 0.7520 (ptmm) cc_final: 0.7111 (pptt) REVERT: C 258 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: a 74 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6114 (mp0) REVERT: a 214 LYS cc_start: 0.8555 (mtmt) cc_final: 0.8040 (mtpp) REVERT: a 276 ASP cc_start: 0.8278 (p0) cc_final: 0.7965 (p0) REVERT: a 287 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7846 (mm) REVERT: a 314 ARG cc_start: 0.6720 (ttm170) cc_final: 0.6258 (ttm170) REVERT: b 50 HIS cc_start: 0.6925 (t-90) cc_final: 0.6672 (t-90) REVERT: b 157 ASP cc_start: 0.8082 (p0) cc_final: 0.7811 (t0) REVERT: b 238 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7461 (mt-10) REVERT: c 156 GLU cc_start: 0.7807 (pt0) cc_final: 0.7364 (tt0) REVERT: c 197 ASP cc_start: 0.8311 (p0) cc_final: 0.7892 (p0) REVERT: c 276 ASP cc_start: 0.8024 (m-30) cc_final: 0.7329 (m-30) REVERT: c 318 MET cc_start: 0.7418 (mpp) cc_final: 0.7127 (mpm) outliers start: 47 outliers final: 38 residues processed: 246 average time/residue: 1.3721 time to fit residues: 373.3820 Evaluate side-chains 258 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 84 HIS Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 324 LEU Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 208 GLN Chi-restraints excluded: chain a residue 287 ILE Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 177 GLU Chi-restraints excluded: chain b residue 238 GLU Chi-restraints excluded: chain b residue 346 VAL Chi-restraints excluded: chain c residue 17 SER Chi-restraints excluded: chain c residue 22 ILE Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 65 ASN Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 228 THR Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 324 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 7.9990 chunk 170 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 147 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 160 optimal weight: 0.7980 chunk 67 optimal weight: 20.0000 chunk 164 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 208 GLN b 293 HIS c 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.199863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.131517 restraints weight = 16400.784| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.86 r_work: 0.3305 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16514 Z= 0.342 Angle : 0.603 8.492 22402 Z= 0.314 Chirality : 0.045 0.142 2387 Planarity : 0.004 0.046 2862 Dihedral : 4.921 42.277 2168 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 2.97 % Allowed : 20.93 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: -1.48 (0.18), residues: 2022 helix: 1.54 (0.36), residues: 226 sheet: -1.88 (0.23), residues: 510 loop : -1.06 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.014 0.002 PHE c 277 TYR 0.018 0.002 TYR c 256 ARG 0.014 0.001 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6516.76 seconds wall clock time: 114 minutes 27.13 seconds (6867.13 seconds total)