Starting phenix.real_space_refine on Sun Jul 21 22:48:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/07_2024/8wbe_37422_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/07_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_37422/07_2024/8wbe_37422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/07_2024/8wbe_37422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/07_2024/8wbe_37422_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbe_37422/07_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-5388/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: 9.35, 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: 6.22 Conformation dependent library (CDL) restraints added in 3.0 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: 2.06 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: 4.97 Time building geometry restraints manager: 6.77 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 2.520 nonbonded pdb=" O THR B 262 " pdb=" NH2 ARG B 294 " model vdw 2.198 2.520 nonbonded pdb=" O ASP b 23 " pdb=" OG1 THR b 27 " model vdw 2.203 2.440 nonbonded pdb=" O THR c 262 " pdb=" NH2 ARG c 294 " model vdw 2.217 2.520 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.226 2.520 ... (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 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: 3.580 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: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.450 Find NCS groups from input model: 0.850 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:11.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.190 ------------------------------------------------------------------------------- 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 : 1.911 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: 1.2287 time to fit residues: 472.2982 Evaluate side-chains 244 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 1.871 ------------------------------------------------------------------------------- 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: 0.9990 chunk 153 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN C 240 GLN C 254 HIS a 48 ASN b 48 ASN b 76 ASN b 84 HIS c 166 ASN c 181 HIS c 240 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16514 Z= 0.351 Angle : 0.590 7.527 22402 Z= 0.312 Chirality : 0.045 0.139 2387 Planarity : 0.004 0.041 2862 Dihedral : 5.021 44.195 2172 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.92 % Allowed : 10.18 % Favored : 86.91 % 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: -1.64 (0.18), residues: 2022 helix: 1.30 (0.37), residues: 225 sheet: -1.84 (0.22), residues: 535 loop : -1.18 (0.17), residues: 1262 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 0.031 0.002 PHE b 20 TYR 0.016 0.002 TYR c 256 ARG 0.006 0.001 ARG B 294 *********************** 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 291 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 240 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7131 (m-90) cc_final: 0.6626 (p-90) REVERT: A 70 GLN cc_start: 0.7413 (tt0) cc_final: 0.6955 (tt0) REVERT: A 81 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6672 (tt0) REVERT: A 102 ARG cc_start: 0.7854 (mmm-85) cc_final: 0.7309 (mmt90) REVERT: A 214 LYS cc_start: 0.8656 (mtmt) cc_final: 0.8447 (mtmm) REVERT: A 272 LYS cc_start: 0.8817 (mttp) cc_final: 0.8339 (mtpm) REVERT: A 309 THR cc_start: 0.8497 (m) cc_final: 0.8177 (p) REVERT: B 31 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7166 (mm-40) REVERT: B 59 SER cc_start: 0.8870 (m) cc_final: 0.8543 (p) REVERT: B 70 GLN cc_start: 0.7126 (mt0) cc_final: 0.6800 (mp10) REVERT: B 76 ASN cc_start: 0.5958 (m-40) cc_final: 0.5543 (m110) REVERT: B 89 VAL cc_start: 0.6816 (t) cc_final: 0.6297 (m) REVERT: B 142 GLU cc_start: 0.6320 (pt0) cc_final: 0.5731 (tm-30) REVERT: B 154 GLU cc_start: 0.7580 (pt0) cc_final: 0.7077 (pt0) REVERT: B 168 TRP cc_start: 0.7750 (m100) cc_final: 0.7422 (m100) REVERT: B 274 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7502 (tp30) REVERT: B 340 GLU cc_start: 0.5690 (tm-30) cc_final: 0.5480 (tm-30) REVERT: C 12 GLU cc_start: 0.7138 (tt0) cc_final: 0.6722 (tt0) REVERT: C 74 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6089 (mp0) REVERT: C 101 LYS cc_start: 0.6865 (mptt) cc_final: 0.6583 (mppt) REVERT: C 177 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6807 (tt0) REVERT: C 214 LYS cc_start: 0.7520 (ptmm) cc_final: 0.7082 (pptt) REVERT: C 274 GLU cc_start: 0.7183 (tp30) cc_final: 0.6951 (tp30) REVERT: a 30 GLU cc_start: 0.7891 (tt0) cc_final: 0.7369 (tt0) REVERT: a 74 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6288 (mp0) REVERT: a 214 LYS cc_start: 0.8621 (mtmt) cc_final: 0.8139 (mtpp) REVERT: a 287 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7901 (mm) REVERT: a 314 ARG cc_start: 0.6698 (ttm170) cc_final: 0.6395 (ttm170) REVERT: b 147 ARG cc_start: 0.6354 (ptm160) cc_final: 0.6016 (ptm160) REVERT: b 157 ASP cc_start: 0.8102 (p0) cc_final: 0.7737 (t0) REVERT: b 345 MET cc_start: 0.5234 (OUTLIER) cc_final: 0.4873 (ptm) REVERT: c 41 ARG cc_start: 0.7393 (ttt90) cc_final: 0.7171 (tpt90) REVERT: c 99 LYS cc_start: 0.6854 (ttmt) cc_final: 0.6544 (ttpp) REVERT: c 147 ARG cc_start: 0.5137 (ptm-80) cc_final: 0.4876 (ptm-80) REVERT: c 154 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6603 (mt-10) REVERT: c 168 TRP cc_start: 0.6771 (m100) cc_final: 0.6452 (m100) REVERT: c 197 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.7919 (p0) REVERT: c 318 MET cc_start: 0.7492 (mpp) cc_final: 0.7230 (mpm) REVERT: c 340 GLU cc_start: 0.4681 (tp30) cc_final: 0.4356 (tp30) outliers start: 51 outliers final: 24 residues processed: 268 average time/residue: 1.2347 time to fit residues: 366.7304 Evaluate side-chains 253 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 223 time to evaluate : 1.957 ------------------------------------------------------------------------------- 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 81 GLU 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 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 283 THR 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 345 MET 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 197 ASP Chi-restraints excluded: chain c residue 209 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 124 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 183 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 48 ASN a 65 ASN b 48 ASN b 208 GLN c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 349 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 16514 Z= 0.330 Angle : 0.567 6.524 22402 Z= 0.298 Chirality : 0.044 0.137 2387 Planarity : 0.004 0.034 2862 Dihedral : 4.904 35.924 2168 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.77 % Allowed : 13.49 % Favored : 82.73 % 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: -1.55 (0.19), residues: 2022 helix: 1.37 (0.36), residues: 222 sheet: -1.93 (0.23), residues: 503 loop : -1.07 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 80 HIS 0.005 0.001 HIS a 50 PHE 0.022 0.002 PHE b 20 TYR 0.017 0.002 TYR c 256 ARG 0.004 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 309 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 243 time to evaluate : 1.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7120 (m-90) cc_final: 0.6883 (m100) REVERT: A 70 GLN cc_start: 0.7311 (tt0) cc_final: 0.6927 (tt0) REVERT: A 81 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: A 272 LYS cc_start: 0.8838 (mttp) cc_final: 0.8338 (mtpm) REVERT: A 309 THR cc_start: 0.8510 (m) cc_final: 0.8127 (p) REVERT: B 31 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7233 (mm-40) REVERT: B 59 SER cc_start: 0.8835 (m) cc_final: 0.8518 (p) REVERT: B 70 GLN cc_start: 0.7107 (mt0) cc_final: 0.6745 (mp10) REVERT: B 76 ASN cc_start: 0.6106 (m-40) cc_final: 0.5759 (m110) REVERT: B 89 VAL cc_start: 0.6822 (t) cc_final: 0.6304 (m) REVERT: B 142 GLU cc_start: 0.6382 (pt0) cc_final: 0.5806 (tm-30) REVERT: B 154 GLU cc_start: 0.7640 (pt0) cc_final: 0.7137 (pt0) REVERT: B 168 TRP cc_start: 0.7765 (m100) cc_final: 0.7511 (m100) REVERT: B 274 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7503 (tp30) REVERT: C 14 LYS cc_start: 0.8349 (tptm) cc_final: 0.8056 (tptp) REVERT: C 62 ARG cc_start: 0.6920 (ppt170) cc_final: 0.6653 (ttp80) REVERT: C 74 GLU cc_start: 0.6430 (mt-10) cc_final: 0.5977 (mp0) REVERT: C 101 LYS cc_start: 0.6910 (mptt) cc_final: 0.6646 (mppt) REVERT: C 177 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6674 (tt0) REVERT: C 214 LYS cc_start: 0.7536 (ptmm) cc_final: 0.7104 (pptt) REVERT: C 274 GLU cc_start: 0.7264 (tp30) cc_final: 0.7021 (tp30) REVERT: a 30 GLU cc_start: 0.7869 (tt0) cc_final: 0.7358 (tt0) REVERT: a 74 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6287 (mp0) REVERT: a 101 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7816 (mttt) REVERT: a 214 LYS cc_start: 0.8613 (mtmt) cc_final: 0.7556 (mmmt) REVERT: a 287 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7896 (mm) REVERT: a 314 ARG cc_start: 0.6620 (ttm170) cc_final: 0.6339 (ttm170) REVERT: b 157 ASP cc_start: 0.8120 (p0) cc_final: 0.7760 (t0) REVERT: c 41 ARG cc_start: 0.7386 (ttt90) cc_final: 0.7080 (tpt90) REVERT: c 148 ARG cc_start: 0.4753 (OUTLIER) cc_final: 0.3315 (tpp80) REVERT: c 154 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: c 168 TRP cc_start: 0.6794 (m100) cc_final: 0.6589 (m100) REVERT: c 197 ASP cc_start: 0.8379 (OUTLIER) cc_final: 0.7908 (p0) REVERT: c 276 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: c 318 MET cc_start: 0.7524 (mpp) cc_final: 0.7262 (mpm) REVERT: c 340 GLU cc_start: 0.4815 (tp30) cc_final: 0.4473 (tp30) REVERT: c 349 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6929 (mp10) outliers start: 66 outliers final: 34 residues processed: 277 average time/residue: 1.2541 time to fit residues: 384.8168 Evaluate side-chains 266 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 223 time to evaluate : 1.772 ------------------------------------------------------------------------------- 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 81 GLU 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 317 THR 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 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 148 ARG Chi-restraints excluded: chain c residue 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 197 ASP Chi-restraints excluded: chain c residue 209 THR Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 262 THR Chi-restraints excluded: chain c residue 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 349 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN a 35 GLN a 48 ASN b 48 ASN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16514 Z= 0.405 Angle : 0.605 7.598 22402 Z= 0.318 Chirality : 0.045 0.169 2387 Planarity : 0.004 0.034 2862 Dihedral : 5.070 40.849 2168 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.12 % Favored : 92.83 % Rotamer: Outliers : 4.80 % Allowed : 14.64 % Favored : 80.56 % 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: 1.33 (0.36), residues: 222 sheet: -1.92 (0.23), residues: 489 loop : -1.18 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 330 HIS 0.006 0.001 HIS c 269 PHE 0.018 0.002 PHE b 20 TYR 0.017 0.002 TYR A 256 ARG 0.007 0.001 ARG B 294 *********************** 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 324 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 240 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7127 (m-90) cc_final: 0.6626 (p-90) REVERT: A 30 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: A 70 GLN cc_start: 0.7329 (tt0) cc_final: 0.6903 (tt0) REVERT: A 272 LYS cc_start: 0.8831 (mttp) cc_final: 0.8324 (mtpm) REVERT: A 309 THR cc_start: 0.8497 (m) cc_final: 0.8063 (p) REVERT: B 31 GLN cc_start: 0.7856 (OUTLIER) cc_final: 0.7285 (mm-40) REVERT: B 59 SER cc_start: 0.8853 (m) cc_final: 0.8535 (p) REVERT: B 70 GLN cc_start: 0.7178 (mt0) cc_final: 0.6783 (mp10) REVERT: B 89 VAL cc_start: 0.6856 (t) cc_final: 0.6298 (m) REVERT: B 142 GLU cc_start: 0.6469 (pt0) cc_final: 0.5803 (tm-30) REVERT: B 147 ARG cc_start: 0.7670 (mtp85) cc_final: 0.7344 (mtp85) REVERT: B 168 TRP cc_start: 0.7715 (m100) cc_final: 0.7497 (m100) REVERT: B 213 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7858 (pt0) REVERT: B 238 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7610 (mm-30) REVERT: B 274 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7493 (tp30) REVERT: C 14 LYS cc_start: 0.8326 (tptm) cc_final: 0.8047 (tptp) REVERT: C 62 ARG cc_start: 0.7004 (ppt170) cc_final: 0.6669 (ttp80) REVERT: C 74 GLU cc_start: 0.6469 (mt-10) cc_final: 0.5994 (mp0) REVERT: C 101 LYS cc_start: 0.6937 (mptt) cc_final: 0.6641 (mppt) REVERT: C 177 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6583 (tt0) REVERT: C 214 LYS cc_start: 0.7513 (ptmm) cc_final: 0.7097 (pptt) REVERT: C 274 GLU cc_start: 0.7284 (tp30) cc_final: 0.7049 (tp30) REVERT: a 30 GLU cc_start: 0.7873 (tt0) cc_final: 0.7315 (tt0) REVERT: a 74 GLU cc_start: 0.6628 (mt-10) cc_final: 0.6285 (mp0) REVERT: a 101 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.7779 (mttt) REVERT: a 214 LYS cc_start: 0.8631 (mtmt) cc_final: 0.7557 (mmmt) REVERT: a 287 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7887 (mm) REVERT: a 314 ARG cc_start: 0.6625 (ttm170) cc_final: 0.6375 (ttm170) REVERT: b 157 ASP cc_start: 0.8113 (p0) cc_final: 0.7708 (t0) REVERT: b 180 ASP cc_start: 0.8447 (t0) cc_final: 0.8233 (t0) REVERT: c 154 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.6784 (mt-10) REVERT: c 168 TRP cc_start: 0.6795 (m100) cc_final: 0.6528 (m100) REVERT: c 197 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8095 (p0) REVERT: c 276 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: c 318 MET cc_start: 0.7512 (mpp) cc_final: 0.7255 (mpm) REVERT: c 340 GLU cc_start: 0.4818 (tp30) cc_final: 0.4499 (tp30) REVERT: c 349 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6886 (mp10) outliers start: 84 outliers final: 42 residues processed: 291 average time/residue: 1.1796 time to fit residues: 382.3058 Evaluate side-chains 271 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 220 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 30 GLU 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 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 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 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 27 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 C residue 283 THR Chi-restraints excluded: chain C residue 317 THR 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 287 ILE 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 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 154 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 197 ASP 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 276 ASP Chi-restraints excluded: chain c residue 324 LEU Chi-restraints excluded: chain c residue 349 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 6.9990 chunk 110 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 175 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN B 208 GLN a 35 GLN a 48 ASN b 48 ASN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 349 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16514 Z= 0.292 Angle : 0.552 7.113 22402 Z= 0.290 Chirality : 0.043 0.137 2387 Planarity : 0.003 0.034 2862 Dihedral : 4.942 42.598 2168 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.77 % Allowed : 16.70 % Favored : 79.53 % 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: -1.51 (0.19), residues: 2022 helix: 1.41 (0.36), residues: 224 sheet: -1.82 (0.23), residues: 489 loop : -1.11 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.004 0.001 HIS b 293 PHE 0.013 0.001 PHE b 20 TYR 0.017 0.001 TYR c 256 ARG 0.006 0.000 ARG b 336 *********************** 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 310 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 244 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7135 (m-90) cc_final: 0.6903 (m100) REVERT: A 70 GLN cc_start: 0.7310 (tt0) cc_final: 0.6896 (tt0) REVERT: A 272 LYS cc_start: 0.8806 (mttp) cc_final: 0.8309 (mtpm) REVERT: B 31 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7278 (mm-40) REVERT: B 59 SER cc_start: 0.8835 (m) cc_final: 0.8516 (p) REVERT: B 60 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8603 (p) REVERT: B 70 GLN cc_start: 0.7194 (mt0) cc_final: 0.6810 (mp10) REVERT: B 142 GLU cc_start: 0.6529 (pt0) cc_final: 0.5925 (tm-30) REVERT: B 147 ARG cc_start: 0.7702 (mtp85) cc_final: 0.7375 (mtp85) REVERT: B 154 GLU cc_start: 0.7529 (pt0) cc_final: 0.7113 (pt0) REVERT: B 157 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: B 274 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7428 (tp30) REVERT: C 14 LYS cc_start: 0.8333 (tptm) cc_final: 0.8039 (tptp) REVERT: C 62 ARG cc_start: 0.6984 (ppt170) cc_final: 0.6431 (ttp-110) REVERT: C 74 GLU cc_start: 0.6447 (mt-10) cc_final: 0.5987 (mp0) REVERT: C 101 LYS cc_start: 0.6867 (mptt) cc_final: 0.6557 (mppt) REVERT: C 177 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6585 (tt0) REVERT: C 214 LYS cc_start: 0.7518 (ptmm) cc_final: 0.7106 (pptt) REVERT: C 258 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.6487 (tm-30) REVERT: a 30 GLU cc_start: 0.7873 (tt0) cc_final: 0.7322 (tt0) REVERT: a 74 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6239 (mp0) REVERT: a 214 LYS cc_start: 0.8602 (mtmt) cc_final: 0.7549 (mmmt) REVERT: a 287 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7900 (mm) REVERT: a 314 ARG cc_start: 0.6617 (ttm170) cc_final: 0.6407 (ttm170) REVERT: b 96 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8150 (t) REVERT: b 180 ASP cc_start: 0.8445 (t0) cc_final: 0.8212 (t0) REVERT: c 154 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6763 (mt-10) REVERT: c 197 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.7857 (p0) REVERT: c 219 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7791 (pt0) REVERT: c 276 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7308 (m-30) REVERT: c 318 MET cc_start: 0.7459 (mpp) cc_final: 0.7173 (mpm) REVERT: c 340 GLU cc_start: 0.4785 (tp30) cc_final: 0.4514 (tp30) outliers start: 66 outliers final: 39 residues processed: 281 average time/residue: 1.2371 time to fit residues: 386.1353 Evaluate side-chains 283 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 140 THR Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 164 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 157 ASP Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 57 ILE 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 283 THR Chi-restraints excluded: chain C residue 317 THR 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 324 LEU Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain b residue 61 THR Chi-restraints excluded: chain b residue 96 VAL Chi-restraints excluded: chain b residue 177 GLU 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 154 GLU Chi-restraints excluded: chain c residue 197 ASP 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 262 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: 0.6980 chunk 114 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN a 48 ASN b 48 ASN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16514 Z= 0.236 Angle : 0.526 7.410 22402 Z= 0.277 Chirality : 0.043 0.132 2387 Planarity : 0.003 0.032 2862 Dihedral : 4.740 43.275 2168 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.66 % Allowed : 17.78 % Favored : 78.56 % 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: -1.39 (0.19), residues: 2022 helix: 1.53 (0.36), residues: 224 sheet: -1.80 (0.24), residues: 469 loop : -1.03 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.012 0.001 PHE B 160 TYR 0.018 0.001 TYR c 256 ARG 0.006 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 304 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 240 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7134 (m-90) cc_final: 0.6614 (p-90) REVERT: A 70 GLN cc_start: 0.7333 (tt0) cc_final: 0.6912 (tt0) REVERT: A 272 LYS cc_start: 0.8787 (mttp) cc_final: 0.8297 (mtpm) REVERT: B 31 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7286 (mm-40) REVERT: B 59 SER cc_start: 0.8865 (m) cc_final: 0.8558 (p) REVERT: B 60 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8585 (p) REVERT: B 70 GLN cc_start: 0.7182 (mt0) cc_final: 0.6813 (mp10) REVERT: B 142 GLU cc_start: 0.6558 (pt0) cc_final: 0.5855 (pp20) REVERT: B 147 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7429 (mtp85) REVERT: B 154 GLU cc_start: 0.7539 (pt0) cc_final: 0.7195 (pt0) REVERT: B 162 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5449 (mtp) REVERT: B 274 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7392 (tp30) REVERT: C 1 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: C 14 LYS cc_start: 0.8299 (tptm) cc_final: 0.7937 (tptp) REVERT: C 62 ARG cc_start: 0.6937 (ppt170) cc_final: 0.6363 (ttp-110) REVERT: C 74 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5922 (mp0) REVERT: C 101 LYS cc_start: 0.6815 (mptt) cc_final: 0.6516 (mppt) REVERT: C 148 ARG cc_start: 0.5043 (tpt-90) cc_final: 0.4706 (tpt-90) REVERT: C 177 GLU cc_start: 0.7288 (mt-10) cc_final: 0.6566 (tt0) REVERT: C 214 LYS cc_start: 0.7534 (ptmm) cc_final: 0.7129 (pptt) REVERT: C 258 GLN cc_start: 0.7363 (OUTLIER) cc_final: 0.6402 (tm-30) REVERT: a 30 GLU cc_start: 0.7904 (tt0) cc_final: 0.7351 (tt0) REVERT: a 74 GLU cc_start: 0.6611 (mt-10) cc_final: 0.6222 (mp0) REVERT: a 214 LYS cc_start: 0.8567 (mtmt) cc_final: 0.8069 (mtpp) REVERT: a 287 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7916 (mm) REVERT: b 157 ASP cc_start: 0.8103 (p0) cc_final: 0.7798 (t0) REVERT: b 180 ASP cc_start: 0.8385 (t0) cc_final: 0.8171 (t0) REVERT: c 154 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6758 (mt-10) REVERT: c 219 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7733 (pt0) REVERT: c 276 ASP cc_start: 0.7994 (m-30) cc_final: 0.7294 (m-30) REVERT: c 318 MET cc_start: 0.7421 (mpp) cc_final: 0.7159 (mpm) REVERT: c 340 GLU cc_start: 0.4875 (tp30) cc_final: 0.4562 (tp30) outliers start: 64 outliers final: 39 residues processed: 279 average time/residue: 1.2536 time to fit residues: 387.7209 Evaluate side-chains 282 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 60 THR Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 27 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 317 THR 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 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 307 LEU 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 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 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: 0.5980 chunk 111 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN a 48 ASN a 269 HIS b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16514 Z= 0.160 Angle : 0.487 7.943 22402 Z= 0.256 Chirality : 0.041 0.131 2387 Planarity : 0.003 0.031 2862 Dihedral : 4.465 42.222 2168 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.74 % Allowed : 19.55 % Favored : 77.70 % 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: -1.22 (0.19), residues: 2022 helix: 1.68 (0.37), residues: 224 sheet: -1.82 (0.23), residues: 493 loop : -0.82 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.012 0.001 PHE a 277 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 276 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7102 (m-90) cc_final: 0.6847 (m100) REVERT: A 70 GLN cc_start: 0.7287 (tt0) cc_final: 0.6896 (tt0) REVERT: A 272 LYS cc_start: 0.8756 (mttp) cc_final: 0.8265 (mtpm) REVERT: B 59 SER cc_start: 0.8878 (m) cc_final: 0.8560 (p) REVERT: B 60 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 70 GLN cc_start: 0.7190 (mt0) cc_final: 0.6798 (mp10) REVERT: B 89 VAL cc_start: 0.6839 (t) cc_final: 0.6329 (m) REVERT: B 142 GLU cc_start: 0.6552 (pt0) cc_final: 0.5837 (pp20) REVERT: B 147 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7430 (mtp85) REVERT: B 154 GLU cc_start: 0.7529 (pt0) cc_final: 0.7212 (pt0) REVERT: B 274 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7346 (tp30) REVERT: B 310 GLN cc_start: 0.6107 (OUTLIER) cc_final: 0.5801 (mp10) REVERT: C 1 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: C 14 LYS cc_start: 0.8202 (tptm) cc_final: 0.7826 (tptp) REVERT: C 62 ARG cc_start: 0.6858 (ppt170) cc_final: 0.6319 (ttp-110) REVERT: C 74 GLU cc_start: 0.6405 (mt-10) cc_final: 0.5865 (mp0) REVERT: C 101 LYS cc_start: 0.6752 (mptt) cc_final: 0.6394 (mppt) REVERT: C 177 GLU cc_start: 0.7250 (mt-10) cc_final: 0.6546 (tt0) REVERT: C 214 LYS cc_start: 0.7542 (ptmm) cc_final: 0.7133 (pptt) REVERT: C 258 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.6420 (tm-30) REVERT: a 30 GLU cc_start: 0.7907 (tt0) cc_final: 0.7324 (tt0) REVERT: a 74 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6130 (mp0) REVERT: a 214 LYS cc_start: 0.8545 (mtmt) cc_final: 0.8062 (mtpp) REVERT: b 96 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8123 (t) REVERT: b 157 ASP cc_start: 0.8072 (p0) cc_final: 0.7793 (t0) REVERT: c 154 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6726 (mt-10) REVERT: c 156 GLU cc_start: 0.7841 (pt0) cc_final: 0.7349 (tt0) REVERT: c 219 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7671 (pt0) REVERT: c 276 ASP cc_start: 0.8010 (m-30) cc_final: 0.7262 (m-30) REVERT: c 318 MET cc_start: 0.7406 (mpp) cc_final: 0.7122 (mpm) REVERT: c 340 GLU cc_start: 0.4884 (tp30) cc_final: 0.4549 (tp30) outliers start: 48 outliers final: 31 residues processed: 258 average time/residue: 1.2531 time to fit residues: 358.8110 Evaluate side-chains 255 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 217 time to evaluate : 1.882 ------------------------------------------------------------------------------- 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 204 SER 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 22 ILE Chi-restraints excluded: chain B residue 60 THR 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 310 GLN Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 27 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 264 THR Chi-restraints excluded: chain C residue 329 CYS Chi-restraints excluded: chain a residue 70 GLN 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 96 VAL Chi-restraints excluded: chain b residue 148 ARG Chi-restraints excluded: chain b residue 307 LEU 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 212 ILE Chi-restraints excluded: chain c residue 218 ILE Chi-restraints excluded: chain c residue 219 GLU 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: 5.9990 chunk 77 optimal weight: 8.9990 chunk 116 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16514 Z= 0.295 Angle : 0.558 7.290 22402 Z= 0.291 Chirality : 0.044 0.136 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.743 42.505 2168 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.72 % Allowed : 19.38 % Favored : 76.90 % 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: -1.40 (0.19), residues: 2022 helix: 1.58 (0.36), residues: 224 sheet: -1.94 (0.23), residues: 493 loop : -0.95 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 168 HIS 0.006 0.001 HIS b 293 PHE 0.013 0.002 PHE c 277 TYR 0.018 0.002 TYR c 256 ARG 0.010 0.000 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 296 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 231 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7083 (m-90) cc_final: 0.6561 (p-90) REVERT: A 70 GLN cc_start: 0.7302 (tt0) cc_final: 0.6903 (tt0) REVERT: A 272 LYS cc_start: 0.8801 (mttp) cc_final: 0.8292 (mtpm) REVERT: A 340 GLU cc_start: 0.7687 (tt0) cc_final: 0.7169 (tt0) REVERT: B 31 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7319 (mm-40) REVERT: B 59 SER cc_start: 0.8907 (m) cc_final: 0.8607 (p) REVERT: B 60 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8600 (p) REVERT: B 70 GLN cc_start: 0.7191 (mt0) cc_final: 0.6858 (mp10) REVERT: B 142 GLU cc_start: 0.6656 (pt0) cc_final: 0.6028 (pp20) REVERT: B 147 ARG cc_start: 0.7815 (mtp85) cc_final: 0.7445 (mtp85) REVERT: B 154 GLU cc_start: 0.7546 (pt0) cc_final: 0.7204 (pt0) REVERT: B 274 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7313 (tp30) REVERT: C 1 ASP cc_start: 0.8669 (OUTLIER) cc_final: 0.8017 (m-30) REVERT: C 14 LYS cc_start: 0.8312 (tptm) cc_final: 0.7952 (tptp) REVERT: C 62 ARG cc_start: 0.6957 (ppt170) cc_final: 0.6365 (ttp-110) REVERT: C 74 GLU cc_start: 0.6451 (mt-10) cc_final: 0.5903 (mp0) REVERT: C 101 LYS cc_start: 0.6805 (mptt) cc_final: 0.6514 (mppt) REVERT: C 148 ARG cc_start: 0.5173 (OUTLIER) cc_final: 0.4888 (tpt-90) REVERT: C 177 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6484 (tt0) REVERT: C 214 LYS cc_start: 0.7529 (ptmm) cc_final: 0.7104 (pptt) REVERT: C 258 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6344 (tm-30) REVERT: a 30 GLU cc_start: 0.7906 (tt0) cc_final: 0.7340 (tt0) REVERT: a 74 GLU cc_start: 0.6581 (mt-10) cc_final: 0.6178 (mp0) REVERT: a 101 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.7810 (mttt) REVERT: a 287 ILE cc_start: 0.8212 (OUTLIER) cc_final: 0.7861 (mm) REVERT: b 157 ASP cc_start: 0.8102 (p0) cc_final: 0.7808 (t0) REVERT: c 154 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: c 156 GLU cc_start: 0.7824 (pt0) cc_final: 0.7348 (tt0) REVERT: c 219 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7819 (pt0) REVERT: c 276 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: c 318 MET cc_start: 0.7399 (mpp) cc_final: 0.7122 (mpm) REVERT: c 340 GLU cc_start: 0.4863 (tp30) cc_final: 0.4572 (tp30) outliers start: 65 outliers final: 42 residues processed: 272 average time/residue: 1.2210 time to fit residues: 369.3886 Evaluate side-chains 278 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 226 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 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 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 218 ILE Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 148 ARG 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 265 VAL Chi-restraints excluded: chain C residue 317 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 101 LYS 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 307 LEU Chi-restraints excluded: chain b residue 346 VAL 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 154 GLU 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 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: 4.9990 chunk 186 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.0870 chunk 109 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 180 optimal weight: 9.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN a 48 ASN c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16514 Z= 0.166 Angle : 0.496 7.321 22402 Z= 0.259 Chirality : 0.042 0.138 2387 Planarity : 0.003 0.030 2862 Dihedral : 4.448 40.135 2168 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.80 % Allowed : 20.41 % Favored : 76.79 % 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: -1.21 (0.19), residues: 2022 helix: 1.67 (0.37), residues: 224 sheet: -1.81 (0.23), residues: 493 loop : -0.81 (0.17), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.012 0.001 PHE a 277 TYR 0.018 0.001 TYR c 256 ARG 0.011 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 273 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 224 time to evaluate : 1.871 Fit side-chains revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7098 (m-90) cc_final: 0.6555 (p-90) REVERT: A 70 GLN cc_start: 0.7292 (tt0) cc_final: 0.6903 (tt0) REVERT: A 272 LYS cc_start: 0.8753 (mttp) cc_final: 0.8257 (mtpm) REVERT: B 31 GLN cc_start: 0.7837 (OUTLIER) cc_final: 0.7287 (mm-40) REVERT: B 59 SER cc_start: 0.8887 (m) cc_final: 0.8577 (p) REVERT: B 70 GLN cc_start: 0.7159 (mt0) cc_final: 0.6820 (mp10) REVERT: B 89 VAL cc_start: 0.6829 (t) cc_final: 0.6324 (m) REVERT: B 142 GLU cc_start: 0.6666 (pt0) cc_final: 0.6004 (pp20) REVERT: B 147 ARG cc_start: 0.7845 (mtp85) cc_final: 0.7490 (mtp85) REVERT: B 154 GLU cc_start: 0.7512 (pt0) cc_final: 0.7195 (pt0) REVERT: B 274 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7305 (tp30) REVERT: C 1 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: C 14 LYS cc_start: 0.8228 (tptm) cc_final: 0.7856 (tptp) REVERT: C 62 ARG cc_start: 0.6919 (ppt170) cc_final: 0.6250 (ttp-110) REVERT: C 74 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5895 (mp0) REVERT: C 101 LYS cc_start: 0.6775 (mptt) cc_final: 0.6413 (mppt) REVERT: C 177 GLU cc_start: 0.7200 (mt-10) cc_final: 0.6489 (tt0) REVERT: C 214 LYS cc_start: 0.7504 (ptmm) cc_final: 0.7096 (pptt) REVERT: C 258 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6384 (tm-30) REVERT: C 314 ARG cc_start: 0.5029 (ttm170) cc_final: 0.4805 (ttm170) REVERT: a 30 GLU cc_start: 0.7921 (tt0) cc_final: 0.7366 (tt0) REVERT: a 74 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6146 (mp0) REVERT: a 101 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7780 (mttt) REVERT: a 214 LYS cc_start: 0.8544 (mtmt) cc_final: 0.8061 (mtpp) REVERT: a 314 ARG cc_start: 0.6725 (ttm170) cc_final: 0.6440 (ttm170) REVERT: b 50 HIS cc_start: 0.6907 (t-90) cc_final: 0.6635 (t-90) REVERT: b 157 ASP cc_start: 0.8063 (p0) cc_final: 0.7825 (t0) REVERT: c 154 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6709 (mt-10) REVERT: c 156 GLU cc_start: 0.7806 (pt0) cc_final: 0.7354 (tt0) REVERT: c 219 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: c 276 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: c 318 MET cc_start: 0.7418 (mpp) cc_final: 0.7143 (mpm) outliers start: 49 outliers final: 37 residues processed: 255 average time/residue: 1.2183 time to fit residues: 344.9889 Evaluate side-chains 266 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 222 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 204 SER 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 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL 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 265 VAL Chi-restraints excluded: chain C residue 317 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 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 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 154 GLU 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 262 THR Chi-restraints excluded: chain c residue 276 ASP 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: 5.9990 chunk 191 optimal weight: 0.1980 chunk 117 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 201 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16514 Z= 0.370 Angle : 0.594 9.237 22402 Z= 0.309 Chirality : 0.045 0.138 2387 Planarity : 0.004 0.055 2862 Dihedral : 4.828 40.723 2168 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.48 % Favored : 93.47 % Rotamer: Outliers : 3.20 % Allowed : 19.90 % Favored : 76.90 % 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: -1.48 (0.18), residues: 2022 helix: 1.50 (0.36), residues: 226 sheet: -1.96 (0.23), residues: 489 loop : -1.03 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 168 HIS 0.005 0.001 HIS b 293 PHE 0.016 0.002 PHE c 34 TYR 0.019 0.002 TYR A 256 ARG 0.014 0.001 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 281 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 225 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 TRP cc_start: 0.7099 (m-90) cc_final: 0.6593 (p-90) REVERT: A 70 GLN cc_start: 0.7329 (tt0) cc_final: 0.6934 (tt0) REVERT: A 272 LYS cc_start: 0.8812 (mttp) cc_final: 0.8202 (mtpm) REVERT: A 340 GLU cc_start: 0.7705 (tt0) cc_final: 0.7204 (tt0) REVERT: B 31 GLN cc_start: 0.7885 (OUTLIER) cc_final: 0.7335 (mm-40) REVERT: B 59 SER cc_start: 0.8927 (m) cc_final: 0.8626 (p) REVERT: B 70 GLN cc_start: 0.7188 (mt0) cc_final: 0.6861 (mp10) REVERT: B 142 GLU cc_start: 0.6649 (pt0) cc_final: 0.5929 (pp20) REVERT: B 154 GLU cc_start: 0.7557 (pt0) cc_final: 0.7138 (pt0) REVERT: B 274 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7333 (tp30) REVERT: C 1 ASP cc_start: 0.8688 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: C 14 LYS cc_start: 0.8320 (tptm) cc_final: 0.7954 (tptp) REVERT: C 62 ARG cc_start: 0.6993 (ppt170) cc_final: 0.6357 (ttp-110) REVERT: C 74 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5965 (mp0) REVERT: C 101 LYS cc_start: 0.6905 (mptt) cc_final: 0.6583 (mppt) REVERT: C 148 ARG cc_start: 0.5213 (OUTLIER) cc_final: 0.4903 (tpt-90) REVERT: C 177 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6536 (tt0) REVERT: C 214 LYS cc_start: 0.7524 (ptmm) cc_final: 0.7094 (pptt) REVERT: C 258 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.6386 (tm-30) REVERT: a 30 GLU cc_start: 0.7905 (tt0) cc_final: 0.7324 (tt0) REVERT: a 74 GLU cc_start: 0.6689 (mt-10) cc_final: 0.6261 (mp0) REVERT: a 101 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: a 314 ARG cc_start: 0.6658 (ttm170) cc_final: 0.6368 (ttm170) REVERT: b 50 HIS cc_start: 0.6891 (t-90) cc_final: 0.6625 (t-90) REVERT: b 157 ASP cc_start: 0.8107 (p0) cc_final: 0.7805 (t0) REVERT: c 154 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6706 (mt-10) REVERT: c 156 GLU cc_start: 0.7848 (pt0) cc_final: 0.7369 (tt0) REVERT: c 197 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8112 (p0) REVERT: c 219 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: c 276 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7305 (m-30) REVERT: c 318 MET cc_start: 0.7397 (mpp) cc_final: 0.7125 (mpm) outliers start: 56 outliers final: 42 residues processed: 260 average time/residue: 1.2168 time to fit residues: 351.2628 Evaluate side-chains 273 residues out of total 1749 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 222 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 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 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 297 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 1 ASP Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 148 ARG 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 265 VAL Chi-restraints excluded: chain C residue 317 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 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 346 VAL 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 154 GLU Chi-restraints excluded: chain c residue 197 ASP 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 262 THR Chi-restraints excluded: chain c residue 276 ASP 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: 3.9990 chunk 170 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 160 optimal weight: 0.0570 chunk 67 optimal weight: 20.0000 chunk 164 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 1.5702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 GLN a 35 GLN b 293 HIS c 166 ASN ** c 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.202476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.133717 restraints weight = 16343.012| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.86 r_work: 0.3337 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16514 Z= 0.198 Angle : 0.520 7.434 22402 Z= 0.271 Chirality : 0.042 0.135 2387 Planarity : 0.003 0.053 2862 Dihedral : 4.564 38.199 2168 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.92 % Allowed : 20.41 % Favored : 76.67 % 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: -1.27 (0.19), residues: 2022 helix: 1.64 (0.37), residues: 224 sheet: -1.73 (0.23), residues: 509 loop : -0.90 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 168 HIS 0.007 0.001 HIS b 293 PHE 0.012 0.001 PHE c 34 TYR 0.018 0.001 TYR c 256 ARG 0.015 0.000 ARG C 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6400.55 seconds wall clock time: 112 minutes 10.73 seconds (6730.73 seconds total)