Starting phenix.real_space_refine on Wed Feb 14 08:55:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibu_35345/02_2024/8ibu_35345_trim_updated.pdb" } resolution = 3.51 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5664 2.51 5 N 1538 2.21 5 O 1644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E GLU 88": "OE1" <-> "OE2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 100": "NH1" <-> "NH2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R ARG 136": "NH1" <-> "NH2" Residue "R ARG 145": "NH1" <-> "NH2" Residue "R ARG 153": "NH1" <-> "NH2" Residue "R ARG 156": "NH1" <-> "NH2" Residue "R GLU 180": "OE1" <-> "OE2" Residue "R GLU 234": "OE1" <-> "OE2" Residue "R ARG 246": "NH1" <-> "NH2" Residue "R GLU 273": "OE1" <-> "OE2" Residue "R ARG 318": "NH1" <-> "NH2" Residue "R TYR 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8903 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2591 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2229 Unusual residues: {'ERY': 1} Classifications: {'peptide': 273, 'undetermined': 1} Link IDs: {'PTRANS': 13, 'TRANS': 259, None: 1} Not linked: pdbres="LEU R 369 " pdbres="ERY R 601 " Chain breaks: 2 Time building chain proxies: 5.79, per 1000 atoms: 0.65 Number of scatterers: 8903 At special positions: 0 Unit cell: (119.952, 117.81, 106.029, 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 57 16.00 O 1644 8.00 N 1538 7.00 C 5664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.5% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.778A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 211 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 299 through 316 removed outlier: 3.605A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 357 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 36 through 41 removed outlier: 5.825A pdb=" N ASN B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'G' and resid 7 through 22 Processing helix chain 'G' and resid 29 through 43 removed outlier: 3.659A pdb=" N HIS G 43 " --> pdb=" O TYR G 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 64 Proline residue: R 40 - end of helix removed outlier: 3.731A pdb=" N LEU R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY R 64 " --> pdb=" O VAL R 60 " (cutoff:3.500A) Processing helix chain 'R' and resid 72 through 95 removed outlier: 3.803A pdb=" N TYR R 76 " --> pdb=" O THR R 72 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 108 through 140 removed outlier: 4.249A pdb=" N ARG R 112 " --> pdb=" O PRO R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 176 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 242 through 251 Processing helix chain 'R' and resid 254 through 273 Proline residue: R 259 - end of helix removed outlier: 3.512A pdb=" N SER R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE R 265 " --> pdb=" O LEU R 261 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR R 267 " --> pdb=" O LEU R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 293 through 323 Proline residue: R 313 - end of helix Processing helix chain 'R' and resid 327 through 355 removed outlier: 3.685A pdb=" N TYR R 331 " --> pdb=" O SER R 327 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL R 339 " --> pdb=" O TYR R 335 " (cutoff:3.500A) Proline residue: R 352 - end of helix Processing helix chain 'R' and resid 360 through 368 Processing sheet with id= A, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.295A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A 34 " --> pdb=" O ASN A 195 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 97 through 99 removed outlier: 4.276A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER B 77 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.110A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.134A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 226 through 228 removed outlier: 3.507A pdb=" N ALA B 213 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA B 208 " --> pdb=" O SER B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.914A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 278 through 283 removed outlier: 6.751A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.887A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 336 " --> pdb=" O PHE B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 2 through 6 Processing sheet with id= J, first strand: chain 'E' and resid 114 through 116 removed outlier: 3.612A pdb=" N ALA E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.812A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 3.729A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 384 hydrogen bonds defined for protein. 1104 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: 2.50 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1438 1.32 - 1.44: 2515 1.44 - 1.56: 5046 1.56 - 1.69: 5 1.69 - 1.81: 82 Bond restraints: 9086 Sorted by residual: bond pdb=" C1 ERY R 601 " pdb=" O2 ERY R 601 " ideal model delta sigma weight residual 1.459 1.250 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" CA ASP R 94 " pdb=" C ASP R 94 " ideal model delta sigma weight residual 1.523 1.424 0.100 1.34e-02 5.57e+03 5.53e+01 bond pdb=" C12 ERY R 601 " pdb=" C13 ERY R 601 " ideal model delta sigma weight residual 1.529 1.639 -0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" CA ARG R 318 " pdb=" C ARG R 318 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.26e-02 6.30e+03 2.73e+01 bond pdb=" CA VAL R 316 " pdb=" C VAL R 316 " ideal model delta sigma weight residual 1.522 1.454 0.068 1.38e-02 5.25e+03 2.41e+01 ... (remaining 9081 not shown) Histogram of bond angle deviations from ideal: 98.12 - 105.29: 152 105.29 - 112.46: 4657 112.46 - 119.63: 2844 119.63 - 126.80: 4538 126.80 - 133.97: 131 Bond angle restraints: 12322 Sorted by residual: angle pdb=" N LEU R 95 " pdb=" CA LEU R 95 " pdb=" C LEU R 95 " ideal model delta sigma weight residual 111.28 99.46 11.82 1.09e+00 8.42e-01 1.18e+02 angle pdb=" N ARG R 142 " pdb=" CA ARG R 142 " pdb=" C ARG R 142 " ideal model delta sigma weight residual 110.08 125.03 -14.95 1.38e+00 5.25e-01 1.17e+02 angle pdb=" N VAL R 316 " pdb=" CA VAL R 316 " pdb=" C VAL R 316 " ideal model delta sigma weight residual 111.05 98.12 12.93 1.25e+00 6.40e-01 1.07e+02 angle pdb=" N ARG R 318 " pdb=" CA ARG R 318 " pdb=" C ARG R 318 " ideal model delta sigma weight residual 111.14 103.14 8.00 1.08e+00 8.57e-01 5.48e+01 angle pdb=" N VAL R 148 " pdb=" CA VAL R 148 " pdb=" C VAL R 148 " ideal model delta sigma weight residual 108.45 117.62 -9.17 1.48e+00 4.57e-01 3.84e+01 ... (remaining 12317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.28: 5224 29.28 - 58.56: 162 58.56 - 87.84: 10 87.84 - 117.12: 1 117.12 - 146.40: 2 Dihedral angle restraints: 5399 sinusoidal: 2134 harmonic: 3265 Sorted by residual: dihedral pdb=" C ASP R 94 " pdb=" N ASP R 94 " pdb=" CA ASP R 94 " pdb=" CB ASP R 94 " ideal model delta harmonic sigma weight residual -122.60 -110.69 -11.91 0 2.50e+00 1.60e-01 2.27e+01 dihedral pdb=" C10 ERY R 601 " pdb=" C8 ERY R 601 " pdb=" C9 ERY R 601 " pdb=" C7 ERY R 601 " ideal model delta sinusoidal sigma weight residual 222.86 76.46 146.40 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C11 ERY R 601 " pdb=" C10 ERY R 601 " pdb=" C9 ERY R 601 " pdb=" C8 ERY R 601 " ideal model delta sinusoidal sigma weight residual -71.83 74.08 -145.91 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 5396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.103: 1403 1.103 - 2.207: 0 2.207 - 3.310: 0 3.310 - 4.414: 0 4.414 - 5.517: 4 Chirality restraints: 1407 Sorted by residual: chirality pdb=" C12 ERY R 601 " pdb=" C11 ERY R 601 " pdb=" C13 ERY R 601 " pdb=" C35 ERY R 601 " both_signs ideal model delta sigma weight residual False -2.75 2.77 -5.52 2.00e-01 2.50e+01 7.61e+02 chirality pdb=" C6 ERY R 601 " pdb=" C32 ERY R 601 " pdb=" C5 ERY R 601 " pdb=" C7 ERY R 601 " both_signs ideal model delta sigma weight residual False -2.75 2.72 -5.48 2.00e-01 2.50e+01 7.50e+02 chirality pdb=" C16 ERY R 601 " pdb=" C15 ERY R 601 " pdb=" C17 ERY R 601 " pdb=" C19 ERY R 601 " both_signs ideal model delta sigma weight residual False 2.68 -2.59 5.27 2.00e-01 2.50e+01 6.94e+02 ... (remaining 1404 not shown) Planarity restraints: 1553 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 140 " 0.025 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ILE R 140 " -0.085 2.00e-02 2.50e+03 pdb=" O ILE R 140 " 0.031 2.00e-02 2.50e+03 pdb=" N CYS R 141 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS R 141 " -0.021 2.00e-02 2.50e+03 4.04e-02 1.63e+01 pdb=" C CYS R 141 " 0.070 2.00e-02 2.50e+03 pdb=" O CYS R 141 " -0.026 2.00e-02 2.50e+03 pdb=" N ARG R 142 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 146 " 0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ALA R 146 " -0.064 2.00e-02 2.50e+03 pdb=" O ALA R 146 " 0.024 2.00e-02 2.50e+03 pdb=" N ARG R 147 " 0.021 2.00e-02 2.50e+03 ... (remaining 1550 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2907 2.83 - 3.34: 8109 3.34 - 3.86: 14585 3.86 - 4.38: 16378 4.38 - 4.90: 28295 Nonbonded interactions: 70274 Sorted by model distance: nonbonded pdb=" OG SER B 286 " pdb=" OD2 ASP G 47 " model vdw 2.307 2.440 nonbonded pdb=" OG1 THR R 151 " pdb=" N ARG R 154 " model vdw 2.310 2.520 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.334 2.440 nonbonded pdb=" OG SER B 336 " pdb=" OD1 ASP B 338 " model vdw 2.336 2.440 nonbonded pdb=" O GLU A 207 " pdb=" NE1 TRP A 211 " model vdw 2.344 2.520 ... (remaining 70269 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 2.330 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.370 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.006 0.209 9086 Z= 0.349 Angle : 0.711 14.954 12322 Z= 0.414 Chirality : 0.285 5.517 1407 Planarity : 0.004 0.049 1553 Dihedral : 13.645 146.402 3295 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.73 % Allowed : 6.96 % Favored : 92.31 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.23), residues: 1107 helix: -0.24 (0.24), residues: 382 sheet: -0.81 (0.30), residues: 268 loop : -2.01 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 104 HIS 0.002 0.001 HIS R 128 PHE 0.006 0.001 PHE A 189 TYR 0.011 0.001 TYR R 345 ARG 0.004 0.000 ARG R 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 355 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6439 (mt-10) REVERT: A 24 GLN cc_start: 0.7081 (tp40) cc_final: 0.6633 (mm-40) REVERT: A 306 TYR cc_start: 0.7034 (m-80) cc_final: 0.6720 (m-80) REVERT: A 336 THR cc_start: 0.8119 (p) cc_final: 0.7851 (t) REVERT: A 348 ASP cc_start: 0.7560 (t0) cc_final: 0.7307 (t0) REVERT: A 352 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7825 (mm-40) REVERT: B 51 ARG cc_start: 0.7008 (ptm160) cc_final: 0.6525 (ptm-80) REVERT: B 123 ASP cc_start: 0.7153 (p0) cc_final: 0.6756 (t0) REVERT: B 214 LYS cc_start: 0.7896 (mttt) cc_final: 0.7660 (mttm) REVERT: B 233 ASP cc_start: 0.6920 (t0) cc_final: 0.6149 (t0) REVERT: B 240 PHE cc_start: 0.7891 (t80) cc_final: 0.7604 (t80) REVERT: B 264 GLN cc_start: 0.7241 (pt0) cc_final: 0.6986 (pt0) REVERT: B 328 ASP cc_start: 0.7704 (p0) cc_final: 0.7412 (p0) REVERT: B 330 MET cc_start: 0.8170 (mmm) cc_final: 0.7950 (tpp) REVERT: E 17 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6615 (tpt-90) REVERT: E 67 PHE cc_start: 0.5764 (m-10) cc_final: 0.5223 (m-10) REVERT: E 112 GLN cc_start: 0.7422 (mm-40) cc_final: 0.6968 (mp10) REVERT: E 244 LYS cc_start: 0.7853 (pttp) cc_final: 0.7482 (tttt) REVERT: G 8 ILE cc_start: 0.7110 (mm) cc_final: 0.6811 (tp) REVERT: G 25 ASP cc_start: 0.6767 (m-30) cc_final: 0.6547 (m-30) REVERT: R 49 PHE cc_start: 0.6969 (t80) cc_final: 0.6610 (t80) REVERT: R 68 ASP cc_start: 0.6084 (p0) cc_final: 0.5470 (p0) REVERT: R 70 ARG cc_start: 0.6482 (mmt180) cc_final: 0.5853 (mmm-85) REVERT: R 77 LEU cc_start: 0.7529 (mt) cc_final: 0.7129 (mt) REVERT: R 82 VAL cc_start: 0.7577 (m) cc_final: 0.7332 (p) REVERT: R 88 LEU cc_start: 0.7356 (mt) cc_final: 0.7060 (mt) REVERT: R 94 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7649 (t0) REVERT: R 109 LEU cc_start: 0.5051 (tp) cc_final: 0.4733 (tp) REVERT: R 116 TYR cc_start: 0.6277 (t80) cc_final: 0.6045 (t80) REVERT: R 143 PRO cc_start: 0.6886 (Cg_exo) cc_final: 0.6481 (Cg_endo) REVERT: R 147 ARG cc_start: 0.5450 (OUTLIER) cc_final: 0.5057 (ttm-80) REVERT: R 167 LEU cc_start: 0.6888 (mt) cc_final: 0.6640 (mt) REVERT: R 250 TRP cc_start: 0.5496 (m100) cc_final: 0.3844 (t60) REVERT: R 272 ARG cc_start: 0.5724 (tmm-80) cc_final: 0.4372 (tpp-160) REVERT: R 299 VAL cc_start: 0.7625 (t) cc_final: 0.7388 (t) REVERT: R 331 TYR cc_start: 0.6871 (t80) cc_final: 0.6164 (t80) REVERT: R 335 TYR cc_start: 0.8285 (m-80) cc_final: 0.8036 (m-10) REVERT: R 356 ASN cc_start: 0.7415 (m-40) cc_final: 0.6452 (m-40) REVERT: R 361 LYS cc_start: 0.7199 (mtpp) cc_final: 0.6175 (mmtp) outliers start: 7 outliers final: 0 residues processed: 360 average time/residue: 0.2809 time to fit residues: 128.4552 Evaluate side-chains 216 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 147 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 190 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN B 22 GLN B 49 GLN B 80 GLN B 180 GLN B 235 ASN E 2 GLN E 34 HIS E 38 GLN E 142 GLN E 179 GLN R 74 ASN R 334 GLN R 342 GLN R 356 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9086 Z= 0.270 Angle : 0.937 27.283 12322 Z= 0.388 Chirality : 0.107 2.484 1407 Planarity : 0.005 0.043 1553 Dihedral : 9.014 174.079 1271 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 3.64 % Allowed : 14.97 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1107 helix: 1.16 (0.26), residues: 373 sheet: -0.47 (0.29), residues: 283 loop : -1.34 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 87 HIS 0.006 0.002 HIS B 188 PHE 0.015 0.002 PHE B 204 TYR 0.022 0.002 TYR E 190 ARG 0.006 0.001 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 215 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7301 (tp30) REVERT: A 21 LYS cc_start: 0.7321 (mtpt) cc_final: 0.7083 (pttt) REVERT: A 24 GLN cc_start: 0.7517 (tp40) cc_final: 0.6547 (mm-40) REVERT: A 31 ARG cc_start: 0.7814 (ttm-80) cc_final: 0.7441 (mtt-85) REVERT: A 43 ASN cc_start: 0.6961 (OUTLIER) cc_final: 0.6739 (p0) REVERT: A 261 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7309 (mt0) REVERT: A 348 ASP cc_start: 0.7756 (t0) cc_final: 0.7345 (t0) REVERT: A 352 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7944 (mm-40) REVERT: B 123 ASP cc_start: 0.7544 (p0) cc_final: 0.7171 (t0) REVERT: B 135 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6954 (mp0) REVERT: B 169 THR cc_start: 0.7602 (m) cc_final: 0.7258 (p) REVERT: B 214 LYS cc_start: 0.7981 (mttt) cc_final: 0.7731 (mttm) REVERT: B 228 THR cc_start: 0.8313 (OUTLIER) cc_final: 0.7782 (t) REVERT: B 232 SER cc_start: 0.8311 (t) cc_final: 0.7600 (p) REVERT: B 233 ASP cc_start: 0.6752 (t0) cc_final: 0.5814 (p0) REVERT: B 251 ASP cc_start: 0.8524 (m-30) cc_final: 0.8198 (m-30) REVERT: B 285 LYS cc_start: 0.7916 (tttm) cc_final: 0.7477 (tttt) REVERT: B 289 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8251 (pp) REVERT: B 328 ASP cc_start: 0.7951 (p0) cc_final: 0.7519 (p0) REVERT: B 330 MET cc_start: 0.8258 (mmm) cc_final: 0.7929 (mmt) REVERT: B 339 SER cc_start: 0.8369 (m) cc_final: 0.8041 (p) REVERT: E 17 ARG cc_start: 0.7171 (tpp80) cc_final: 0.6748 (tpt-90) REVERT: E 112 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6664 (mp10) REVERT: E 244 LYS cc_start: 0.7939 (pttp) cc_final: 0.7533 (tttt) REVERT: G 47 ASP cc_start: 0.8075 (t0) cc_final: 0.7814 (t0) REVERT: R 35 LEU cc_start: 0.5848 (mt) cc_final: 0.5419 (tp) REVERT: R 49 PHE cc_start: 0.7038 (t80) cc_final: 0.6550 (t80) REVERT: R 70 ARG cc_start: 0.6419 (mmt180) cc_final: 0.5901 (mmm-85) REVERT: R 250 TRP cc_start: 0.5630 (m100) cc_final: 0.4049 (t60) REVERT: R 272 ARG cc_start: 0.6097 (tmm-80) cc_final: 0.4500 (tpp-160) REVERT: R 331 TYR cc_start: 0.6657 (t80) cc_final: 0.6237 (t80) REVERT: R 356 ASN cc_start: 0.7959 (m110) cc_final: 0.7092 (m110) REVERT: R 361 LYS cc_start: 0.7252 (mtpp) cc_final: 0.6478 (mtpp) outliers start: 35 outliers final: 13 residues processed: 240 average time/residue: 0.2544 time to fit residues: 79.8563 Evaluate side-chains 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 183 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 38 GLN Chi-restraints excluded: chain E residue 75 LYS Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 329 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 81 optimal weight: 0.0070 chunk 99 optimal weight: 0.0670 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9086 Z= 0.167 Angle : 0.878 26.564 12322 Z= 0.351 Chirality : 0.101 2.204 1407 Planarity : 0.004 0.045 1553 Dihedral : 8.468 170.818 1265 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.35 % Favored : 97.56 % Rotamer: Outliers : 2.81 % Allowed : 19.44 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.25), residues: 1107 helix: 1.75 (0.27), residues: 371 sheet: -0.24 (0.29), residues: 287 loop : -1.14 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 87 HIS 0.003 0.001 HIS B 147 PHE 0.022 0.001 PHE R 93 TYR 0.011 0.001 TYR E 102 ARG 0.005 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 196 time to evaluate : 1.239 Fit side-chains REVERT: A 24 GLN cc_start: 0.7498 (tp40) cc_final: 0.6951 (mm-40) REVERT: A 241 LYS cc_start: 0.8450 (tmtt) cc_final: 0.8019 (ttmm) REVERT: A 348 ASP cc_start: 0.7721 (t0) cc_final: 0.7065 (t0) REVERT: A 352 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7822 (mm-40) REVERT: B 9 LEU cc_start: 0.4306 (OUTLIER) cc_final: 0.3838 (mm) REVERT: B 49 GLN cc_start: 0.7409 (OUTLIER) cc_final: 0.6999 (mm110) REVERT: B 123 ASP cc_start: 0.7521 (p0) cc_final: 0.7159 (t0) REVERT: B 135 GLU cc_start: 0.7221 (mm-30) cc_final: 0.6862 (mp0) REVERT: B 169 THR cc_start: 0.7828 (m) cc_final: 0.7389 (p) REVERT: B 217 ASP cc_start: 0.7566 (m-30) cc_final: 0.7358 (t70) REVERT: B 228 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7895 (t) REVERT: B 233 ASP cc_start: 0.6685 (t0) cc_final: 0.5727 (p0) REVERT: B 264 GLN cc_start: 0.8214 (pt0) cc_final: 0.7948 (pt0) REVERT: B 285 LYS cc_start: 0.7893 (tttm) cc_final: 0.7338 (tttt) REVERT: B 330 MET cc_start: 0.8308 (mmm) cc_final: 0.7954 (mmt) REVERT: B 334 THR cc_start: 0.9020 (m) cc_final: 0.8430 (p) REVERT: B 339 SER cc_start: 0.8239 (m) cc_final: 0.7904 (p) REVERT: E 17 ARG cc_start: 0.7287 (tpp80) cc_final: 0.6787 (tpt-90) REVERT: E 33 MET cc_start: 0.8699 (mmp) cc_final: 0.8483 (mmt) REVERT: E 244 LYS cc_start: 0.8010 (pttp) cc_final: 0.7461 (tttt) REVERT: R 35 LEU cc_start: 0.5825 (mt) cc_final: 0.5394 (tp) REVERT: R 49 PHE cc_start: 0.6969 (t80) cc_final: 0.6518 (t80) REVERT: R 70 ARG cc_start: 0.6276 (mmt180) cc_final: 0.5881 (mmm-85) REVERT: R 123 TYR cc_start: 0.7224 (m-80) cc_final: 0.7004 (m-80) REVERT: R 167 LEU cc_start: 0.6863 (mt) cc_final: 0.6467 (mt) REVERT: R 248 MET cc_start: 0.6962 (ppp) cc_final: 0.6677 (ppp) REVERT: R 272 ARG cc_start: 0.5827 (tmm-80) cc_final: 0.4013 (tpp-160) REVERT: R 356 ASN cc_start: 0.7810 (m110) cc_final: 0.6767 (m-40) REVERT: R 361 LYS cc_start: 0.7079 (mtpp) cc_final: 0.6096 (mmtp) outliers start: 27 outliers final: 14 residues processed: 208 average time/residue: 0.2542 time to fit residues: 69.9679 Evaluate side-chains 191 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 228 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 9.9990 chunk 52 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 101 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN B 22 GLN B 244 ASN E 179 GLN G 43 HIS R 293 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 9086 Z= 0.320 Angle : 0.942 26.372 12322 Z= 0.392 Chirality : 0.099 2.114 1407 Planarity : 0.005 0.045 1553 Dihedral : 8.943 162.619 1265 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.52 % Favored : 96.39 % Rotamer: Outliers : 4.78 % Allowed : 21.31 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1107 helix: 1.49 (0.27), residues: 380 sheet: -0.26 (0.30), residues: 276 loop : -0.99 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 104 HIS 0.007 0.002 HIS B 147 PHE 0.018 0.002 PHE E 109 TYR 0.026 0.002 TYR E 190 ARG 0.005 0.001 ARG A 284 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 176 time to evaluate : 1.054 Fit side-chains REVERT: A 24 GLN cc_start: 0.7616 (tp40) cc_final: 0.6894 (mm-40) REVERT: A 31 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7465 (mtt-85) REVERT: A 310 LYS cc_start: 0.7881 (tppt) cc_final: 0.7407 (ttpt) REVERT: A 348 ASP cc_start: 0.7793 (t0) cc_final: 0.7283 (t0) REVERT: B 9 LEU cc_start: 0.4169 (OUTLIER) cc_final: 0.3674 (mm) REVERT: B 123 ASP cc_start: 0.7621 (p0) cc_final: 0.7400 (t0) REVERT: B 135 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6928 (mp0) REVERT: B 169 THR cc_start: 0.8622 (m) cc_final: 0.8266 (p) REVERT: B 217 ASP cc_start: 0.7752 (m-30) cc_final: 0.7499 (t70) REVERT: B 233 ASP cc_start: 0.6658 (t0) cc_final: 0.6431 (t0) REVERT: B 267 MET cc_start: 0.7579 (tpp) cc_final: 0.7372 (ttt) REVERT: B 285 LYS cc_start: 0.7837 (tttm) cc_final: 0.7395 (tttt) REVERT: B 308 ASP cc_start: 0.7758 (p0) cc_final: 0.7444 (p0) REVERT: B 330 MET cc_start: 0.8134 (mmm) cc_final: 0.7853 (mmt) REVERT: B 339 SER cc_start: 0.8754 (m) cc_final: 0.8540 (p) REVERT: E 231 GLN cc_start: 0.8969 (pp30) cc_final: 0.8158 (pp30) REVERT: E 244 LYS cc_start: 0.8024 (pttp) cc_final: 0.7471 (tttt) REVERT: G 18 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8383 (mp) REVERT: R 35 LEU cc_start: 0.5564 (mt) cc_final: 0.5152 (tp) REVERT: R 70 ARG cc_start: 0.6063 (mmt180) cc_final: 0.5733 (mmm-85) REVERT: R 356 ASN cc_start: 0.7987 (m110) cc_final: 0.7211 (m-40) REVERT: R 361 LYS cc_start: 0.7395 (mtpp) cc_final: 0.6245 (mmtp) outliers start: 46 outliers final: 27 residues processed: 202 average time/residue: 0.2222 time to fit residues: 60.6803 Evaluate side-chains 189 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 160 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 158 ASP Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 75 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 0.0870 chunk 44 optimal weight: 6.9990 chunk 91 optimal weight: 0.0770 chunk 74 optimal weight: 9.9990 chunk 0 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN R 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9086 Z= 0.137 Angle : 0.874 25.669 12322 Z= 0.347 Chirality : 0.097 2.125 1407 Planarity : 0.004 0.041 1553 Dihedral : 8.496 163.024 1265 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 2.91 % Allowed : 22.56 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.25), residues: 1107 helix: 1.84 (0.27), residues: 373 sheet: -0.06 (0.30), residues: 283 loop : -0.85 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 302 HIS 0.003 0.001 HIS R 315 PHE 0.016 0.001 PHE B 204 TYR 0.013 0.001 TYR R 345 ARG 0.007 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.055 Fit side-chains REVERT: A 24 GLN cc_start: 0.7549 (tp40) cc_final: 0.6860 (mm-40) REVERT: A 348 ASP cc_start: 0.7810 (t0) cc_final: 0.7344 (t0) REVERT: B 169 THR cc_start: 0.8501 (m) cc_final: 0.8157 (p) REVERT: B 254 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7972 (t) REVERT: B 285 LYS cc_start: 0.7787 (tttm) cc_final: 0.7455 (ttmt) REVERT: B 330 MET cc_start: 0.8143 (mmm) cc_final: 0.7845 (mmt) REVERT: B 339 SER cc_start: 0.8418 (m) cc_final: 0.8165 (p) REVERT: E 183 GLN cc_start: 0.5737 (mt0) cc_final: 0.5390 (mt0) REVERT: E 231 GLN cc_start: 0.8851 (pp30) cc_final: 0.8157 (pp30) REVERT: E 244 LYS cc_start: 0.8077 (pttp) cc_final: 0.7543 (tttt) REVERT: R 35 LEU cc_start: 0.5531 (mt) cc_final: 0.5107 (tp) REVERT: R 70 ARG cc_start: 0.6017 (mmt180) cc_final: 0.5700 (mmm-85) REVERT: R 248 MET cc_start: 0.7028 (ppp) cc_final: 0.6613 (ppp) REVERT: R 329 MET cc_start: 0.4587 (OUTLIER) cc_final: 0.4325 (mtt) REVERT: R 334 GLN cc_start: 0.7665 (OUTLIER) cc_final: 0.7113 (tp-100) REVERT: R 356 ASN cc_start: 0.7690 (m110) cc_final: 0.6873 (m-40) REVERT: R 361 LYS cc_start: 0.7149 (mtpp) cc_final: 0.6151 (mmtp) outliers start: 28 outliers final: 13 residues processed: 187 average time/residue: 0.2218 time to fit residues: 56.7849 Evaluate side-chains 182 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 107 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN E 38 GLN R 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9086 Z= 0.161 Angle : 0.876 26.002 12322 Z= 0.350 Chirality : 0.098 2.125 1407 Planarity : 0.004 0.042 1553 Dihedral : 8.402 162.397 1265 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 3.64 % Allowed : 22.97 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1107 helix: 1.83 (0.27), residues: 375 sheet: 0.05 (0.30), residues: 278 loop : -0.66 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 302 HIS 0.003 0.001 HIS B 147 PHE 0.013 0.001 PHE B 204 TYR 0.019 0.001 TYR R 345 ARG 0.006 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7573 (tp-100) cc_final: 0.6813 (mm-40) REVERT: A 31 ARG cc_start: 0.7722 (ttm-80) cc_final: 0.7360 (mtt-85) REVERT: A 348 ASP cc_start: 0.7756 (t0) cc_final: 0.7314 (t0) REVERT: B 9 LEU cc_start: 0.4165 (OUTLIER) cc_final: 0.3647 (mm) REVERT: B 169 THR cc_start: 0.8522 (m) cc_final: 0.8160 (p) REVERT: B 223 CYS cc_start: 0.7438 (p) cc_final: 0.7090 (p) REVERT: B 254 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8332 (t) REVERT: B 285 LYS cc_start: 0.7790 (tttm) cc_final: 0.7447 (ttmt) REVERT: B 309 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7476 (ttt180) REVERT: B 330 MET cc_start: 0.8209 (mmm) cc_final: 0.7895 (mmt) REVERT: E 183 GLN cc_start: 0.5893 (mt0) cc_final: 0.5552 (mt0) REVERT: E 231 GLN cc_start: 0.8838 (pp30) cc_final: 0.8173 (pp30) REVERT: E 244 LYS cc_start: 0.8081 (pttp) cc_final: 0.7552 (tttt) REVERT: R 35 LEU cc_start: 0.5517 (mt) cc_final: 0.5094 (tp) REVERT: R 70 ARG cc_start: 0.5922 (mmt180) cc_final: 0.5720 (mmm-85) REVERT: R 248 MET cc_start: 0.6959 (ppp) cc_final: 0.6554 (ppp) REVERT: R 329 MET cc_start: 0.4603 (OUTLIER) cc_final: 0.4290 (mtp) REVERT: R 334 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7284 (tp-100) REVERT: R 356 ASN cc_start: 0.7671 (m110) cc_final: 0.6881 (m-40) REVERT: R 361 LYS cc_start: 0.7128 (mtpp) cc_final: 0.6126 (mmtp) outliers start: 35 outliers final: 18 residues processed: 194 average time/residue: 0.2250 time to fit residues: 58.7677 Evaluate side-chains 183 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 0.0770 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 GLN R 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9086 Z= 0.195 Angle : 0.888 25.979 12322 Z= 0.357 Chirality : 0.098 2.127 1407 Planarity : 0.004 0.043 1553 Dihedral : 8.443 164.126 1265 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 4.05 % Allowed : 23.70 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1107 helix: 1.83 (0.27), residues: 374 sheet: -0.01 (0.30), residues: 280 loop : -0.59 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.014 0.001 PHE E 67 TYR 0.018 0.001 TYR R 345 ARG 0.005 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7566 (tp-100) cc_final: 0.6828 (mm-40) REVERT: A 31 ARG cc_start: 0.7731 (ttm-80) cc_final: 0.7354 (mtt-85) REVERT: A 348 ASP cc_start: 0.7826 (t0) cc_final: 0.7404 (t0) REVERT: A 356 ARG cc_start: 0.7059 (ttm-80) cc_final: 0.6797 (mtp-110) REVERT: B 9 LEU cc_start: 0.4157 (OUTLIER) cc_final: 0.3642 (mm) REVERT: B 169 THR cc_start: 0.8614 (m) cc_final: 0.8255 (p) REVERT: B 223 CYS cc_start: 0.7514 (p) cc_final: 0.7162 (p) REVERT: B 285 LYS cc_start: 0.7777 (tttm) cc_final: 0.7354 (tttt) REVERT: B 309 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7537 (ttt180) REVERT: B 330 MET cc_start: 0.8249 (mmm) cc_final: 0.7939 (mmt) REVERT: E 183 GLN cc_start: 0.6067 (mt0) cc_final: 0.5769 (mt0) REVERT: E 231 GLN cc_start: 0.8843 (pp30) cc_final: 0.8160 (pp30) REVERT: E 244 LYS cc_start: 0.8074 (pttp) cc_final: 0.7555 (tttt) REVERT: G 57 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6947 (mp0) REVERT: R 35 LEU cc_start: 0.5387 (mt) cc_final: 0.5011 (tp) REVERT: R 70 ARG cc_start: 0.6239 (mmt180) cc_final: 0.5996 (mmm-85) REVERT: R 102 ARG cc_start: 0.3298 (OUTLIER) cc_final: 0.1474 (tpt170) REVERT: R 334 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7367 (tp-100) REVERT: R 356 ASN cc_start: 0.7718 (m110) cc_final: 0.6921 (m-40) outliers start: 39 outliers final: 25 residues processed: 191 average time/residue: 0.2388 time to fit residues: 60.8970 Evaluate side-chains 187 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 158 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 84 optimal weight: 0.0970 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 0.0470 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9086 Z= 0.148 Angle : 0.878 25.759 12322 Z= 0.349 Chirality : 0.098 2.134 1407 Planarity : 0.004 0.042 1553 Dihedral : 8.353 162.590 1265 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.80 % Favored : 97.11 % Rotamer: Outliers : 3.53 % Allowed : 24.95 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.26), residues: 1107 helix: 1.93 (0.27), residues: 373 sheet: 0.13 (0.30), residues: 272 loop : -0.61 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 302 HIS 0.004 0.001 HIS R 315 PHE 0.014 0.001 PHE B 204 TYR 0.018 0.001 TYR R 345 ARG 0.005 0.000 ARG B 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7519 (tp-100) cc_final: 0.6781 (mm-40) REVERT: A 31 ARG cc_start: 0.7694 (ttm-80) cc_final: 0.7326 (mtt-85) REVERT: A 261 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7571 (mt0) REVERT: A 348 ASP cc_start: 0.7835 (t0) cc_final: 0.7505 (t0) REVERT: B 9 LEU cc_start: 0.4129 (OUTLIER) cc_final: 0.3634 (mm) REVERT: B 169 THR cc_start: 0.8554 (m) cc_final: 0.8201 (p) REVERT: B 223 CYS cc_start: 0.7487 (p) cc_final: 0.7127 (p) REVERT: B 285 LYS cc_start: 0.7757 (tttm) cc_final: 0.7428 (ttmt) REVERT: B 330 MET cc_start: 0.8232 (mmm) cc_final: 0.7922 (mmt) REVERT: E 183 GLN cc_start: 0.6004 (mt0) cc_final: 0.5656 (mt0) REVERT: E 231 GLN cc_start: 0.8819 (pp30) cc_final: 0.8163 (pp30) REVERT: E 244 LYS cc_start: 0.8076 (pttp) cc_final: 0.7566 (tttt) REVERT: G 57 GLU cc_start: 0.7197 (mt-10) cc_final: 0.6997 (mp0) REVERT: R 35 LEU cc_start: 0.5453 (mt) cc_final: 0.5064 (tp) REVERT: R 70 ARG cc_start: 0.6212 (mmt180) cc_final: 0.5966 (mmm-85) REVERT: R 102 ARG cc_start: 0.2834 (OUTLIER) cc_final: 0.1153 (tpp-160) REVERT: R 140 ILE cc_start: 0.8054 (mm) cc_final: 0.7674 (mm) REVERT: R 248 MET cc_start: 0.7148 (ppp) cc_final: 0.6714 (ppp) REVERT: R 329 MET cc_start: 0.4781 (OUTLIER) cc_final: 0.4400 (mtp) REVERT: R 334 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7303 (tp-100) REVERT: R 356 ASN cc_start: 0.7652 (m110) cc_final: 0.6839 (m-40) outliers start: 34 outliers final: 22 residues processed: 191 average time/residue: 0.2312 time to fit residues: 59.5059 Evaluate side-chains 184 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 99 optimal weight: 0.0020 chunk 65 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.5970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9086 Z= 0.232 Angle : 0.902 25.941 12322 Z= 0.367 Chirality : 0.098 2.128 1407 Planarity : 0.004 0.044 1553 Dihedral : 8.456 163.924 1265 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 3.43 % Allowed : 25.47 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.26), residues: 1107 helix: 1.74 (0.27), residues: 379 sheet: -0.01 (0.30), residues: 270 loop : -0.53 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 87 HIS 0.004 0.001 HIS B 147 PHE 0.019 0.001 PHE R 49 TYR 0.025 0.001 TYR R 345 ARG 0.008 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7461 (tp-100) cc_final: 0.6971 (mm110) REVERT: A 31 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7351 (mtt-85) REVERT: A 261 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7599 (mt0) REVERT: A 348 ASP cc_start: 0.7881 (t0) cc_final: 0.7550 (t0) REVERT: B 9 LEU cc_start: 0.4147 (OUTLIER) cc_final: 0.3623 (mm) REVERT: B 169 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8320 (p) REVERT: B 223 CYS cc_start: 0.7543 (p) cc_final: 0.7194 (p) REVERT: B 285 LYS cc_start: 0.7814 (tttm) cc_final: 0.7381 (tttt) REVERT: B 330 MET cc_start: 0.8286 (mmm) cc_final: 0.7972 (mmt) REVERT: E 183 GLN cc_start: 0.6278 (mt0) cc_final: 0.5997 (mt0) REVERT: E 231 GLN cc_start: 0.8844 (pp30) cc_final: 0.8166 (pp30) REVERT: E 244 LYS cc_start: 0.8110 (pttp) cc_final: 0.7597 (tttt) REVERT: R 35 LEU cc_start: 0.5476 (mt) cc_final: 0.5063 (tp) REVERT: R 70 ARG cc_start: 0.6252 (mmt180) cc_final: 0.5995 (mmm-85) REVERT: R 102 ARG cc_start: 0.2831 (OUTLIER) cc_final: 0.1139 (tpp-160) REVERT: R 248 MET cc_start: 0.7148 (ppp) cc_final: 0.6750 (ppp) REVERT: R 329 MET cc_start: 0.4836 (OUTLIER) cc_final: 0.4422 (mtp) REVERT: R 356 ASN cc_start: 0.7667 (m110) cc_final: 0.6835 (m-40) outliers start: 33 outliers final: 26 residues processed: 182 average time/residue: 0.2219 time to fit residues: 54.7188 Evaluate side-chains 186 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 48 LEU Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 308 ILE Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 361 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 69 optimal weight: 0.0070 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN R 334 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.6002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9086 Z= 0.172 Angle : 0.897 25.761 12322 Z= 0.360 Chirality : 0.098 2.130 1407 Planarity : 0.004 0.043 1553 Dihedral : 8.411 165.854 1265 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.07 % Favored : 96.84 % Rotamer: Outliers : 3.12 % Allowed : 25.78 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.26), residues: 1107 helix: 1.77 (0.27), residues: 378 sheet: 0.10 (0.30), residues: 268 loop : -0.51 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 302 HIS 0.003 0.001 HIS B 147 PHE 0.016 0.001 PHE R 314 TYR 0.021 0.001 TYR R 345 ARG 0.009 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLN cc_start: 0.7464 (tp-100) cc_final: 0.6773 (mm-40) REVERT: A 31 ARG cc_start: 0.7727 (ttm-80) cc_final: 0.7365 (mtt-85) REVERT: A 348 ASP cc_start: 0.7807 (t0) cc_final: 0.7490 (t0) REVERT: B 9 LEU cc_start: 0.4205 (OUTLIER) cc_final: 0.3707 (mm) REVERT: B 169 THR cc_start: 0.8595 (OUTLIER) cc_final: 0.8249 (p) REVERT: B 223 CYS cc_start: 0.7539 (p) cc_final: 0.7191 (p) REVERT: B 285 LYS cc_start: 0.7768 (tttm) cc_final: 0.7414 (tttt) REVERT: B 330 MET cc_start: 0.8253 (mmm) cc_final: 0.7952 (mmt) REVERT: E 88 GLU cc_start: 0.7257 (pp20) cc_final: 0.6095 (tm-30) REVERT: E 183 GLN cc_start: 0.6322 (mt0) cc_final: 0.5978 (mt0) REVERT: E 231 GLN cc_start: 0.8818 (pp30) cc_final: 0.8158 (pp30) REVERT: E 244 LYS cc_start: 0.8081 (pttp) cc_final: 0.7543 (tttt) REVERT: R 35 LEU cc_start: 0.5237 (mt) cc_final: 0.4819 (tp) REVERT: R 70 ARG cc_start: 0.6173 (mmt180) cc_final: 0.5875 (mmm-85) REVERT: R 88 LEU cc_start: 0.7630 (mt) cc_final: 0.6995 (mt) REVERT: R 102 ARG cc_start: 0.2825 (OUTLIER) cc_final: 0.1088 (tpp-160) REVERT: R 248 MET cc_start: 0.7125 (ppp) cc_final: 0.6775 (ppp) REVERT: R 356 ASN cc_start: 0.7587 (m110) cc_final: 0.6709 (m-40) outliers start: 30 outliers final: 27 residues processed: 179 average time/residue: 0.2241 time to fit residues: 54.3659 Evaluate side-chains 187 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 9 LEU Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 169 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 TRP Chi-restraints excluded: chain B residue 301 VAL Chi-restraints excluded: chain B residue 312 VAL Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain E residue 5 GLU Chi-restraints excluded: chain E residue 29 SER Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 102 ARG Chi-restraints excluded: chain R residue 109 LEU Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 264 SER Chi-restraints excluded: chain R residue 301 LEU Chi-restraints excluded: chain R residue 305 LEU Chi-restraints excluded: chain R residue 329 MET Chi-restraints excluded: chain R residue 334 GLN Chi-restraints excluded: chain R residue 361 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 90 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 334 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.153197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116748 restraints weight = 12429.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116342 restraints weight = 10118.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118018 restraints weight = 9713.031| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.6443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9086 Z= 0.383 Angle : 0.975 26.087 12322 Z= 0.413 Chirality : 0.100 2.112 1407 Planarity : 0.005 0.046 1553 Dihedral : 8.762 165.745 1265 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 3.64 % Allowed : 26.09 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.25), residues: 1107 helix: 1.35 (0.27), residues: 380 sheet: -0.31 (0.30), residues: 276 loop : -0.54 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 104 HIS 0.007 0.002 HIS B 147 PHE 0.015 0.002 PHE E 67 TYR 0.028 0.002 TYR E 190 ARG 0.007 0.001 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2180.60 seconds wall clock time: 40 minutes 33.67 seconds (2433.67 seconds total)