Starting phenix.real_space_refine on Fri Jan 19 00:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iuk_35724/01_2024/8iuk_35724_updated.pdb" } resolution = 2.67 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= 0.005 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 70 5.16 5 C 6305 2.51 5 N 1716 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 205": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 250": "NH1" <-> "NH2" Residue "A ARG 354": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "E ARG 160": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 308": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9951 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1873 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 4, 'TRANS': 222} Chain breaks: 2 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: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2339 Unusual residues: {'UGU': 1} Classifications: {'peptide': 293, 'undetermined': 1} Link IDs: {'PTRANS': 5, 'TRANS': 287, None: 1} Not linked: pdbres="CYS R 323 " pdbres="UGU R 401 " Chain breaks: 1 Time building chain proxies: 5.23, per 1000 atoms: 0.53 Number of scatterers: 9951 At special positions: 0 Unit cell: (123.6, 91.464, 131.84, 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 70 16.00 O 1860 8.00 N 1716 7.00 C 6305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.02 Conformation dependent library (CDL) restraints added in 1.9 seconds 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2364 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 31.6% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 4.048A pdb=" N VAL A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 231 through 244 removed outlier: 4.433A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 297 through 314 Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'B' and resid 9 through 29 Processing helix chain 'B' and resid 35 through 38 No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'E' and resid 52 through 54 No H-bonds generated for 'chain 'E' and resid 52 through 54' Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 29 through 46 removed outlier: 4.793A pdb=" N LYS G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 30 through 60 removed outlier: 4.735A pdb=" N PHE R 36 " --> pdb=" O PHE R 32 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG R 57 " --> pdb=" O LYS R 53 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N GLN R 60 " --> pdb=" O GLN R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 94 removed outlier: 3.848A pdb=" N SER R 94 " --> pdb=" O PHE R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 101 No H-bonds generated for 'chain 'R' and resid 98 through 101' Processing helix chain 'R' and resid 107 through 138 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 140 through 144 Processing helix chain 'R' and resid 149 through 167 Processing helix chain 'R' and resid 171 through 173 No H-bonds generated for 'chain 'R' and resid 171 through 173' Processing helix chain 'R' and resid 196 through 233 Processing helix chain 'R' and resid 245 through 278 removed outlier: 3.513A pdb=" N CYS R 256 " --> pdb=" O LEU R 252 " (cutoff:3.500A) Proline residue: R 264 - end of helix removed outlier: 7.525A pdb=" N ASN R 277 " --> pdb=" O GLY R 273 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N HIS R 278 " --> pdb=" O ILE R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'R' and resid 300 through 304 Processing helix chain 'R' and resid 309 through 322 Processing sheet with id= A, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.581A pdb=" N TYR A 325 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA A 220 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A 201 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY A 46 " --> pdb=" O VAL A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.910A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS B 96 " --> pdb=" O ILE B 86 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 105 through 110 removed outlier: 7.166A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.890A 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: 6.917A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 164 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 172 " --> pdb=" O THR B 164 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.528A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.521A pdb=" N GLY B 249 " --> pdb=" O ASN B 235 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE B 237 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ALA B 247 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE B 239 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ALA B 245 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.286A 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: 6.768A pdb=" N GLY B 293 " --> pdb=" O THR B 279 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 281 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LEU B 291 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N PHE B 283 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N LEU B 289 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 311 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.038A 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 56 removed outlier: 7.019A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (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 9 through 11 removed outlier: 3.698A pdb=" N ALA E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG E 37 " --> pdb=" O TRP E 46 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TRP E 46 " --> pdb=" O ARG E 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.827A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 243 through 245 removed outlier: 3.682A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.813A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.623A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1290 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: 2.82 Time building geometry restraints manager: 4.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2067 1.33 - 1.45: 2408 1.45 - 1.57: 5568 1.57 - 1.69: 3 1.69 - 1.81: 100 Bond restraints: 10146 Sorted by residual: bond pdb=" C12 UGU R 401 " pdb=" C8 UGU R 401 " ideal model delta sigma weight residual 1.671 1.347 0.324 2.00e-02 2.50e+03 2.62e+02 bond pdb=" C11 UGU R 401 " pdb=" C12 UGU R 401 " ideal model delta sigma weight residual 1.306 1.591 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C10 UGU R 401 " pdb=" C11 UGU R 401 " ideal model delta sigma weight residual 1.711 1.588 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C7 UGU R 401 " pdb=" C8 UGU R 401 " ideal model delta sigma weight residual 1.405 1.519 -0.114 2.00e-02 2.50e+03 3.26e+01 bond pdb=" CA GLU A 14 " pdb=" C GLU A 14 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.30e-02 5.92e+03 2.76e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.38: 274 107.38 - 114.04: 5735 114.04 - 120.69: 4127 120.69 - 127.34: 3484 127.34 - 133.99: 98 Bond angle restraints: 13718 Sorted by residual: angle pdb=" C5 UGU R 401 " pdb=" C6 UGU R 401 " pdb=" C7 UGU R 401 " ideal model delta sigma weight residual 152.65 119.50 33.15 3.00e+00 1.11e-01 1.22e+02 angle pdb=" N ALA A 13 " pdb=" CA ALA A 13 " pdb=" C ALA A 13 " ideal model delta sigma weight residual 111.36 104.11 7.25 1.09e+00 8.42e-01 4.43e+01 angle pdb=" N LYS A 16 " pdb=" CA LYS A 16 " pdb=" C LYS A 16 " ideal model delta sigma weight residual 112.68 104.22 8.46 1.33e+00 5.65e-01 4.04e+01 angle pdb=" O ALA A 13 " pdb=" C ALA A 13 " pdb=" N GLU A 14 " ideal model delta sigma weight residual 122.15 128.35 -6.20 1.14e+00 7.69e-01 2.96e+01 angle pdb=" CA ALA A 13 " pdb=" C ALA A 13 " pdb=" N GLU A 14 " ideal model delta sigma weight residual 117.39 111.05 6.34 1.24e+00 6.50e-01 2.62e+01 ... (remaining 13713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 5910 21.70 - 43.41: 111 43.41 - 65.11: 12 65.11 - 86.81: 4 86.81 - 108.52: 1 Dihedral angle restraints: 6038 sinusoidal: 2371 harmonic: 3667 Sorted by residual: dihedral pdb=" C2 UGU R 401 " pdb=" C3 UGU R 401 " pdb=" C4 UGU R 401 " pdb=" C5 UGU R 401 " ideal model delta sinusoidal sigma weight residual 113.76 -137.72 -108.52 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CB MET R 292 " pdb=" CG MET R 292 " pdb=" SD MET R 292 " pdb=" CE MET R 292 " ideal model delta sinusoidal sigma weight residual -60.00 -0.27 -59.73 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N PHE R 32 " pdb=" CA PHE R 32 " pdb=" CB PHE R 32 " pdb=" CG PHE R 32 " ideal model delta sinusoidal sigma weight residual -60.00 -115.24 55.24 3 1.50e+01 4.44e-03 9.33e+00 ... (remaining 6035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.134: 1550 1.134 - 2.267: 0 2.267 - 3.401: 0 3.401 - 4.534: 0 4.534 - 5.668: 1 Chirality restraints: 1551 Sorted by residual: chirality pdb=" C12 UGU R 401 " pdb=" C11 UGU R 401 " pdb=" C13 UGU R 401 " pdb=" C8 UGU R 401 " both_signs ideal model delta sigma weight residual False -2.72 2.94 -5.67 2.00e-01 2.50e+01 8.03e+02 chirality pdb=" C11 UGU R 401 " pdb=" C10 UGU R 401 " pdb=" C12 UGU R 401 " pdb=" O4 UGU R 401 " both_signs ideal model delta sigma weight residual False 2.50 2.96 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" C8 UGU R 401 " pdb=" C12 UGU R 401 " pdb=" C7 UGU R 401 " pdb=" C9 UGU R 401 " both_signs ideal model delta sigma weight residual False -2.89 -2.53 -0.36 2.00e-01 2.50e+01 3.22e+00 ... (remaining 1548 not shown) Planarity restraints: 1738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG R 291 " 0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C ARG R 291 " -0.041 2.00e-02 2.50e+03 pdb=" O ARG R 291 " 0.015 2.00e-02 2.50e+03 pdb=" N MET R 292 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 16 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C LYS A 16 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS A 16 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 17 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 325 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 326 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 326 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 326 " -0.020 5.00e-02 4.00e+02 ... (remaining 1735 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2580 2.80 - 3.33: 9017 3.33 - 3.85: 16221 3.85 - 4.38: 18258 4.38 - 4.90: 32681 Nonbonded interactions: 78757 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.280 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.283 2.440 nonbonded pdb=" O GLY R 40 " pdb=" ND2 ASN R 44 " model vdw 2.294 2.520 nonbonded pdb=" OE2 GLU B 265 " pdb=" OG1 THR B 268 " model vdw 2.294 2.440 nonbonded pdb=" O GLY R 80 " pdb=" ND2 ASN R 84 " model vdw 2.306 2.520 ... (remaining 78752 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 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: 0.980 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: 4.170 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 29.590 Find NCS groups from input model: 0.290 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:11.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 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 0.324 10146 Z= 0.377 Angle : 0.563 33.149 13718 Z= 0.308 Chirality : 0.150 5.668 1551 Planarity : 0.003 0.037 1738 Dihedral : 8.259 108.518 3665 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 0.37 % Allowed : 4.88 % Favored : 94.75 % 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: -0.68 (0.22), residues: 1248 helix: 1.26 (0.25), residues: 408 sheet: -0.50 (0.29), residues: 288 loop : -1.77 (0.22), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 295 HIS 0.002 0.000 HIS A 322 PHE 0.006 0.001 PHE A 189 TYR 0.006 0.000 TYR E 101 ARG 0.002 0.000 ARG R 133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 394 time to evaluate : 1.206 Fit side-chains REVERT: A 23 LYS cc_start: 0.7132 (mttm) cc_final: 0.6586 (mptt) REVERT: A 26 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 31 LYS cc_start: 0.7647 (mttp) cc_final: 0.7338 (mtpt) REVERT: A 195 ASN cc_start: 0.8152 (m-40) cc_final: 0.7936 (m110) REVERT: A 197 HIS cc_start: 0.5832 (m170) cc_final: 0.5574 (m170) REVERT: A 235 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6390 (tt0) REVERT: A 241 LYS cc_start: 0.7772 (tttt) cc_final: 0.7548 (ttmp) REVERT: A 257 PHE cc_start: 0.7494 (m-10) cc_final: 0.7267 (m-80) REVERT: A 262 ASP cc_start: 0.7449 (p0) cc_final: 0.6955 (p0) REVERT: A 286 THR cc_start: 0.7056 (t) cc_final: 0.6727 (m) REVERT: E 4 VAL cc_start: 0.6784 (t) cc_final: 0.6542 (m) REVERT: E 155 VAL cc_start: 0.8088 (t) cc_final: 0.7823 (t) outliers start: 4 outliers final: 2 residues processed: 395 average time/residue: 1.1891 time to fit residues: 502.3276 Evaluate side-chains 194 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 192 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain E residue 92 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.0040 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 213 GLN A 238 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 336 ASN A 350 GLN B 181 GLN B 235 ASN B 264 GLN B 271 HIS B 273 ASN E 34 HIS E 112 GLN E 142 GLN E 179 GLN E 183 GLN E 186 GLN E 194 ASN N 13 GLN N 39 GLN N 77 ASN R 244 HIS R 250 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10146 Z= 0.246 Angle : 0.642 11.165 13718 Z= 0.320 Chirality : 0.044 0.219 1551 Planarity : 0.004 0.046 1738 Dihedral : 5.789 54.292 1397 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.25 % Allowed : 16.31 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1248 helix: 1.87 (0.25), residues: 406 sheet: -0.01 (0.28), residues: 319 loop : -0.91 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 337 HIS 0.009 0.002 HIS B 147 PHE 0.023 0.002 PHE N 103 TYR 0.025 0.002 TYR E 190 ARG 0.005 0.001 ARG B 261 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 233 time to evaluate : 1.233 Fit side-chains REVERT: A 23 LYS cc_start: 0.7374 (mttm) cc_final: 0.6988 (mptt) REVERT: A 188 LYS cc_start: 0.8172 (mttt) cc_final: 0.7897 (mmtp) REVERT: A 197 HIS cc_start: 0.6731 (m170) cc_final: 0.6429 (m170) REVERT: A 231 ASN cc_start: 0.8143 (m-40) cc_final: 0.7859 (m-40) REVERT: A 286 THR cc_start: 0.7580 (t) cc_final: 0.7268 (m) REVERT: A 315 THR cc_start: 0.7704 (m) cc_final: 0.7465 (p) REVERT: B 18 GLN cc_start: 0.6807 (tm-30) cc_final: 0.6566 (tm-30) REVERT: B 27 ARG cc_start: 0.7085 (ttm170) cc_final: 0.6209 (ttm-80) REVERT: B 64 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.6919 (t80) REVERT: B 135 GLU cc_start: 0.7738 (mp0) cc_final: 0.7525 (mp0) REVERT: B 191 ASP cc_start: 0.6813 (m-30) cc_final: 0.6503 (m-30) REVERT: B 224 ARG cc_start: 0.7556 (mtp85) cc_final: 0.7261 (mtp85) REVERT: B 264 GLN cc_start: 0.7167 (tt0) cc_final: 0.6501 (tt0) REVERT: B 279 THR cc_start: 0.9025 (m) cc_final: 0.8513 (p) REVERT: B 308 ASP cc_start: 0.7133 (m-30) cc_final: 0.6925 (m-30) REVERT: E 81 GLN cc_start: 0.7894 (tp40) cc_final: 0.7674 (mm-40) REVERT: R 207 PHE cc_start: 0.7758 (t80) cc_final: 0.7532 (t80) outliers start: 57 outliers final: 23 residues processed: 265 average time/residue: 1.2160 time to fit residues: 345.1893 Evaluate side-chains 211 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 336 ASN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN E 183 GLN E 186 GLN N 13 GLN N 77 ASN N 82 GLN N 123 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10146 Z= 0.345 Angle : 0.682 10.886 13718 Z= 0.354 Chirality : 0.047 0.206 1551 Planarity : 0.004 0.050 1738 Dihedral : 6.081 59.521 1392 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 5.53 % Allowed : 18.34 % Favored : 76.13 % 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: 0.41 (0.23), residues: 1248 helix: 1.62 (0.25), residues: 409 sheet: 0.10 (0.27), residues: 325 loop : -0.66 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 295 HIS 0.008 0.002 HIS A 322 PHE 0.024 0.002 PHE B 297 TYR 0.030 0.002 TYR E 190 ARG 0.008 0.001 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 189 time to evaluate : 1.197 Fit side-chains revert: symmetry clash REVERT: A 23 LYS cc_start: 0.7433 (mttm) cc_final: 0.7039 (mptp) REVERT: A 243 ILE cc_start: 0.8652 (mt) cc_final: 0.8450 (mm) REVERT: A 262 ASP cc_start: 0.8053 (p0) cc_final: 0.7846 (p0) REVERT: A 274 LYS cc_start: 0.7738 (pmtt) cc_final: 0.7492 (ptpp) REVERT: A 286 THR cc_start: 0.7757 (t) cc_final: 0.7474 (m) REVERT: A 339 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7829 (mtm180) REVERT: B 18 GLN cc_start: 0.6672 (tm-30) cc_final: 0.6372 (tm-30) REVERT: B 64 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.6922 (t80) REVERT: B 66 MET cc_start: 0.8489 (ppp) cc_final: 0.8244 (ppp) REVERT: B 219 ARG cc_start: 0.6582 (mmt180) cc_final: 0.6167 (mmt180) REVERT: B 279 THR cc_start: 0.8971 (m) cc_final: 0.8390 (p) REVERT: E 137 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6566 (p0) REVERT: N 38 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7593 (ptm160) REVERT: N 43 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.6885 (mtmt) REVERT: R 208 LEU cc_start: 0.8210 (mt) cc_final: 0.7942 (mt) outliers start: 60 outliers final: 31 residues processed: 229 average time/residue: 1.2698 time to fit residues: 311.2274 Evaluate side-chains 199 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 238 ASN A 261 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN B 298 ASN E 81 GLN E 186 GLN N 77 ASN R 81 HIS R 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10146 Z= 0.172 Angle : 0.533 10.231 13718 Z= 0.277 Chirality : 0.042 0.156 1551 Planarity : 0.004 0.051 1738 Dihedral : 5.306 53.251 1392 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.88 % Allowed : 20.18 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1248 helix: 2.04 (0.25), residues: 412 sheet: 0.33 (0.29), residues: 313 loop : -0.49 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 PHE 0.015 0.001 PHE B 156 TYR 0.019 0.001 TYR E 190 ARG 0.007 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 167 time to evaluate : 1.098 Fit side-chains REVERT: A 23 LYS cc_start: 0.7385 (mttm) cc_final: 0.6989 (mptt) REVERT: A 188 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7049 (mmtp) REVERT: A 274 LYS cc_start: 0.7834 (pmtt) cc_final: 0.7573 (ptpp) REVERT: B 18 GLN cc_start: 0.6700 (tm-30) cc_final: 0.6443 (tm-30) REVERT: B 40 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6651 (p0) REVERT: B 60 LEU cc_start: 0.8720 (tt) cc_final: 0.8423 (mp) REVERT: B 64 TYR cc_start: 0.8592 (OUTLIER) cc_final: 0.6789 (t80) REVERT: B 219 ARG cc_start: 0.6665 (mmt180) cc_final: 0.6360 (mmt180) REVERT: B 224 ARG cc_start: 0.7544 (mtp85) cc_final: 0.7209 (mtm180) REVERT: B 279 THR cc_start: 0.8919 (m) cc_final: 0.8453 (p) REVERT: E 137 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6547 (p0) REVERT: E 201 ASP cc_start: 0.6813 (t0) cc_final: 0.6410 (t0) REVERT: N 38 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7410 (ptm160) REVERT: R 208 LEU cc_start: 0.8184 (mt) cc_final: 0.7921 (mt) outliers start: 53 outliers final: 29 residues processed: 206 average time/residue: 1.3307 time to fit residues: 292.2826 Evaluate side-chains 189 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 155 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 188 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 278 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 89 optimal weight: 0.0060 chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10146 Z= 0.172 Angle : 0.520 9.182 13718 Z= 0.271 Chirality : 0.042 0.154 1551 Planarity : 0.004 0.052 1738 Dihedral : 5.018 50.006 1392 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.25 % Allowed : 20.92 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.24), residues: 1248 helix: 2.30 (0.25), residues: 408 sheet: 0.30 (0.29), residues: 317 loop : -0.38 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 295 HIS 0.010 0.001 HIS A 197 PHE 0.018 0.001 PHE A 189 TYR 0.019 0.001 TYR E 190 ARG 0.007 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 158 time to evaluate : 1.175 Fit side-chains REVERT: A 16 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7745 (mtmt) REVERT: A 23 LYS cc_start: 0.7376 (mttm) cc_final: 0.6995 (mptt) REVERT: A 193 LYS cc_start: 0.7768 (mmtm) cc_final: 0.7391 (mppt) REVERT: B 18 GLN cc_start: 0.6713 (tm-30) cc_final: 0.6459 (tm-30) REVERT: B 40 ASN cc_start: 0.7328 (OUTLIER) cc_final: 0.6658 (p0) REVERT: B 60 LEU cc_start: 0.8737 (tt) cc_final: 0.8382 (mp) REVERT: B 64 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.6844 (t80) REVERT: B 180 GLN cc_start: 0.7343 (OUTLIER) cc_final: 0.6339 (mp10) REVERT: B 219 ARG cc_start: 0.6711 (mmt180) cc_final: 0.6100 (mmt180) REVERT: B 279 THR cc_start: 0.8924 (m) cc_final: 0.8486 (p) REVERT: E 73 ASP cc_start: 0.8122 (m-30) cc_final: 0.7872 (m-30) REVERT: E 160 ARG cc_start: 0.7459 (ttm170) cc_final: 0.7201 (ttp-170) REVERT: E 201 ASP cc_start: 0.6828 (t0) cc_final: 0.6422 (t0) REVERT: G 12 ARG cc_start: 0.6261 (ptp-170) cc_final: 0.6054 (ptp-170) REVERT: N 38 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7393 (ptm160) REVERT: R 208 LEU cc_start: 0.8220 (mt) cc_final: 0.7961 (mt) outliers start: 57 outliers final: 41 residues processed: 199 average time/residue: 1.2974 time to fit residues: 275.8360 Evaluate side-chains 196 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 186 GLN N 77 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10146 Z= 0.272 Angle : 0.599 9.860 13718 Z= 0.313 Chirality : 0.044 0.179 1551 Planarity : 0.004 0.054 1738 Dihedral : 5.292 44.939 1392 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.81 % Allowed : 20.09 % Favored : 74.10 % 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: 0.90 (0.24), residues: 1248 helix: 2.13 (0.25), residues: 407 sheet: 0.26 (0.28), residues: 323 loop : -0.37 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 295 HIS 0.018 0.002 HIS A 197 PHE 0.017 0.002 PHE A 189 TYR 0.025 0.002 TYR E 190 ARG 0.006 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 152 time to evaluate : 1.181 Fit side-chains REVERT: A 16 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (mtmt) REVERT: A 23 LYS cc_start: 0.7378 (mttm) cc_final: 0.7002 (mptp) REVERT: A 339 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7931 (mtm180) REVERT: B 18 GLN cc_start: 0.6726 (tm-30) cc_final: 0.6449 (tm-30) REVERT: B 40 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6543 (p0) REVERT: B 60 LEU cc_start: 0.8694 (tt) cc_final: 0.8392 (mp) REVERT: B 64 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.6898 (t80) REVERT: B 219 ARG cc_start: 0.6634 (mmt180) cc_final: 0.6335 (mmt180) REVERT: B 279 THR cc_start: 0.8938 (m) cc_final: 0.8332 (p) REVERT: B 319 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7983 (ptm160) REVERT: E 137 ASP cc_start: 0.6880 (OUTLIER) cc_final: 0.6621 (p0) REVERT: E 201 ASP cc_start: 0.6883 (t0) cc_final: 0.6484 (t0) REVERT: N 38 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7515 (ptm160) REVERT: N 89 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: R 208 LEU cc_start: 0.8229 (mt) cc_final: 0.7966 (mt) outliers start: 63 outliers final: 46 residues processed: 203 average time/residue: 1.2873 time to fit residues: 279.2444 Evaluate side-chains 202 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 148 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 94 SER Chi-restraints excluded: chain R residue 106 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 230 VAL Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 87 optimal weight: 0.0000 chunk 67 optimal weight: 20.0000 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** B 273 ASN N 77 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.7353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10146 Z= 0.212 Angle : 0.553 9.557 13718 Z= 0.289 Chirality : 0.043 0.175 1551 Planarity : 0.004 0.054 1738 Dihedral : 5.078 40.539 1392 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 6.45 % Allowed : 20.00 % Favored : 73.55 % 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: 0.99 (0.23), residues: 1248 helix: 2.24 (0.25), residues: 408 sheet: 0.30 (0.29), residues: 311 loop : -0.34 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 295 HIS 0.012 0.001 HIS A 197 PHE 0.017 0.001 PHE A 189 TYR 0.021 0.001 TYR E 190 ARG 0.007 0.001 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 157 time to evaluate : 1.112 Fit side-chains REVERT: A 16 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7754 (mtmt) REVERT: A 23 LYS cc_start: 0.7373 (mttm) cc_final: 0.6989 (mptp) REVERT: A 52 LYS cc_start: 0.8169 (OUTLIER) cc_final: 0.7806 (ptpt) REVERT: A 232 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7579 (mmm-85) REVERT: A 339 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7921 (mtm180) REVERT: B 18 GLN cc_start: 0.6688 (tm-30) cc_final: 0.6383 (tm-30) REVERT: B 19 LEU cc_start: 0.7060 (mt) cc_final: 0.6472 (mt) REVERT: B 60 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 64 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.6816 (t80) REVERT: B 180 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.6427 (mp10) REVERT: B 219 ARG cc_start: 0.6664 (mmt180) cc_final: 0.6430 (mmt180) REVERT: B 279 THR cc_start: 0.8925 (m) cc_final: 0.8349 (p) REVERT: B 319 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7967 (ptm160) REVERT: E 137 ASP cc_start: 0.7067 (OUTLIER) cc_final: 0.6822 (p0) REVERT: E 201 ASP cc_start: 0.6839 (t0) cc_final: 0.6444 (t0) REVERT: N 19 ARG cc_start: 0.7901 (ttt-90) cc_final: 0.7596 (ttt-90) REVERT: N 38 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7492 (ptm160) REVERT: N 43 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.6744 (mtmt) REVERT: N 89 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: R 208 LEU cc_start: 0.8216 (mt) cc_final: 0.7956 (mt) outliers start: 70 outliers final: 45 residues processed: 210 average time/residue: 1.3333 time to fit residues: 299.8025 Evaluate side-chains 208 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 230 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 36 optimal weight: 0.0470 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 1.2080 ------------------------------------------------------------------------------- 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** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10146 Z= 0.162 Angle : 0.516 9.523 13718 Z= 0.270 Chirality : 0.041 0.166 1551 Planarity : 0.004 0.053 1738 Dihedral : 4.684 34.090 1392 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.16 % Allowed : 21.20 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1248 helix: 2.46 (0.25), residues: 407 sheet: 0.43 (0.29), residues: 306 loop : -0.29 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.011 0.001 HIS A 197 PHE 0.017 0.001 PHE A 189 TYR 0.017 0.001 TYR E 190 ARG 0.007 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 161 time to evaluate : 1.282 Fit side-chains REVERT: A 16 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7742 (mtmt) REVERT: A 23 LYS cc_start: 0.7340 (mttm) cc_final: 0.6955 (mptp) REVERT: B 18 GLN cc_start: 0.6648 (tm-30) cc_final: 0.6364 (tm-30) REVERT: B 19 LEU cc_start: 0.7058 (mt) cc_final: 0.6475 (mt) REVERT: B 24 ARG cc_start: 0.6626 (OUTLIER) cc_final: 0.6178 (ttp-170) REVERT: B 40 ASN cc_start: 0.7184 (m-40) cc_final: 0.6566 (p0) REVERT: B 60 LEU cc_start: 0.8653 (tt) cc_final: 0.8349 (mp) REVERT: B 219 ARG cc_start: 0.6646 (mmt180) cc_final: 0.6253 (mmt180) REVERT: B 319 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7995 (ptm160) REVERT: E 201 ASP cc_start: 0.6728 (t0) cc_final: 0.6335 (t0) REVERT: N 38 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7376 (ptm160) REVERT: N 43 LYS cc_start: 0.7431 (OUTLIER) cc_final: 0.6669 (mtmt) REVERT: N 89 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6695 (pm20) REVERT: R 208 LEU cc_start: 0.8210 (mt) cc_final: 0.7948 (mt) outliers start: 56 outliers final: 41 residues processed: 203 average time/residue: 1.3192 time to fit residues: 285.5787 Evaluate side-chains 207 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 160 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 230 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 0.0570 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.7302 ------------------------------------------------------------------------------- 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** N 77 ASN N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10146 Z= 0.143 Angle : 0.508 9.100 13718 Z= 0.265 Chirality : 0.041 0.155 1551 Planarity : 0.004 0.052 1738 Dihedral : 4.501 32.017 1392 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.96 % Allowed : 23.23 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1248 helix: 2.56 (0.25), residues: 408 sheet: 0.46 (0.29), residues: 306 loop : -0.26 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 295 HIS 0.010 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.016 0.001 TYR A 36 ARG 0.010 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 165 time to evaluate : 1.178 Fit side-chains REVERT: A 16 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7720 (mtmt) REVERT: A 23 LYS cc_start: 0.7324 (mttm) cc_final: 0.6938 (mptt) REVERT: A 52 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7777 (ptpt) REVERT: B 18 GLN cc_start: 0.6667 (tm-30) cc_final: 0.6381 (tm-30) REVERT: B 19 LEU cc_start: 0.7057 (mt) cc_final: 0.6484 (mt) REVERT: B 40 ASN cc_start: 0.7152 (m-40) cc_final: 0.6533 (p0) REVERT: B 60 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 64 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7677 (t80) REVERT: B 151 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7825 (mm) REVERT: B 219 ARG cc_start: 0.6655 (mmt180) cc_final: 0.6178 (mmt180) REVERT: B 279 THR cc_start: 0.8925 (m) cc_final: 0.8577 (p) REVERT: B 319 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7898 (ptm160) REVERT: E 75 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7293 (ptpt) REVERT: E 201 ASP cc_start: 0.6627 (t0) cc_final: 0.6236 (t0) REVERT: N 19 ARG cc_start: 0.7913 (ttt-90) cc_final: 0.7631 (ttt-90) REVERT: N 38 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7343 (ptm160) REVERT: N 43 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6574 (mtmt) REVERT: R 208 LEU cc_start: 0.8195 (mt) cc_final: 0.7934 (mt) outliers start: 43 outliers final: 29 residues processed: 195 average time/residue: 1.3736 time to fit residues: 285.4254 Evaluate side-chains 199 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 162 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 120 GLN N 123 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.7217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10146 Z= 0.140 Angle : 0.505 9.066 13718 Z= 0.263 Chirality : 0.041 0.161 1551 Planarity : 0.004 0.050 1738 Dihedral : 4.272 29.303 1392 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.59 % Allowed : 23.69 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.24), residues: 1248 helix: 2.57 (0.25), residues: 408 sheet: 0.53 (0.29), residues: 306 loop : -0.23 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.011 0.001 HIS A 197 PHE 0.017 0.001 PHE A 189 TYR 0.016 0.001 TYR A 36 ARG 0.014 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.652 Fit side-chains REVERT: A 16 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7693 (mtmt) REVERT: A 23 LYS cc_start: 0.7338 (mttm) cc_final: 0.6899 (mptt) REVERT: A 239 ASP cc_start: 0.7396 (m-30) cc_final: 0.7050 (t0) REVERT: B 18 GLN cc_start: 0.6664 (tm-30) cc_final: 0.6405 (tm-30) REVERT: B 19 LEU cc_start: 0.7042 (mt) cc_final: 0.6462 (mt) REVERT: B 40 ASN cc_start: 0.7136 (m-40) cc_final: 0.6529 (p0) REVERT: B 60 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8360 (mp) REVERT: B 64 TYR cc_start: 0.8524 (OUTLIER) cc_final: 0.6699 (t80) REVERT: B 151 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7813 (mm) REVERT: B 219 ARG cc_start: 0.6685 (mmt180) cc_final: 0.6264 (mmt180) REVERT: B 279 THR cc_start: 0.8805 (m) cc_final: 0.8474 (p) REVERT: B 319 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7859 (ptm160) REVERT: E 81 GLN cc_start: 0.8031 (tp40) cc_final: 0.7712 (mm-40) REVERT: E 160 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6868 (ttm170) REVERT: E 201 ASP cc_start: 0.6540 (t0) cc_final: 0.6160 (t0) REVERT: N 38 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7271 (ptm160) REVERT: R 208 LEU cc_start: 0.8175 (mt) cc_final: 0.7926 (mt) outliers start: 39 outliers final: 28 residues processed: 194 average time/residue: 1.3783 time to fit residues: 284.8550 Evaluate side-chains 197 residues out of total 1087 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 163 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 208 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 62 SER Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 230 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 14 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108747 restraints weight = 13100.440| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.68 r_work: 0.3163 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.7228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 10146 Z= 0.187 Angle : 0.830 59.175 13718 Z= 0.482 Chirality : 0.043 0.537 1551 Planarity : 0.004 0.050 1738 Dihedral : 4.336 29.341 1392 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.59 % Allowed : 23.78 % Favored : 72.63 % Cbeta Deviations : 0.08 % 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: 1.29 (0.24), residues: 1248 helix: 2.51 (0.25), residues: 408 sheet: 0.54 (0.30), residues: 306 loop : -0.23 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.009 0.001 HIS A 197 PHE 0.017 0.001 PHE A 189 TYR 0.016 0.001 TYR A 36 ARG 0.014 0.001 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4988.19 seconds wall clock time: 88 minutes 52.47 seconds (5332.47 seconds total)