Starting phenix.real_space_refine on Wed Apr 30 18:53:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuk_35724/04_2025/8iuk_35724.cif" } 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. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9951 Number of models: 1 Model: "" Number of chains: 7 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: 2314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2314 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 5, 'TRANS': 287} Chain breaks: 1 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'UGU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.99, per 1000 atoms: 0.60 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 - 3.00 Amino acid : True - 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 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... Secondary structure from input PDB file: 29 helices and 15 sheets defined 35.4% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 4.048A pdb=" N VAL A 19 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.609A pdb=" N ILE A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 230 through 245 removed outlier: 4.129A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.794A pdb=" N GLY A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.575A pdb=" N PHE A 282 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 315 Processing helix chain 'A' and resid 335 through 358 Processing helix chain 'B' and resid 9 through 30 removed outlier: 3.508A pdb=" N CYS B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.687A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 removed outlier: 3.577A pdb=" N GLY E 55 " --> pdb=" O SER E 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 52 through 55' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 28 through 44 removed outlier: 3.927A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.912A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.663A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 59 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) Processing helix chain 'R' and resid 64 through 93 Processing helix chain 'R' and resid 97 through 102 removed outlier: 3.882A pdb=" N PHE R 101 " --> pdb=" O GLU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 139 Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 139 through 145 Processing helix chain 'R' and resid 148 through 168 Processing helix chain 'R' and resid 170 through 174 removed outlier: 3.949A pdb=" N HIS R 174 " --> pdb=" O ILE R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 234 removed outlier: 4.068A pdb=" N ARG R 199 " --> pdb=" O ASP R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 276 removed outlier: 3.513A pdb=" N CYS R 256 " --> pdb=" O LEU R 252 " (cutoff:3.500A) Proline residue: R 264 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 282 through 299 removed outlier: 4.019A pdb=" N THR R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 299 through 305 Processing helix chain 'R' and resid 308 through 323 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 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) removed outlier: 7.239A pdb=" N ARG A 41 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ILE A 222 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU A 43 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASP A 226 " --> pdb=" O LEU A 45 " (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: 3.581A pdb=" N TYR A 325 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.586A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 341 " --> pdb=" O LEU B 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.913A pdb=" N ALA B 65 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B 86 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AA4, 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=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 4.002A pdb=" N CYS B 153 " --> pdb=" O SER B 165 " (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: 6.556A pdb=" N LEU B 173 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing sheet with id=AA6, 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: 6.439A pdb=" N ALA B 213 " --> pdb=" O THR B 226 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N THR B 226 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 215 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing sheet with id=AA7, 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: 6.239A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, 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: 6.451A pdb=" N CYS B 299 " --> pdb=" O VAL B 312 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL B 312 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 301 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 6.188A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.631A pdb=" N THR E 141 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG E 160 " --> pdb=" O THR E 141 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 186 through 189 removed outlier: 6.729A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AB4, 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=AB5, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.029A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 178 through 179 removed outlier: 3.509A pdb=" N PHE R 187 " --> pdb=" O LYS R 178 " (cutoff:3.500A) 472 hydrogen bonds defined for protein. 1350 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: 3.46 Time building geometry restraints manager: 3.01 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 1.548 1.347 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C10 UGU R 401 " pdb=" C9 UGU R 401 " ideal model delta sigma weight residual 1.535 1.357 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" C8 UGU R 401 " pdb=" C9 UGU R 401 " ideal model delta sigma weight residual 1.531 1.663 -0.132 2.00e-02 2.50e+03 4.36e+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 bond pdb=" CA SER A 12 " pdb=" CB SER A 12 " ideal model delta sigma weight residual 1.526 1.455 0.072 1.44e-02 4.82e+03 2.47e+01 ... (remaining 10141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 13664 3.10 - 6.20: 40 6.20 - 9.30: 10 9.30 - 12.39: 2 12.39 - 15.49: 2 Bond angle restraints: 13718 Sorted by residual: 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=" C11 UGU R 401 " pdb=" C12 UGU R 401 " pdb=" C13 UGU R 401 " ideal model delta sigma weight residual 117.79 102.30 15.49 3.00e+00 1.11e-01 2.67e+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 - 16.50: 5851 16.50 - 32.99: 162 32.99 - 49.49: 32 49.49 - 65.99: 7 65.99 - 82.48: 2 Dihedral angle restraints: 6054 sinusoidal: 2387 harmonic: 3667 Sorted by residual: 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 dihedral pdb=" CG ARG R 291 " pdb=" CD ARG R 291 " pdb=" NE ARG R 291 " pdb=" CZ ARG R 291 " ideal model delta sinusoidal sigma weight residual -180.00 -139.72 -40.28 2 1.50e+01 4.44e-03 8.92e+00 ... (remaining 6051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1506 0.104 - 0.207: 39 0.207 - 0.311: 3 0.311 - 0.415: 1 0.415 - 0.518: 2 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 2.42 2.94 -0.52 2.00e-01 2.50e+01 6.71e+00 chirality pdb=" C9 UGU R 401 " pdb=" C10 UGU R 401 " pdb=" C8 UGU R 401 " pdb=" O3 UGU R 401 " both_signs ideal model delta sigma weight residual False -2.72 -2.22 -0.51 2.00e-01 2.50e+01 6.38e+00 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 2.60 2.96 -0.36 2.00e-01 2.50e+01 3.19e+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: 2570 2.80 - 3.33: 9013 3.33 - 3.85: 16178 3.85 - 4.38: 18230 4.38 - 4.90: 32670 Nonbonded interactions: 78661 Sorted by model distance: nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.280 3.040 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.283 3.040 nonbonded pdb=" O GLY R 40 " pdb=" ND2 ASN R 44 " model vdw 2.294 3.120 nonbonded pdb=" OE2 GLU B 265 " pdb=" OG1 THR B 268 " model vdw 2.294 3.040 nonbonded pdb=" O GLY R 80 " pdb=" ND2 ASN R 84 " model vdw 2.306 3.120 ... (remaining 78656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 1.070 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: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.300 Find NCS groups from input model: 0.140 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: 0.010 Load rotamer database and sin/cos tables:16.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 44.700 ------------------------------------------------------------------------------- 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 : 0.004 0.201 10149 Z= 0.250 Angle : 0.525 15.493 13724 Z= 0.300 Chirality : 0.044 0.518 1551 Planarity : 0.003 0.037 1738 Dihedral : 8.040 82.485 3681 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 Details of bonding type rmsd hydrogen bonds : bond 0.10373 ( 472) hydrogen bonds : angle 4.56636 ( 1350) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.52246 ( 6) covalent geometry : bond 0.00423 (10146) covalent geometry : angle 0.52466 (13718) *********************** 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 to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 1.015 Fit side-chains REVERT: A 23 LYS cc_start: 0.7132 (mttm) cc_final: 0.6575 (mptt) REVERT: A 26 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7149 (mt-10) REVERT: A 31 LYS cc_start: 0.7647 (mttp) cc_final: 0.7339 (mtpt) REVERT: A 195 ASN cc_start: 0.8152 (m-40) cc_final: 0.7933 (m110) REVERT: A 197 HIS cc_start: 0.5832 (m170) cc_final: 0.5575 (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: 0.7001 (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: 1.2575 time to fit residues: 531.5675 Evaluate side-chains 192 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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: 8.9990 chunk 52 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS A 336 ASN A 350 GLN B 235 ASN B 264 GLN B 271 HIS B 273 ASN E 34 HIS E 142 GLN E 179 GLN E 183 GLN E 186 GLN E 194 ASN G 58 ASN N 13 GLN N 35 ASN N 39 GLN N 77 ASN R 244 HIS R 250 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106841 restraints weight = 12941.442| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.74 r_work: 0.3112 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.6565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 10149 Z= 0.343 Angle : 0.846 12.379 13724 Z= 0.443 Chirality : 0.054 0.261 1551 Planarity : 0.006 0.049 1738 Dihedral : 7.248 57.464 1413 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.62 % Allowed : 16.04 % Favored : 78.34 % 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: -0.08 (0.22), residues: 1248 helix: 1.12 (0.24), residues: 412 sheet: -0.02 (0.28), residues: 310 loop : -0.97 (0.25), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP R 295 HIS 0.013 0.003 HIS A 322 PHE 0.028 0.003 PHE B 156 TYR 0.035 0.003 TYR E 190 ARG 0.010 0.002 ARG B 319 Details of bonding type rmsd hydrogen bonds : bond 0.05361 ( 472) hydrogen bonds : angle 4.91054 ( 1350) SS BOND : bond 0.01095 ( 3) SS BOND : angle 1.45683 ( 6) covalent geometry : bond 0.00800 (10146) covalent geometry : angle 0.84590 (13718) *********************** 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 285 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 224 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: A 234 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: A 262 ASP cc_start: 0.8271 (p0) cc_final: 0.8058 (p0) REVERT: A 286 THR cc_start: 0.8058 (t) cc_final: 0.7824 (m) REVERT: A 315 THR cc_start: 0.8594 (m) cc_final: 0.8344 (p) REVERT: B 18 GLN cc_start: 0.6681 (tm-30) cc_final: 0.6429 (tm-30) REVERT: B 64 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8168 (t80) REVERT: B 200 ASP cc_start: 0.6663 (p0) cc_final: 0.6410 (p0) REVERT: B 222 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7824 (pp-130) REVERT: B 259 ASP cc_start: 0.7750 (t70) cc_final: 0.7378 (t0) REVERT: E 72 ASP cc_start: 0.7747 (t70) cc_final: 0.7491 (t70) REVERT: G 28 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7546 (mptp) REVERT: N 38 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8270 (ptm160) REVERT: R 59 ARG cc_start: 0.7310 (ttp80) cc_final: 0.7021 (ptm160) REVERT: R 90 PHE cc_start: 0.7797 (t80) cc_final: 0.7573 (t80) REVERT: R 154 MET cc_start: 0.7609 (ptp) cc_final: 0.6968 (mmp) REVERT: R 208 LEU cc_start: 0.8331 (mt) cc_final: 0.8030 (mt) REVERT: R 313 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7433 (ptpt) outliers start: 61 outliers final: 25 residues processed: 264 average time/residue: 1.2579 time to fit residues: 354.8330 Evaluate side-chains 196 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 311 VAL 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 151 LEU Chi-restraints excluded: chain B residue 222 MET 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 139 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 SER 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 28 LYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 269 MET Chi-restraints excluded: chain R residue 313 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 43 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 67 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN B 298 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN E 186 GLN N 77 ASN N 123 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.136471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.106330 restraints weight = 13164.022| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.79 r_work: 0.3140 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.6800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10149 Z= 0.144 Angle : 0.579 9.306 13724 Z= 0.301 Chirality : 0.043 0.182 1551 Planarity : 0.004 0.048 1738 Dihedral : 6.366 54.027 1410 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 6.08 % Allowed : 18.99 % 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: 0.73 (0.23), residues: 1248 helix: 2.05 (0.25), residues: 408 sheet: 0.16 (0.29), residues: 311 loop : -0.51 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 295 HIS 0.009 0.002 HIS A 197 PHE 0.014 0.002 PHE A 189 TYR 0.021 0.001 TYR E 190 ARG 0.004 0.001 ARG B 202 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 472) hydrogen bonds : angle 4.37380 ( 1350) SS BOND : bond 0.00206 ( 3) SS BOND : angle 0.54919 ( 6) covalent geometry : bond 0.00327 (10146) covalent geometry : angle 0.57863 (13718) *********************** 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 243 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 0.925 Fit side-chains REVERT: A 193 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7303 (mtmt) REVERT: A 227 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8431 (m) REVERT: A 262 ASP cc_start: 0.8171 (p0) cc_final: 0.7936 (p0) REVERT: B 18 GLN cc_start: 0.6683 (tm-30) cc_final: 0.6377 (tm-30) REVERT: B 40 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6727 (p0) REVERT: B 64 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7855 (t80) REVERT: B 144 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8035 (pp) REVERT: B 177 GLU cc_start: 0.7238 (tp30) cc_final: 0.6739 (tt0) REVERT: B 259 ASP cc_start: 0.7738 (t70) cc_final: 0.7297 (t0) REVERT: G 12 ARG cc_start: 0.6348 (ptp-170) cc_final: 0.6137 (ptp-170) REVERT: N 46 GLU cc_start: 0.8400 (tt0) cc_final: 0.8059 (tt0) REVERT: N 105 ARG cc_start: 0.6556 (ttm110) cc_final: 0.6352 (mtm180) REVERT: R 90 PHE cc_start: 0.7825 (t80) cc_final: 0.7557 (t80) REVERT: R 154 MET cc_start: 0.7466 (ptp) cc_final: 0.6695 (mmp) REVERT: R 208 LEU cc_start: 0.8164 (mt) cc_final: 0.7873 (mt) outliers start: 66 outliers final: 34 residues processed: 222 average time/residue: 1.3343 time to fit residues: 317.9467 Evaluate side-chains 193 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 40 ASN 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET 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 139 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 SER 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 30 SER 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 43 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 234 SER Chi-restraints excluded: chain R residue 278 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 0.0770 chunk 43 optimal weight: 0.0570 chunk 52 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 183 GLN N 77 ASN R 180 GLN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.109102 restraints weight = 13034.435| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.67 r_work: 0.3145 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10149 Z= 0.106 Angle : 0.520 9.132 13724 Z= 0.271 Chirality : 0.041 0.185 1551 Planarity : 0.003 0.048 1738 Dihedral : 5.788 57.899 1408 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.35 % Allowed : 21.01 % 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: 1.14 (0.24), residues: 1248 helix: 2.55 (0.25), residues: 408 sheet: 0.34 (0.30), residues: 308 loop : -0.37 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 PHE 0.017 0.001 PHE A 189 TYR 0.017 0.001 TYR E 190 ARG 0.005 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.03339 ( 472) hydrogen bonds : angle 4.10309 ( 1350) SS BOND : bond 0.00161 ( 3) SS BOND : angle 0.42511 ( 6) covalent geometry : bond 0.00230 (10146) covalent geometry : angle 0.51971 (13718) *********************** 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 226 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 168 time to evaluate : 1.238 Fit side-chains REVERT: A 274 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7724 (ptpp) REVERT: B 18 GLN cc_start: 0.6735 (tm-30) cc_final: 0.6480 (tm-30) REVERT: B 40 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6660 (p0) REVERT: B 64 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8798 (t80) REVERT: B 144 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8043 (pp) REVERT: B 259 ASP cc_start: 0.7742 (t70) cc_final: 0.7334 (t0) REVERT: E 73 ASP cc_start: 0.8300 (m-30) cc_final: 0.8021 (m-30) REVERT: E 149 VAL cc_start: 0.6034 (p) cc_final: 0.5654 (m) REVERT: G 12 ARG cc_start: 0.6442 (ptp-170) cc_final: 0.6231 (ptp-170) REVERT: N 46 GLU cc_start: 0.8445 (tt0) cc_final: 0.8113 (tt0) REVERT: R 90 PHE cc_start: 0.7855 (t80) cc_final: 0.7599 (t80) REVERT: R 154 MET cc_start: 0.7517 (ptp) cc_final: 0.6773 (mmp) REVERT: R 208 LEU cc_start: 0.8256 (mt) cc_final: 0.7978 (mt) outliers start: 58 outliers final: 31 residues processed: 207 average time/residue: 1.3351 time to fit residues: 294.9622 Evaluate side-chains 195 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 59 MET Chi-restraints excluded: chain A residue 184 ILE 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 313 ILE 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET 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 139 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL 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 234 SER 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 13 optimal weight: 9.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN E 183 GLN N 77 ASN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.106434 restraints weight = 13075.800| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.72 r_work: 0.3102 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.7012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10149 Z= 0.127 Angle : 0.552 9.620 13724 Z= 0.287 Chirality : 0.042 0.171 1551 Planarity : 0.004 0.050 1738 Dihedral : 5.547 51.552 1408 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.35 % Allowed : 20.65 % Favored : 74.01 % 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: 1.23 (0.24), residues: 1248 helix: 2.66 (0.25), residues: 408 sheet: 0.26 (0.29), residues: 328 loop : -0.28 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 295 HIS 0.013 0.001 HIS A 197 PHE 0.018 0.001 PHE A 189 TYR 0.022 0.001 TYR E 190 ARG 0.003 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.03574 ( 472) hydrogen bonds : angle 4.15189 ( 1350) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.54314 ( 6) covalent geometry : bond 0.00285 (10146) covalent geometry : angle 0.55168 (13718) *********************** 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 223 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.187 Fit side-chains REVERT: A 227 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8388 (m) REVERT: B 18 GLN cc_start: 0.6811 (tm-30) cc_final: 0.6529 (tm-30) REVERT: B 40 ASN cc_start: 0.7334 (OUTLIER) cc_final: 0.6679 (p0) REVERT: B 64 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.8031 (t80) REVERT: B 144 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8085 (pp) REVERT: B 259 ASP cc_start: 0.7734 (t70) cc_final: 0.7374 (t0) REVERT: E 81 GLN cc_start: 0.7960 (tp40) cc_final: 0.7760 (tp40) REVERT: E 149 VAL cc_start: 0.6194 (p) cc_final: 0.5806 (m) REVERT: E 201 ASP cc_start: 0.7067 (t0) cc_final: 0.6671 (t0) REVERT: N 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8115 (tt0) REVERT: N 89 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: R 90 PHE cc_start: 0.7912 (t80) cc_final: 0.7643 (t80) REVERT: R 154 MET cc_start: 0.7604 (ptp) cc_final: 0.6837 (mmp) REVERT: R 208 LEU cc_start: 0.8286 (mt) cc_final: 0.7996 (mt) outliers start: 58 outliers final: 42 residues processed: 206 average time/residue: 1.3805 time to fit residues: 304.2929 Evaluate side-chains 200 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 227 SER Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 330 CYS 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 222 MET 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 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 197 SER Chi-restraints excluded: chain E residue 220 GLU 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 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 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 89 VAL 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 234 SER 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 117 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.131348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.101614 restraints weight = 13186.018| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 1.74 r_work: 0.3019 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.7550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10149 Z= 0.229 Angle : 0.680 10.581 13724 Z= 0.357 Chirality : 0.046 0.205 1551 Planarity : 0.004 0.049 1738 Dihedral : 5.515 46.595 1408 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.53 % Allowed : 21.01 % Favored : 73.46 % 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: 0.83 (0.23), residues: 1248 helix: 2.20 (0.25), residues: 404 sheet: 0.19 (0.28), residues: 326 loop : -0.48 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 295 HIS 0.016 0.002 HIS A 197 PHE 0.021 0.002 PHE A 223 TYR 0.031 0.002 TYR E 190 ARG 0.005 0.001 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 472) hydrogen bonds : angle 4.65167 ( 1350) SS BOND : bond 0.00393 ( 3) SS BOND : angle 0.71127 ( 6) covalent geometry : bond 0.00531 (10146) covalent geometry : angle 0.67955 (13718) *********************** 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 214 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 1.172 Fit side-chains REVERT: A 321 ARG cc_start: 0.7553 (ptp90) cc_final: 0.7324 (mpp-170) REVERT: B 18 GLN cc_start: 0.6840 (tm-30) cc_final: 0.6546 (tm-30) REVERT: B 24 ARG cc_start: 0.6885 (OUTLIER) cc_final: 0.6547 (ttp-170) REVERT: B 40 ASN cc_start: 0.7248 (OUTLIER) cc_final: 0.6666 (p0) REVERT: B 64 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8036 (t80) REVERT: B 144 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8266 (pp) REVERT: B 259 ASP cc_start: 0.7812 (t70) cc_final: 0.7444 (t0) REVERT: E 81 GLN cc_start: 0.7937 (tp40) cc_final: 0.7736 (tp40) REVERT: E 156 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.7942 (t) REVERT: E 158 SER cc_start: 0.7934 (t) cc_final: 0.7691 (m) REVERT: E 201 ASP cc_start: 0.7326 (t0) cc_final: 0.6964 (t0) REVERT: N 19 ARG cc_start: 0.7924 (ttt-90) cc_final: 0.7615 (ttt-90) REVERT: N 89 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6992 (pm20) REVERT: R 90 PHE cc_start: 0.7970 (t80) cc_final: 0.7750 (t80) REVERT: R 154 MET cc_start: 0.7611 (ptp) cc_final: 0.6928 (mmp) REVERT: R 208 LEU cc_start: 0.8326 (mt) cc_final: 0.8014 (mt) outliers start: 60 outliers final: 38 residues processed: 200 average time/residue: 1.3365 time to fit residues: 285.1711 Evaluate side-chains 187 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 143 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 59 MET 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 330 CYS Chi-restraints excluded: chain B residue 24 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 222 MET 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 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 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 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 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 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 89 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN G 58 ASN N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.133382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.103544 restraints weight = 13217.376| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.82 r_work: 0.3041 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10149 Z= 0.151 Angle : 0.579 9.901 13724 Z= 0.305 Chirality : 0.043 0.174 1551 Planarity : 0.004 0.050 1738 Dihedral : 4.906 47.677 1408 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.88 % Allowed : 21.94 % Favored : 73.18 % 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: 2.45 (0.25), residues: 403 sheet: 0.16 (0.29), residues: 312 loop : -0.40 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 295 HIS 0.011 0.002 HIS A 197 PHE 0.015 0.002 PHE A 189 TYR 0.022 0.001 TYR E 190 ARG 0.007 0.001 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 472) hydrogen bonds : angle 4.41248 ( 1350) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.59962 ( 6) covalent geometry : bond 0.00344 (10146) covalent geometry : angle 0.57933 (13718) *********************** 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 214 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 161 time to evaluate : 1.019 Fit side-chains REVERT: A 321 ARG cc_start: 0.7560 (ptp90) cc_final: 0.7256 (mpp-170) REVERT: B 18 GLN cc_start: 0.6749 (tm-30) cc_final: 0.6463 (tm-30) REVERT: B 19 LEU cc_start: 0.7342 (mt) cc_final: 0.6789 (mt) REVERT: B 40 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6651 (p0) REVERT: B 64 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.7976 (t80) REVERT: B 144 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8212 (pp) REVERT: B 259 ASP cc_start: 0.7792 (t70) cc_final: 0.7425 (t0) REVERT: E 149 VAL cc_start: 0.6524 (p) cc_final: 0.6064 (m) REVERT: E 156 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.7942 (t) REVERT: E 158 SER cc_start: 0.8016 (t) cc_final: 0.7586 (p) REVERT: E 160 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7602 (ttp-170) REVERT: E 201 ASP cc_start: 0.7201 (t0) cc_final: 0.6831 (t0) REVERT: E 247 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5690 (tm) REVERT: N 19 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7643 (ttt-90) REVERT: N 38 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8122 (ptm160) REVERT: N 89 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: R 90 PHE cc_start: 0.7981 (t80) cc_final: 0.7762 (t80) REVERT: R 154 MET cc_start: 0.7572 (ptp) cc_final: 0.6922 (mmp) REVERT: R 208 LEU cc_start: 0.8292 (mt) cc_final: 0.7987 (mt) outliers start: 53 outliers final: 39 residues processed: 199 average time/residue: 1.3229 time to fit residues: 280.6061 Evaluate side-chains 193 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 147 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 59 MET 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 330 CYS 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 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET 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 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 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 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 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 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 89 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105961 restraints weight = 13156.487| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.79 r_work: 0.3130 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.7387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10149 Z= 0.109 Angle : 0.533 9.512 13724 Z= 0.280 Chirality : 0.042 0.159 1551 Planarity : 0.004 0.052 1738 Dihedral : 4.514 48.941 1408 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.70 % Allowed : 22.86 % Favored : 72.44 % 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: 1.22 (0.24), residues: 1248 helix: 2.71 (0.25), residues: 406 sheet: 0.25 (0.29), residues: 308 loop : -0.32 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 295 HIS 0.009 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.019 0.001 TYR A 36 ARG 0.008 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.03426 ( 472) hydrogen bonds : angle 4.18225 ( 1350) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.51606 ( 6) covalent geometry : bond 0.00241 (10146) covalent geometry : angle 0.53289 (13718) *********************** 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 208 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 157 time to evaluate : 1.030 Fit side-chains REVERT: B 18 GLN cc_start: 0.6730 (tm-30) cc_final: 0.6466 (tm-30) REVERT: B 19 LEU cc_start: 0.7332 (mt) cc_final: 0.6784 (mt) REVERT: B 40 ASN cc_start: 0.7219 (OUTLIER) cc_final: 0.6631 (p0) REVERT: B 47 ARG cc_start: 0.7164 (OUTLIER) cc_final: 0.6689 (ttm170) REVERT: B 64 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.7899 (t80) REVERT: B 144 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8099 (pp) REVERT: E 81 GLN cc_start: 0.7855 (tp40) cc_final: 0.7525 (mm-40) REVERT: E 149 VAL cc_start: 0.6539 (p) cc_final: 0.6137 (m) REVERT: E 156 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.7924 (t) REVERT: E 160 ARG cc_start: 0.7781 (ttm170) cc_final: 0.7536 (ttp-170) REVERT: E 163 LYS cc_start: 0.8285 (ptmm) cc_final: 0.8045 (ptmt) REVERT: E 201 ASP cc_start: 0.7022 (t0) cc_final: 0.6654 (t0) REVERT: N 19 ARG cc_start: 0.7969 (ttt-90) cc_final: 0.7690 (ttt-90) REVERT: N 46 GLU cc_start: 0.8379 (tt0) cc_final: 0.8061 (tt0) REVERT: N 89 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: R 154 MET cc_start: 0.7483 (ptp) cc_final: 0.6816 (mmp) REVERT: R 208 LEU cc_start: 0.8271 (mt) cc_final: 0.7971 (mt) outliers start: 51 outliers final: 34 residues processed: 193 average time/residue: 1.4806 time to fit residues: 305.8130 Evaluate side-chains 185 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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 330 CYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU 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 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain E residue 247 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 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 122 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 164 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 108 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106371 restraints weight = 13100.484| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.80 r_work: 0.3112 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.7352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10149 Z= 0.107 Angle : 0.529 9.633 13724 Z= 0.277 Chirality : 0.041 0.153 1551 Planarity : 0.004 0.056 1738 Dihedral : 4.425 50.348 1408 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.24 % Allowed : 23.59 % Favored : 72.17 % 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: 1.37 (0.24), residues: 1248 helix: 2.80 (0.25), residues: 409 sheet: 0.35 (0.29), residues: 313 loop : -0.23 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 295 HIS 0.009 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.019 0.001 TYR A 36 ARG 0.009 0.000 ARG E 180 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 472) hydrogen bonds : angle 4.09489 ( 1350) SS BOND : bond 0.00146 ( 3) SS BOND : angle 0.45078 ( 6) covalent geometry : bond 0.00236 (10146) covalent geometry : angle 0.52887 (13718) *********************** 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 203 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 1.114 Fit side-chains REVERT: B 18 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6496 (tm-30) REVERT: B 19 LEU cc_start: 0.7342 (mt) cc_final: 0.6763 (mt) REVERT: B 40 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6610 (p0) REVERT: B 47 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6699 (ttm170) REVERT: B 64 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8817 (t80) REVERT: B 144 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8082 (pp) REVERT: B 219 ARG cc_start: 0.6940 (mmt180) cc_final: 0.6686 (mmt180) REVERT: E 156 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.7933 (t) REVERT: E 160 ARG cc_start: 0.7824 (ttm170) cc_final: 0.7572 (ttp-170) REVERT: E 201 ASP cc_start: 0.6948 (t0) cc_final: 0.6525 (t0) REVERT: N 19 ARG cc_start: 0.7980 (ttt-90) cc_final: 0.7701 (ttt-90) REVERT: N 46 GLU cc_start: 0.8433 (tt0) cc_final: 0.8118 (tt0) REVERT: N 89 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6905 (pm20) REVERT: R 154 MET cc_start: 0.7558 (ptp) cc_final: 0.6820 (mmp) REVERT: R 208 LEU cc_start: 0.8287 (mt) cc_final: 0.7991 (mt) REVERT: R 269 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7853 (tpt) outliers start: 46 outliers final: 32 residues processed: 190 average time/residue: 1.4597 time to fit residues: 295.7477 Evaluate side-chains 190 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 151 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER 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 330 CYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 144 LEU 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 10 LEU 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 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain E residue 224 VAL 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 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 122 THR Chi-restraints excluded: chain N residue 125 THR 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 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 70 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103165 restraints weight = 13091.499| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.74 r_work: 0.3052 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10149 Z= 0.175 Angle : 0.621 10.215 13724 Z= 0.326 Chirality : 0.044 0.172 1551 Planarity : 0.004 0.059 1738 Dihedral : 4.958 49.440 1408 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 4.15 % Allowed : 24.52 % Favored : 71.34 % 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: 1.14 (0.24), residues: 1248 helix: 2.54 (0.25), residues: 404 sheet: 0.27 (0.29), residues: 319 loop : -0.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 295 HIS 0.012 0.002 HIS A 197 PHE 0.016 0.002 PHE A 189 TYR 0.025 0.002 TYR E 190 ARG 0.014 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 472) hydrogen bonds : angle 4.40314 ( 1350) SS BOND : bond 0.00281 ( 3) SS BOND : angle 0.65336 ( 6) covalent geometry : bond 0.00407 (10146) covalent geometry : angle 0.62130 (13718) ********************** 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 194 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 1.194 Fit side-chains REVERT: B 18 GLN cc_start: 0.6779 (tm-30) cc_final: 0.6491 (tm-30) REVERT: B 19 LEU cc_start: 0.7350 (mt) cc_final: 0.6774 (mt) REVERT: B 40 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.6704 (p0) REVERT: B 47 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6688 (ttm170) REVERT: B 64 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 144 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8217 (pp) REVERT: E 149 VAL cc_start: 0.6703 (p) cc_final: 0.6343 (m) REVERT: E 156 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.7950 (t) REVERT: E 158 SER cc_start: 0.7980 (t) cc_final: 0.7558 (p) REVERT: E 201 ASP cc_start: 0.7142 (t0) cc_final: 0.6766 (t0) REVERT: N 46 GLU cc_start: 0.8458 (tt0) cc_final: 0.8122 (tt0) REVERT: N 89 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.6902 (pm20) REVERT: R 154 MET cc_start: 0.7576 (ptp) cc_final: 0.6888 (mmp) REVERT: R 208 LEU cc_start: 0.8290 (mt) cc_final: 0.7980 (mt) REVERT: R 269 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7878 (tpt) outliers start: 45 outliers final: 35 residues processed: 182 average time/residue: 1.4123 time to fit residues: 273.9955 Evaluate side-chains 189 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 147 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 201 VAL 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 330 CYS Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 144 LEU 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 10 LEU 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 197 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR 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 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 122 THR Chi-restraints excluded: chain N residue 125 THR 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 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 91 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.133717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104358 restraints weight = 13067.662| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.74 r_work: 0.3072 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.7630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10149 Z= 0.141 Angle : 0.583 9.964 13724 Z= 0.306 Chirality : 0.043 0.167 1551 Planarity : 0.004 0.056 1738 Dihedral : 4.843 51.336 1408 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.33 % Allowed : 24.15 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1248 helix: 2.58 (0.25), residues: 404 sheet: 0.32 (0.29), residues: 321 loop : -0.29 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 295 HIS 0.010 0.001 HIS A 197 PHE 0.015 0.001 PHE A 189 TYR 0.020 0.001 TYR A 36 ARG 0.009 0.001 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03785 ( 472) hydrogen bonds : angle 4.32043 ( 1350) SS BOND : bond 0.00212 ( 3) SS BOND : angle 0.56406 ( 6) covalent geometry : bond 0.00322 (10146) covalent geometry : angle 0.58347 (13718) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9332.39 seconds wall clock time: 163 minutes 39.44 seconds (9819.44 seconds total)