Starting phenix.real_space_refine on Fri Feb 14 05:15:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuk_35724/02_2025/8iuk_35724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuk_35724/02_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_35724/02_2025/8iuk_35724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuk_35724/02_2025/8iuk_35724.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuk_35724/02_2025/8iuk_35724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuk_35724/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.90, per 1000 atoms: 0.59 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: 2.67 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: 1.23 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: 3.24 Time building geometry restraints manager: 2.98 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.040 Find NCS groups from input model: 0.130 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:12.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.350 ------------------------------------------------------------------------------- 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 10146 Z= 0.272 Angle : 0.525 15.493 13718 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 *********************** 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 : 1.133 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: 1.2162 time to fit residues: 513.5806 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 : 1.155 ------------------------------------------------------------------------------- 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 = 12941.441| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.74 r_work: 0.3112 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- 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 10146 Z= 0.520 Angle : 0.846 12.379 13718 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 *********************** 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 : 1.071 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: 0.8057 (p0) REVERT: A 286 THR cc_start: 0.8058 (t) cc_final: 0.7824 (m) REVERT: A 315 THR cc_start: 0.8593 (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: 0.8929 (OUTLIER) cc_final: 0.8168 (t80) REVERT: B 200 ASP cc_start: 0.6661 (p0) cc_final: 0.6408 (p0) REVERT: B 222 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.7823 (pp-130) REVERT: B 259 ASP cc_start: 0.7750 (t70) cc_final: 0.7378 (t0) REVERT: E 72 ASP cc_start: 0.7748 (t70) cc_final: 0.7492 (t70) REVERT: G 28 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7547 (mptp) REVERT: N 38 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8269 (ptm160) REVERT: R 59 ARG cc_start: 0.7310 (ttp80) cc_final: 0.7020 (ptm160) REVERT: R 90 PHE cc_start: 0.7797 (t80) cc_final: 0.7574 (t80) REVERT: R 154 MET cc_start: 0.7607 (ptp) cc_final: 0.6968 (mmp) REVERT: R 208 LEU cc_start: 0.8331 (mt) cc_final: 0.8031 (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: 1.3056 time to fit residues: 367.6258 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 : 1.315 ------------------------------------------------------------------------------- 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: 1.9990 chunk 67 optimal weight: 0.0070 chunk 69 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 8 optimal weight: 0.1980 chunk 91 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 overall best weight: 0.4802 ------------------------------------------------------------------------------- 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 E 183 GLN E 186 GLN N 77 ASN N 123 GLN R 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.141166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112144 restraints weight = 13165.695| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.75 r_work: 0.3198 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.6527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10146 Z= 0.135 Angle : 0.513 8.286 13718 Z= 0.266 Chirality : 0.041 0.189 1551 Planarity : 0.003 0.047 1738 Dihedral : 6.009 58.128 1410 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 4.98 % Allowed : 19.91 % Favored : 75.12 % 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: 0.84 (0.24), residues: 1248 helix: 2.18 (0.25), residues: 414 sheet: 0.28 (0.29), residues: 307 loop : -0.57 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 295 HIS 0.004 0.001 HIS A 322 PHE 0.015 0.001 PHE A 189 TYR 0.014 0.001 TYR A 36 ARG 0.003 0.000 ARG G 12 *********************** 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 241 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 187 time to evaluate : 1.263 Fit side-chains REVERT: A 217 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7151 (p0) REVERT: A 262 ASP cc_start: 0.8191 (p0) cc_final: 0.7973 (p0) REVERT: B 18 GLN cc_start: 0.6719 (tm-30) cc_final: 0.6427 (tm-30) REVERT: B 32 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7330 (p0) REVERT: B 40 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.6767 (p0) REVERT: B 144 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7901 (pp) REVERT: B 177 GLU cc_start: 0.7036 (tp30) cc_final: 0.6657 (tt0) REVERT: B 200 ASP cc_start: 0.6677 (p0) cc_final: 0.6468 (p0) REVERT: B 222 MET cc_start: 0.8119 (OUTLIER) cc_final: 0.7788 (pp-130) REVERT: B 259 ASP cc_start: 0.7737 (t70) cc_final: 0.7303 (t0) REVERT: B 265 GLU cc_start: 0.8231 (tt0) cc_final: 0.8018 (tt0) REVERT: N 46 GLU cc_start: 0.8381 (tt0) cc_final: 0.8062 (tt0) REVERT: N 105 ARG cc_start: 0.6577 (ttm110) cc_final: 0.6373 (mtm180) REVERT: R 90 PHE cc_start: 0.7751 (t80) cc_final: 0.7512 (t80) REVERT: R 154 MET cc_start: 0.7534 (ptp) cc_final: 0.6752 (mmp) REVERT: R 208 LEU cc_start: 0.8207 (mt) cc_final: 0.7978 (mt) outliers start: 54 outliers final: 20 residues processed: 222 average time/residue: 1.3769 time to fit residues: 326.8960 Evaluate side-chains 194 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 217 ASP Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 40 ASN Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 166 LEU 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 17 SER Chi-restraints excluded: chain N residue 30 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 234 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 43 optimal weight: 0.0670 chunk 52 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 110 optimal weight: 0.0040 chunk 80 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 overall best weight: 0.8232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN B 298 ASN E 183 GLN E 186 GLN N 77 ASN N 123 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.139961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.110877 restraints weight = 13039.946| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.73 r_work: 0.3172 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.6574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10146 Z= 0.141 Angle : 0.512 9.612 13718 Z= 0.266 Chirality : 0.041 0.181 1551 Planarity : 0.003 0.048 1738 Dihedral : 5.646 58.474 1408 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.42 % Allowed : 22.03 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1248 helix: 2.49 (0.25), residues: 418 sheet: 0.37 (0.29), residues: 317 loop : -0.39 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 PHE 0.018 0.001 PHE R 207 TYR 0.015 0.001 TYR E 190 ARG 0.005 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 169 time to evaluate : 1.215 Fit side-chains REVERT: A 193 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7360 (mtmt) REVERT: A 217 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.7107 (p0) REVERT: A 284 ARG cc_start: 0.7949 (mpp-170) cc_final: 0.7599 (ptp90) REVERT: B 18 GLN cc_start: 0.6719 (tm-30) cc_final: 0.6439 (tm-30) REVERT: B 32 ASP cc_start: 0.7676 (p0) cc_final: 0.7474 (p0) REVERT: B 40 ASN cc_start: 0.7379 (OUTLIER) cc_final: 0.6723 (p0) REVERT: B 60 LEU cc_start: 0.8619 (tt) cc_final: 0.8400 (mp) REVERT: B 64 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8553 (t80) REVERT: B 140 VAL cc_start: 0.8862 (p) cc_final: 0.8656 (t) REVERT: B 144 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7955 (pp) REVERT: B 177 GLU cc_start: 0.7035 (tp30) cc_final: 0.6609 (tt0) REVERT: B 200 ASP cc_start: 0.6781 (p0) cc_final: 0.6560 (p0) REVERT: B 222 MET cc_start: 0.8146 (OUTLIER) cc_final: 0.7894 (pp-130) REVERT: B 259 ASP cc_start: 0.7737 (t70) cc_final: 0.7314 (t0) REVERT: E 73 ASP cc_start: 0.8361 (m-30) cc_final: 0.8039 (m-30) REVERT: E 86 ARG cc_start: 0.6781 (mtt180) cc_final: 0.6467 (ptp-170) REVERT: N 46 GLU cc_start: 0.8394 (tt0) cc_final: 0.8081 (tt0) REVERT: R 90 PHE cc_start: 0.7765 (t80) cc_final: 0.7538 (t80) REVERT: R 154 MET cc_start: 0.7538 (ptp) cc_final: 0.6733 (mmp) REVERT: R 208 LEU cc_start: 0.8187 (mt) cc_final: 0.7934 (mt) outliers start: 48 outliers final: 26 residues processed: 198 average time/residue: 1.2950 time to fit residues: 274.0769 Evaluate side-chains 187 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 187 THR Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 217 ASP 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 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 139 VAL 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 18 LEU 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 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 234 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 39 optimal weight: 7.9990 chunk 92 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 0.0470 chunk 82 optimal weight: 7.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- 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 183 GLN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.133190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102924 restraints weight = 13075.754| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.79 r_work: 0.3042 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.7253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 10146 Z= 0.303 Angle : 0.645 9.919 13718 Z= 0.337 Chirality : 0.046 0.196 1551 Planarity : 0.004 0.049 1738 Dihedral : 5.821 49.200 1408 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.44 % Allowed : 21.84 % Favored : 72.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1248 helix: 2.29 (0.25), residues: 403 sheet: 0.22 (0.29), residues: 317 loop : -0.37 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 295 HIS 0.019 0.002 HIS A 197 PHE 0.016 0.002 PHE A 189 TYR 0.031 0.002 TYR E 190 ARG 0.007 0.001 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 161 time to evaluate : 0.905 Fit side-chains REVERT: B 18 GLN cc_start: 0.6804 (tm-30) cc_final: 0.6492 (tm-30) REVERT: B 32 ASP cc_start: 0.7922 (p0) cc_final: 0.7594 (p0) REVERT: B 40 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6726 (p0) REVERT: B 64 TYR cc_start: 0.8997 (OUTLIER) cc_final: 0.8126 (t80) REVERT: B 140 VAL cc_start: 0.9013 (p) cc_final: 0.8784 (t) REVERT: B 144 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8187 (pp) REVERT: B 259 ASP cc_start: 0.7777 (t70) cc_final: 0.7407 (t0) REVERT: E 73 ASP cc_start: 0.8282 (m-30) cc_final: 0.8063 (m-30) REVERT: E 201 ASP cc_start: 0.7177 (t0) cc_final: 0.6812 (t0) REVERT: N 89 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: R 90 PHE cc_start: 0.7912 (t80) cc_final: 0.7618 (t80) REVERT: R 154 MET cc_start: 0.7553 (ptp) cc_final: 0.6863 (mmp) REVERT: R 208 LEU cc_start: 0.8324 (mt) cc_final: 0.8007 (mt) outliers start: 59 outliers final: 35 residues processed: 206 average time/residue: 1.3240 time to fit residues: 291.0909 Evaluate side-chains 186 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 147 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 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 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 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 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: 0.9980 chunk 116 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.135594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.105344 restraints weight = 13125.306| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.87 r_work: 0.3130 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.7154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10146 Z= 0.162 Angle : 0.536 8.955 13718 Z= 0.280 Chirality : 0.041 0.163 1551 Planarity : 0.004 0.049 1738 Dihedral : 4.835 49.388 1408 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.96 % Allowed : 23.23 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.24), residues: 1248 helix: 2.59 (0.25), residues: 409 sheet: 0.23 (0.29), residues: 309 loop : -0.26 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 295 HIS 0.011 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.019 0.001 TYR A 36 ARG 0.006 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.196 Fit side-chains REVERT: A 321 ARG cc_start: 0.7304 (ptp90) cc_final: 0.7052 (mtm-85) REVERT: B 18 GLN cc_start: 0.6788 (tm-30) cc_final: 0.6522 (tm-30) REVERT: B 32 ASP cc_start: 0.7873 (p0) cc_final: 0.7465 (p0) REVERT: B 40 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.6669 (p0) REVERT: B 64 TYR cc_start: 0.8988 (OUTLIER) cc_final: 0.8201 (t80) REVERT: B 140 VAL cc_start: 0.8917 (p) cc_final: 0.8692 (t) REVERT: B 259 ASP cc_start: 0.7665 (t70) cc_final: 0.7271 (t0) REVERT: E 81 GLN cc_start: 0.8023 (tp40) cc_final: 0.7777 (tp40) REVERT: E 149 VAL cc_start: 0.6355 (p) cc_final: 0.6024 (m) REVERT: E 201 ASP cc_start: 0.7021 (t0) cc_final: 0.6640 (t0) REVERT: N 19 ARG cc_start: 0.7940 (ttt-90) cc_final: 0.7641 (ttt-90) REVERT: N 46 GLU cc_start: 0.8370 (tt0) cc_final: 0.8041 (tt0) REVERT: N 89 GLU cc_start: 0.7354 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: R 90 PHE cc_start: 0.7886 (t80) cc_final: 0.7645 (t80) REVERT: R 154 MET cc_start: 0.7401 (ptp) cc_final: 0.6671 (mmp) REVERT: R 208 LEU cc_start: 0.8257 (mt) cc_final: 0.7942 (mt) outliers start: 43 outliers final: 29 residues processed: 195 average time/residue: 1.4044 time to fit residues: 291.5762 Evaluate side-chains 188 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 225 VAL 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 64 TYR 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 90 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 224 VAL Chi-restraints excluded: chain G residue 18 LEU 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 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 94 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 234 SER 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: 10.0000 chunk 18 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 70 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 4 optimal weight: 0.0040 chunk 57 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 overall best weight: 2.5398 ------------------------------------------------------------------------------- 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** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN R 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103176 restraints weight = 13225.970| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.71 r_work: 0.3071 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10146 Z= 0.255 Angle : 0.602 9.997 13718 Z= 0.317 Chirality : 0.044 0.177 1551 Planarity : 0.004 0.049 1738 Dihedral : 4.933 48.301 1408 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.52 % Allowed : 22.95 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.23), residues: 1248 helix: 2.44 (0.25), residues: 404 sheet: 0.23 (0.28), residues: 325 loop : -0.29 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 295 HIS 0.010 0.002 HIS A 197 PHE 0.016 0.002 PHE A 189 TYR 0.027 0.002 TYR E 190 ARG 0.005 0.001 ARG E 180 *********************** 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 208 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 1.226 Fit side-chains REVERT: A 321 ARG cc_start: 0.7461 (ptp90) cc_final: 0.7225 (mpp-170) REVERT: B 18 GLN cc_start: 0.6785 (tm-30) cc_final: 0.6508 (tm-30) REVERT: B 19 LEU cc_start: 0.7379 (mt) cc_final: 0.6781 (mt) REVERT: B 32 ASP cc_start: 0.7961 (p0) cc_final: 0.7745 (p0) REVERT: B 40 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6655 (p0) REVERT: B 64 TYR cc_start: 0.8992 (OUTLIER) cc_final: 0.8023 (t80) REVERT: B 140 VAL cc_start: 0.8984 (p) cc_final: 0.8748 (t) REVERT: B 259 ASP cc_start: 0.7734 (t70) cc_final: 0.7372 (t0) REVERT: E 18 LYS cc_start: 0.8004 (tttm) cc_final: 0.7804 (tttp) REVERT: E 81 GLN cc_start: 0.7975 (tp40) cc_final: 0.7690 (tp40) REVERT: E 149 VAL cc_start: 0.6398 (p) cc_final: 0.5931 (m) REVERT: E 156 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.7928 (t) REVERT: E 201 ASP cc_start: 0.7094 (t0) cc_final: 0.6722 (t0) REVERT: N 46 GLU cc_start: 0.8412 (tt0) cc_final: 0.8074 (tt0) REVERT: R 90 PHE cc_start: 0.7979 (t80) cc_final: 0.7774 (t80) REVERT: R 154 MET cc_start: 0.7518 (ptp) cc_final: 0.6849 (mmp) REVERT: R 208 LEU cc_start: 0.8285 (mt) cc_final: 0.7980 (mt) outliers start: 49 outliers final: 36 residues processed: 193 average time/residue: 1.4038 time to fit residues: 288.3344 Evaluate side-chains 194 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 70 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 267 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 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 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 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 263 SER 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: 2.9990 chunk 78 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** 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 = 0.3683 r_free = 0.3683 target = 0.136387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.106582 restraints weight = 13159.268| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.86 r_work: 0.3156 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10146 Z= 0.139 Angle : 0.508 8.801 13718 Z= 0.267 Chirality : 0.041 0.158 1551 Planarity : 0.004 0.055 1738 Dihedral : 4.355 50.677 1408 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.50 % Allowed : 24.61 % Favored : 71.89 % 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: 1.34 (0.24), residues: 1248 helix: 2.75 (0.25), residues: 406 sheet: 0.39 (0.29), residues: 305 loop : -0.22 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 295 HIS 0.009 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.018 0.001 TYR A 36 ARG 0.009 0.000 ARG E 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2496 Ramachandran restraints generated. 1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.162 Fit side-chains REVERT: A 34 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: A 321 ARG cc_start: 0.7395 (ptp90) cc_final: 0.7116 (mpp-170) REVERT: B 18 GLN cc_start: 0.6760 (tm-30) cc_final: 0.6505 (tm-30) REVERT: B 19 LEU cc_start: 0.7317 (mt) cc_final: 0.6749 (mt) REVERT: B 32 ASP cc_start: 0.8041 (p0) cc_final: 0.7551 (p0) REVERT: B 40 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.6642 (p0) REVERT: B 64 TYR cc_start: 0.8960 (OUTLIER) cc_final: 0.8500 (t80) REVERT: B 140 VAL cc_start: 0.8800 (p) cc_final: 0.8581 (t) REVERT: B 219 ARG cc_start: 0.7033 (mmt180) cc_final: 0.6826 (mmt180) REVERT: B 259 ASP cc_start: 0.7620 (t70) cc_final: 0.7238 (t0) REVERT: E 201 ASP cc_start: 0.6898 (t0) cc_final: 0.6522 (t0) REVERT: N 19 ARG cc_start: 0.7964 (ttt-90) cc_final: 0.7645 (ttt-90) REVERT: N 46 GLU cc_start: 0.8346 (tt0) cc_final: 0.8008 (tt0) REVERT: R 90 PHE cc_start: 0.7959 (t80) cc_final: 0.7726 (t80) REVERT: R 154 MET cc_start: 0.7416 (ptp) cc_final: 0.6673 (mmp) REVERT: R 208 LEU cc_start: 0.8248 (mt) cc_final: 0.7957 (mt) outliers start: 38 outliers final: 26 residues processed: 189 average time/residue: 1.4032 time to fit residues: 282.2985 Evaluate side-chains 184 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 34 GLN 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 64 TYR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 267 MET 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 166 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 R 297 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105119 restraints weight = 13128.992| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.84 r_work: 0.3077 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10146 Z= 0.189 Angle : 0.555 9.485 13718 Z= 0.291 Chirality : 0.042 0.160 1551 Planarity : 0.004 0.057 1738 Dihedral : 4.563 49.824 1408 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.52 % Allowed : 23.87 % Favored : 71.61 % 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: 1.34 (0.24), residues: 1248 helix: 2.69 (0.25), residues: 405 sheet: 0.39 (0.29), residues: 322 loop : -0.20 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 295 HIS 0.010 0.001 HIS A 197 PHE 0.016 0.001 PHE A 189 TYR 0.021 0.001 TYR E 190 ARG 0.008 0.000 ARG E 180 *********************** 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 210 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 161 time to evaluate : 1.145 Fit side-chains REVERT: A 321 ARG cc_start: 0.7549 (ptp90) cc_final: 0.7251 (mpp-170) REVERT: B 18 GLN cc_start: 0.6776 (tm-30) cc_final: 0.6511 (tm-30) REVERT: B 19 LEU cc_start: 0.7346 (mt) cc_final: 0.6770 (mt) REVERT: B 32 ASP cc_start: 0.8096 (p0) cc_final: 0.7576 (p0) REVERT: B 40 ASN cc_start: 0.7276 (OUTLIER) cc_final: 0.6645 (p0) REVERT: B 64 TYR cc_start: 0.8998 (OUTLIER) cc_final: 0.8213 (t80) REVERT: B 140 VAL cc_start: 0.8931 (p) cc_final: 0.8684 (t) REVERT: B 219 ARG cc_start: 0.7002 (mmt180) cc_final: 0.6715 (mmt180) REVERT: E 201 ASP cc_start: 0.7035 (t0) cc_final: 0.6698 (t0) REVERT: G 12 ARG cc_start: 0.6104 (ptp-170) cc_final: 0.5896 (ptp-170) REVERT: N 19 ARG cc_start: 0.7959 (ttt-90) cc_final: 0.7666 (ttt-90) REVERT: N 46 GLU cc_start: 0.8508 (tt0) cc_final: 0.8172 (tt0) REVERT: N 89 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: R 154 MET cc_start: 0.7569 (ptp) cc_final: 0.6859 (mmp) REVERT: R 208 LEU cc_start: 0.8266 (mt) cc_final: 0.7970 (mt) REVERT: R 269 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7850 (tpt) outliers start: 49 outliers final: 35 residues processed: 193 average time/residue: 1.3878 time to fit residues: 285.6241 Evaluate side-chains 196 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 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 267 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 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 166 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 215 THR 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 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 263 SER 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: 8.9990 chunk 90 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 115 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.0980 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 49 GLN B 345 ASN G 58 ASN N 77 ASN N 123 GLN R 189 ASN R 297 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.132213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.102421 restraints weight = 13125.245| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.79 r_work: 0.3017 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.7721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10146 Z= 0.297 Angle : 0.648 9.920 13718 Z= 0.340 Chirality : 0.046 0.188 1551 Planarity : 0.005 0.059 1738 Dihedral : 5.178 49.061 1408 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.61 % Allowed : 23.78 % Favored : 71.61 % 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: 1.05 (0.23), residues: 1248 helix: 2.33 (0.25), residues: 404 sheet: 0.28 (0.28), residues: 324 loop : -0.29 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 295 HIS 0.013 0.002 HIS A 197 PHE 0.018 0.002 PHE A 223 TYR 0.026 0.002 TYR E 190 ARG 0.008 0.001 ARG E 180 ********************** 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 215 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.047 Fit side-chains REVERT: A 321 ARG cc_start: 0.7642 (ptp90) cc_final: 0.7326 (mpp-170) REVERT: B 18 GLN cc_start: 0.6893 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 19 LEU cc_start: 0.7343 (mt) cc_final: 0.6759 (mt) REVERT: B 32 ASP cc_start: 0.8126 (p0) cc_final: 0.7612 (p0) REVERT: B 40 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6695 (p0) REVERT: B 64 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8091 (t80) REVERT: E 149 VAL cc_start: 0.6648 (p) cc_final: 0.6255 (m) REVERT: E 156 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.7953 (t) REVERT: E 158 SER cc_start: 0.8002 (t) cc_final: 0.7550 (p) REVERT: E 201 ASP cc_start: 0.7243 (t0) cc_final: 0.6922 (t0) REVERT: N 19 ARG cc_start: 0.7953 (ttt-90) cc_final: 0.7629 (ttt-90) REVERT: N 38 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.8180 (ptm160) REVERT: N 89 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: R 154 MET cc_start: 0.7617 (ptp) cc_final: 0.6936 (mmp) REVERT: R 208 LEU cc_start: 0.8307 (mt) cc_final: 0.7977 (mt) REVERT: R 269 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7880 (tpt) outliers start: 50 outliers final: 36 residues processed: 205 average time/residue: 1.4287 time to fit residues: 311.2495 Evaluate side-chains 200 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 158 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 222 MET Chi-restraints excluded: chain B residue 267 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 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 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 38 ARG Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 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: 3.9990 chunk 62 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 49 GLN N 77 ASN N 123 GLN R 189 ASN R 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.131494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101938 restraints weight = 13156.583| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.71 r_work: 0.3039 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.7851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10146 Z= 0.313 Angle : 0.662 10.168 13718 Z= 0.346 Chirality : 0.046 0.183 1551 Planarity : 0.005 0.059 1738 Dihedral : 5.374 54.791 1408 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: 0.95 (0.23), residues: 1248 helix: 2.20 (0.25), residues: 404 sheet: 0.23 (0.28), residues: 324 loop : -0.30 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 295 HIS 0.013 0.002 HIS A 197 PHE 0.019 0.002 PHE A 223 TYR 0.025 0.002 TYR E 190 ARG 0.010 0.001 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9008.26 seconds wall clock time: 159 minutes 32.32 seconds (9572.32 seconds total)