Starting phenix.real_space_refine on Sat Aug 23 04:50:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iuk_35724/08_2025/8iuk_35724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iuk_35724/08_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_35724/08_2025/8iuk_35724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iuk_35724/08_2025/8iuk_35724.map" model { file = "/net/cci-nas-00/data/ceres_data/8iuk_35724/08_2025/8iuk_35724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iuk_35724/08_2025/8iuk_35724.cif" } resolution = 2.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6305 2.51 5 N 1716 2.21 5 O 1860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.56, per 1000 atoms: 0.26 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: 1.09 Conformation dependent library (CDL) restraints added in 438.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.40 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: 1.71 Time building geometry restraints manager: 1.37 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.570 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.201 10149 Z= 0.250 Angle : 0.525 15.493 13724 Z= 0.300 Chirality : 0.044 0.518 1551 Planarity : 0.003 0.037 1738 Dihedral : 8.040 82.485 3681 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG R 133 TYR 0.006 0.000 TYR E 101 PHE 0.006 0.001 PHE A 189 TRP 0.005 0.001 TRP R 295 HIS 0.002 0.000 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00423 (10146) covalent geometry : angle 0.52466 (13718) SS BOND : bond 0.00150 ( 3) SS BOND : angle 0.52246 ( 6) hydrogen bonds : bond 0.10373 ( 472) hydrogen bonds : angle 4.56636 ( 1350) *********************** 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 : 0.417 Fit side-chains REVERT: A 23 LYS cc_start: 0.7132 (mttm) cc_final: 0.6586 (mptt) REVERT: A 26 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7141 (mt-10) REVERT: A 31 LYS cc_start: 0.7647 (mttp) cc_final: 0.7338 (mtpt) REVERT: A 195 ASN cc_start: 0.8152 (m-40) cc_final: 0.7936 (m110) REVERT: A 197 HIS cc_start: 0.5832 (m170) cc_final: 0.5574 (m170) REVERT: A 235 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6390 (tt0) REVERT: A 241 LYS cc_start: 0.7772 (tttt) cc_final: 0.7548 (ttmp) REVERT: A 257 PHE cc_start: 0.7494 (m-10) cc_final: 0.7267 (m-80) REVERT: A 262 ASP cc_start: 0.7449 (p0) cc_final: 0.6955 (p0) REVERT: A 286 THR cc_start: 0.7056 (t) cc_final: 0.6727 (m) REVERT: E 4 VAL cc_start: 0.6784 (t) cc_final: 0.6542 (m) REVERT: E 155 VAL cc_start: 0.8088 (t) cc_final: 0.7823 (t) outliers start: 4 outliers final: 2 residues processed: 395 average time/residue: 0.6268 time to fit residues: 264.1990 Evaluate side-chains 194 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 0.382 ------------------------------------------------------------------------------- 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 108 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.0030 chunk 33 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 213 GLN A 261 GLN A 327 HIS A 350 GLN B 235 ASN B 264 GLN B 273 ASN B 298 ASN E 34 HIS E 142 GLN E 179 GLN E 183 GLN N 13 GLN N 39 GLN N 77 ASN N 123 GLN R 81 HIS R 180 GLN 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 = 0.4061 r_free = 0.4061 target = 0.169574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.141450 restraints weight = 13416.288| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.86 r_work: 0.3640 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10149 Z= 0.105 Angle : 0.511 9.012 13724 Z= 0.261 Chirality : 0.041 0.173 1551 Planarity : 0.003 0.042 1738 Dihedral : 5.347 57.278 1413 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.61 % Allowed : 16.22 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.23), residues: 1248 helix: 2.33 (0.26), residues: 409 sheet: 0.02 (0.29), residues: 289 loop : -1.13 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 72 TYR 0.010 0.001 TYR A 36 PHE 0.016 0.001 PHE A 223 TRP 0.015 0.001 TRP R 295 HIS 0.007 0.001 HIS E 167 Details of bonding type rmsd covalent geometry : bond 0.00224 (10146) covalent geometry : angle 0.51093 (13718) SS BOND : bond 0.00287 ( 3) SS BOND : angle 0.90799 ( 6) hydrogen bonds : bond 0.02678 ( 472) hydrogen bonds : angle 3.64336 ( 1350) *********************** 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 272 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 222 time to evaluate : 0.323 Fit side-chains REVERT: A 257 PHE cc_start: 0.8339 (m-10) cc_final: 0.8005 (m-80) REVERT: A 286 THR cc_start: 0.7471 (t) cc_final: 0.7150 (m) REVERT: B 222 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7224 (pp-130) REVERT: E 4 VAL cc_start: 0.7119 (t) cc_final: 0.6904 (p) REVERT: E 180 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7470 (mtt90) REVERT: E 183 GLN cc_start: 0.5814 (mt0) cc_final: 0.5400 (mp10) REVERT: G 18 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6790 (mt) REVERT: N 80 TYR cc_start: 0.6890 (m-80) cc_final: 0.6666 (m-80) REVERT: N 123 GLN cc_start: 0.7644 (tp-100) cc_final: 0.7357 (tp40) REVERT: R 155 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5257 (ptp) outliers start: 50 outliers final: 17 residues processed: 252 average time/residue: 0.6736 time to fit residues: 180.6356 Evaluate side-chains 200 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 155 MET Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 12 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN A 327 HIS A 336 ASN B 181 GLN ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 HIS B 273 ASN E 186 GLN N 13 GLN N 77 ASN R 297 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111053 restraints weight = 13133.273| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.66 r_work: 0.3152 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.6346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10149 Z= 0.195 Angle : 0.661 12.056 13724 Z= 0.344 Chirality : 0.046 0.201 1551 Planarity : 0.004 0.044 1738 Dihedral : 6.160 55.449 1408 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.79 % Allowed : 18.25 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.23), residues: 1248 helix: 2.07 (0.25), residues: 411 sheet: 0.10 (0.28), residues: 314 loop : -0.56 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 12 TYR 0.032 0.002 TYR E 190 PHE 0.020 0.002 PHE N 103 TRP 0.016 0.002 TRP A 248 HIS 0.007 0.002 HIS E 232 Details of bonding type rmsd covalent geometry : bond 0.00445 (10146) covalent geometry : angle 0.66136 (13718) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.85270 ( 6) hydrogen bonds : bond 0.04228 ( 472) hydrogen bonds : angle 4.48944 ( 1350) *********************** 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 262 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 210 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 234 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8223 (tm-30) REVERT: A 281 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7782 (tm-30) REVERT: A 286 THR cc_start: 0.8110 (t) cc_final: 0.7883 (m) REVERT: B 27 ARG cc_start: 0.7411 (ttm170) cc_final: 0.7158 (ttm-80) REVERT: B 64 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8124 (t80) REVERT: B 177 GLU cc_start: 0.7124 (tp30) cc_final: 0.6736 (tt0) REVERT: B 222 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7914 (pp-130) REVERT: B 259 ASP cc_start: 0.7827 (t70) cc_final: 0.7369 (t0) REVERT: E 86 ARG cc_start: 0.6790 (ptp-170) cc_final: 0.6580 (mtt180) REVERT: E 201 ASP cc_start: 0.7228 (t0) cc_final: 0.6904 (t0) REVERT: G 28 LYS cc_start: 0.8319 (OUTLIER) cc_final: 0.7488 (mptp) REVERT: G 57 GLU cc_start: 0.6894 (mp0) cc_final: 0.6680 (mp0) REVERT: G 58 ASN cc_start: 0.4840 (t0) cc_final: 0.4436 (t160) REVERT: N 46 GLU cc_start: 0.8508 (tt0) cc_final: 0.8203 (tt0) REVERT: N 123 GLN cc_start: 0.8064 (tp-100) cc_final: 0.7804 (tp40) REVERT: R 59 ARG cc_start: 0.7241 (ttp80) cc_final: 0.7036 (ptm160) REVERT: R 90 PHE cc_start: 0.7642 (t80) cc_final: 0.7395 (t80) REVERT: R 154 MET cc_start: 0.7515 (ptp) cc_final: 0.7249 (ptt) REVERT: R 208 LEU cc_start: 0.8217 (mt) cc_final: 0.7919 (mt) REVERT: R 291 ARG cc_start: 0.7561 (mmt90) cc_final: 0.7261 (mmm-85) outliers start: 52 outliers final: 25 residues processed: 243 average time/residue: 0.6390 time to fit residues: 165.8784 Evaluate side-chains 196 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 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 G residue 18 LEU Chi-restraints excluded: chain G residue 28 LYS 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 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 Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 112 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 87 optimal weight: 0.0980 chunk 52 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN E 183 GLN E 186 GLN N 77 ASN N 82 GLN R 297 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108676 restraints weight = 13280.802| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.69 r_work: 0.3123 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.6614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10149 Z= 0.136 Angle : 0.565 9.785 13724 Z= 0.293 Chirality : 0.043 0.168 1551 Planarity : 0.004 0.046 1738 Dihedral : 5.922 56.476 1408 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.07 % Allowed : 21.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.24), residues: 1248 helix: 2.39 (0.25), residues: 408 sheet: 0.21 (0.28), residues: 315 loop : -0.34 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 139 TYR 0.020 0.001 TYR E 190 PHE 0.015 0.002 PHE A 189 TRP 0.015 0.002 TRP R 295 HIS 0.009 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00311 (10146) covalent geometry : angle 0.56492 (13718) SS BOND : bond 0.00195 ( 3) SS BOND : angle 0.49555 ( 6) hydrogen bonds : bond 0.03681 ( 472) hydrogen bonds : angle 4.24510 ( 1350) *********************** 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 222 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 167 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 217 ASP cc_start: 0.7799 (p0) cc_final: 0.7551 (p0) REVERT: A 234 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8245 (tm-30) REVERT: A 281 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7824 (tm-30) REVERT: B 60 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8393 (mp) REVERT: B 64 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8011 (t80) REVERT: B 219 ARG cc_start: 0.7444 (mmt90) cc_final: 0.7201 (mmt90) REVERT: B 222 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7955 (pp-130) REVERT: B 259 ASP cc_start: 0.7800 (t70) cc_final: 0.7377 (t0) REVERT: B 265 GLU cc_start: 0.8196 (tt0) cc_final: 0.7975 (tt0) REVERT: N 46 GLU cc_start: 0.8501 (tt0) cc_final: 0.8183 (tt0) REVERT: N 123 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7791 (tp40) REVERT: R 90 PHE cc_start: 0.7684 (t80) cc_final: 0.7452 (t80) REVERT: R 154 MET cc_start: 0.7588 (ptp) cc_final: 0.6763 (mmp) REVERT: R 208 LEU cc_start: 0.8176 (mt) cc_final: 0.7905 (mt) REVERT: R 291 ARG cc_start: 0.7540 (mmt90) cc_final: 0.7279 (mmm-85) outliers start: 55 outliers final: 31 residues processed: 205 average time/residue: 0.6864 time to fit residues: 149.7430 Evaluate side-chains 189 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 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 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 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS E 183 GLN E 186 GLN N 77 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 = 0.3690 r_free = 0.3690 target = 0.137428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108283 restraints weight = 13181.330| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.69 r_work: 0.3132 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10149 Z= 0.124 Angle : 0.541 9.436 13724 Z= 0.281 Chirality : 0.042 0.171 1551 Planarity : 0.004 0.047 1738 Dihedral : 5.726 59.706 1408 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.07 % Allowed : 21.66 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (0.24), residues: 1248 helix: 2.58 (0.25), residues: 409 sheet: 0.29 (0.29), residues: 315 loop : -0.22 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 139 TYR 0.019 0.001 TYR E 190 PHE 0.015 0.001 PHE A 189 TRP 0.014 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00280 (10146) covalent geometry : angle 0.54096 (13718) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.46992 ( 6) hydrogen bonds : bond 0.03482 ( 472) hydrogen bonds : angle 4.19492 ( 1350) *********************** 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 218 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 0.412 Fit side-chains REVERT: A 234 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8276 (tm-30) REVERT: A 281 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7822 (tm-30) REVERT: B 64 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.7977 (t80) REVERT: B 177 GLU cc_start: 0.7204 (tp30) cc_final: 0.6707 (tt0) REVERT: B 222 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (pp-130) REVERT: B 259 ASP cc_start: 0.7701 (t70) cc_final: 0.7313 (t0) REVERT: N 46 GLU cc_start: 0.8442 (tt0) cc_final: 0.8110 (tt0) REVERT: N 123 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7774 (tp40) REVERT: R 90 PHE cc_start: 0.7762 (t80) cc_final: 0.7559 (t80) REVERT: R 154 MET cc_start: 0.7577 (ptp) cc_final: 0.6777 (mmp) REVERT: R 161 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.7287 (mt) REVERT: R 208 LEU cc_start: 0.8193 (mt) cc_final: 0.7916 (mt) REVERT: R 291 ARG cc_start: 0.7498 (mmt90) cc_final: 0.7244 (mmm-85) outliers start: 55 outliers final: 38 residues processed: 200 average time/residue: 0.6905 time to fit residues: 146.9260 Evaluate side-chains 196 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 154 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 234 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 222 MET Chi-restraints excluded: chain B residue 279 THR 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 199 VAL 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 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 161 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 Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 54 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 120 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN E 183 GLN N 77 ASN N 123 GLN R 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.137810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110429 restraints weight = 13225.174| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.62 r_work: 0.3168 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10149 Z= 0.106 Angle : 0.511 9.524 13724 Z= 0.266 Chirality : 0.041 0.157 1551 Planarity : 0.003 0.048 1738 Dihedral : 5.311 54.995 1408 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.16 % Allowed : 22.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.24), residues: 1248 helix: 2.76 (0.25), residues: 409 sheet: 0.31 (0.29), residues: 319 loop : -0.12 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.016 0.001 TYR E 190 PHE 0.016 0.001 PHE A 189 TRP 0.013 0.001 TRP R 295 HIS 0.004 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00235 (10146) covalent geometry : angle 0.51118 (13718) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.49316 ( 6) hydrogen bonds : bond 0.03230 ( 472) hydrogen bonds : angle 4.07843 ( 1350) *********************** 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 223 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 167 time to evaluate : 0.453 Fit side-chains revert: symmetry clash REVERT: A 217 ASP cc_start: 0.7368 (p0) cc_final: 0.7019 (p0) REVERT: A 234 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8240 (tm-30) REVERT: B 47 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6653 (ttm170) REVERT: B 64 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7921 (t80) REVERT: B 224 ARG cc_start: 0.8083 (mtp85) cc_final: 0.7501 (mmt180) REVERT: B 259 ASP cc_start: 0.7695 (t70) cc_final: 0.7314 (t0) REVERT: E 137 ASP cc_start: 0.6754 (OUTLIER) cc_final: 0.6465 (p0) REVERT: N 46 GLU cc_start: 0.8395 (tt0) cc_final: 0.8058 (tt0) REVERT: N 123 GLN cc_start: 0.7975 (tp40) cc_final: 0.7585 (tp-100) REVERT: R 90 PHE cc_start: 0.7762 (t80) cc_final: 0.7526 (t80) REVERT: R 154 MET cc_start: 0.7513 (ptp) cc_final: 0.6752 (mmp) REVERT: R 161 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.7346 (mt) REVERT: R 208 LEU cc_start: 0.8263 (mt) cc_final: 0.7982 (mt) REVERT: R 291 ARG cc_start: 0.7441 (mmt90) cc_final: 0.7174 (mmm-85) outliers start: 56 outliers final: 34 residues processed: 202 average time/residue: 0.7162 time to fit residues: 153.7778 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 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 234 GLN Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 279 THR 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 137 ASP 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 199 VAL 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 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 161 LEU Chi-restraints excluded: chain R residue 263 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN E 183 GLN N 77 ASN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.132434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.103133 restraints weight = 13204.032| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.78 r_work: 0.3028 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.7449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 10149 Z= 0.218 Angle : 0.664 10.651 13724 Z= 0.349 Chirality : 0.047 0.197 1551 Planarity : 0.004 0.048 1738 Dihedral : 5.340 46.910 1408 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.90 % Allowed : 21.75 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.24), residues: 1248 helix: 2.26 (0.25), residues: 404 sheet: 0.42 (0.29), residues: 314 loop : -0.31 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 180 TYR 0.026 0.002 TYR E 190 PHE 0.018 0.002 PHE A 189 TRP 0.015 0.002 TRP R 295 HIS 0.016 0.002 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00516 (10146) covalent geometry : angle 0.66413 (13718) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.79146 ( 6) hydrogen bonds : bond 0.04356 ( 472) hydrogen bonds : angle 4.58986 ( 1350) *********************** 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 228 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 164 time to evaluate : 0.505 Fit side-chains REVERT: A 321 ARG cc_start: 0.7626 (ptp90) cc_final: 0.7376 (mtm-85) REVERT: B 47 ARG cc_start: 0.7156 (OUTLIER) cc_final: 0.6742 (ttm170) REVERT: B 64 TYR cc_start: 0.9025 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 259 ASP cc_start: 0.7826 (t70) cc_final: 0.7495 (t0) REVERT: G 12 ARG cc_start: 0.6546 (ptp90) cc_final: 0.6165 (ptp-170) REVERT: N 89 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: N 123 GLN cc_start: 0.8001 (tp40) cc_final: 0.7667 (tp-100) REVERT: R 90 PHE cc_start: 0.7924 (t80) cc_final: 0.7713 (t80) REVERT: R 154 MET cc_start: 0.7747 (ptp) cc_final: 0.6951 (mmp) REVERT: R 208 LEU cc_start: 0.8370 (mt) cc_final: 0.8028 (mt) REVERT: R 291 ARG cc_start: 0.7666 (mmt90) cc_final: 0.7431 (mmm-85) outliers start: 64 outliers final: 45 residues processed: 209 average time/residue: 0.7144 time to fit residues: 158.5238 Evaluate side-chains 201 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 48 ASP 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 311 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 22 SER Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 43 LYS Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 57 optimal weight: 0.0060 chunk 68 optimal weight: 0.0060 chunk 90 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.0770 chunk 74 optimal weight: 6.9990 overall best weight: 0.5772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 271 HIS N 77 ASN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.137311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109562 restraints weight = 13084.849| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.61 r_work: 0.3162 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10149 Z= 0.100 Angle : 0.517 9.127 13724 Z= 0.272 Chirality : 0.041 0.169 1551 Planarity : 0.004 0.049 1738 Dihedral : 4.362 47.505 1408 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.32 % Allowed : 23.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.24), residues: 1248 helix: 2.70 (0.25), residues: 405 sheet: 0.37 (0.29), residues: 316 loop : -0.11 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.026 0.001 TYR E 235 PHE 0.018 0.001 PHE A 189 TRP 0.014 0.001 TRP R 295 HIS 0.008 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00213 (10146) covalent geometry : angle 0.51726 (13718) SS BOND : bond 0.00111 ( 3) SS BOND : angle 0.45444 ( 6) hydrogen bonds : bond 0.03219 ( 472) hydrogen bonds : angle 4.13574 ( 1350) *********************** 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 201 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 0.470 Fit side-chains REVERT: A 217 ASP cc_start: 0.7357 (p0) cc_final: 0.7056 (p0) REVERT: A 321 ARG cc_start: 0.7440 (ptp90) cc_final: 0.7192 (mpp-170) REVERT: B 47 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6732 (ttm170) REVERT: B 64 TYR cc_start: 0.8978 (OUTLIER) cc_final: 0.8090 (t80) REVERT: B 259 ASP cc_start: 0.7679 (t70) cc_final: 0.7362 (t0) REVERT: E 75 LYS cc_start: 0.7704 (mtmt) cc_final: 0.7479 (ptpt) REVERT: E 137 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6879 (p0) REVERT: G 12 ARG cc_start: 0.6375 (ptp90) cc_final: 0.5970 (ptp-170) REVERT: N 46 GLU cc_start: 0.8355 (tt0) cc_final: 0.8052 (tt0) REVERT: N 123 GLN cc_start: 0.7951 (tp40) cc_final: 0.7653 (tp-100) REVERT: R 90 PHE cc_start: 0.7969 (t80) cc_final: 0.7750 (t80) REVERT: R 154 MET cc_start: 0.7517 (ptp) cc_final: 0.6805 (mmp) REVERT: R 208 LEU cc_start: 0.8262 (mt) cc_final: 0.7993 (mt) REVERT: R 291 ARG cc_start: 0.7436 (mmt90) cc_final: 0.7154 (mmm-85) outliers start: 36 outliers final: 21 residues processed: 187 average time/residue: 0.7184 time to fit residues: 142.7729 Evaluate side-chains 176 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 137 ASP 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 199 VAL Chi-restraints excluded: chain E residue 224 VAL Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 15 optimal weight: 0.4980 chunk 121 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 5 optimal weight: 0.0770 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS 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 = 0.3693 r_free = 0.3693 target = 0.137208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110147 restraints weight = 13209.794| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.54 r_work: 0.3194 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.7157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10149 Z= 0.101 Angle : 0.519 9.292 13724 Z= 0.273 Chirality : 0.041 0.189 1551 Planarity : 0.004 0.049 1738 Dihedral : 4.219 47.895 1408 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.86 % Allowed : 25.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.24), residues: 1248 helix: 2.73 (0.25), residues: 405 sheet: 0.43 (0.29), residues: 331 loop : -0.05 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 180 TYR 0.029 0.001 TYR E 235 PHE 0.022 0.001 PHE A 189 TRP 0.012 0.001 TRP R 295 HIS 0.011 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00219 (10146) covalent geometry : angle 0.51921 (13718) SS BOND : bond 0.00089 ( 3) SS BOND : angle 0.44172 ( 6) hydrogen bonds : bond 0.03189 ( 472) hydrogen bonds : angle 4.07296 ( 1350) *********************** 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 185 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.432 Fit side-chains REVERT: A 193 LYS cc_start: 0.7981 (mmtm) cc_final: 0.7581 (mppt) REVERT: A 217 ASP cc_start: 0.7229 (p0) cc_final: 0.6898 (p0) REVERT: A 262 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7934 (p0) REVERT: A 321 ARG cc_start: 0.7315 (ptp90) cc_final: 0.7097 (mpp-170) REVERT: B 47 ARG cc_start: 0.7055 (OUTLIER) cc_final: 0.6652 (ttm170) REVERT: B 64 TYR cc_start: 0.8952 (OUTLIER) cc_final: 0.8113 (t80) REVERT: B 259 ASP cc_start: 0.7622 (t70) cc_final: 0.7297 (t0) REVERT: E 73 ASP cc_start: 0.8011 (m-30) cc_final: 0.7808 (m-30) REVERT: E 137 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6898 (p0) REVERT: E 160 ARG cc_start: 0.7732 (ttm170) cc_final: 0.7501 (tmm-80) REVERT: N 46 GLU cc_start: 0.8359 (tt0) cc_final: 0.8020 (tt0) REVERT: N 105 ARG cc_start: 0.6588 (ttm110) cc_final: 0.6324 (mtm180) REVERT: N 123 GLN cc_start: 0.7942 (tp40) cc_final: 0.7650 (tp-100) REVERT: R 154 MET cc_start: 0.7428 (ptp) cc_final: 0.6753 (mmp) REVERT: R 208 LEU cc_start: 0.8249 (mt) cc_final: 0.7966 (mt) REVERT: R 269 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7793 (tpt) REVERT: R 291 ARG cc_start: 0.7387 (mmt90) cc_final: 0.7127 (mmm-85) outliers start: 31 outliers final: 22 residues processed: 177 average time/residue: 0.7275 time to fit residues: 136.6049 Evaluate side-chains 170 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 ASP Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 137 ASP 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 199 VAL 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 110 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU 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 92 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 160 ASN N 77 ASN R 297 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.135098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105086 restraints weight = 13175.880| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.80 r_work: 0.3123 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10149 Z= 0.124 Angle : 0.558 9.948 13724 Z= 0.293 Chirality : 0.042 0.207 1551 Planarity : 0.004 0.054 1738 Dihedral : 4.451 49.657 1408 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.13 % Allowed : 25.44 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.24), residues: 1248 helix: 2.69 (0.25), residues: 405 sheet: 0.35 (0.29), residues: 323 loop : -0.05 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 180 TYR 0.024 0.001 TYR E 235 PHE 0.023 0.001 PHE A 189 TRP 0.014 0.001 TRP R 295 HIS 0.015 0.001 HIS A 197 Details of bonding type rmsd covalent geometry : bond 0.00281 (10146) covalent geometry : angle 0.55797 (13718) SS BOND : bond 0.00180 ( 3) SS BOND : angle 0.47604 ( 6) hydrogen bonds : bond 0.03489 ( 472) hydrogen bonds : angle 4.17516 ( 1350) ********************** 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 185 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.405 Fit side-chains REVERT: A 186 GLU cc_start: 0.7716 (tt0) cc_final: 0.7470 (tt0) REVERT: A 217 ASP cc_start: 0.7556 (p0) cc_final: 0.7211 (p0) REVERT: A 262 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7944 (p0) REVERT: A 321 ARG cc_start: 0.7467 (ptp90) cc_final: 0.7194 (mpp-170) REVERT: B 47 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6682 (ttm170) REVERT: B 64 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8010 (t80) REVERT: B 259 ASP cc_start: 0.7718 (t70) cc_final: 0.7289 (t0) REVERT: B 267 MET cc_start: 0.8425 (tpt) cc_final: 0.8158 (tpt) REVERT: E 81 GLN cc_start: 0.7915 (tp40) cc_final: 0.7594 (mm-40) REVERT: E 156 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7855 (t) REVERT: N 46 GLU cc_start: 0.8395 (tt0) cc_final: 0.8040 (tt0) REVERT: N 123 GLN cc_start: 0.7968 (tp40) cc_final: 0.7611 (tp-100) REVERT: R 154 MET cc_start: 0.7568 (ptp) cc_final: 0.6699 (mmp) REVERT: R 208 LEU cc_start: 0.8200 (mt) cc_final: 0.7881 (mt) REVERT: R 269 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7825 (tpt) REVERT: R 291 ARG cc_start: 0.7362 (mmt90) cc_final: 0.7104 (mmm-85) outliers start: 34 outliers final: 20 residues processed: 175 average time/residue: 0.7242 time to fit residues: 134.8346 Evaluate side-chains 171 residues out of total 1087 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 ASP Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 279 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 199 VAL 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 110 VAL Chi-restraints excluded: chain R residue 109 SER Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.4909 > 50: distance: 55 - 72: 13.975 distance: 66 - 72: 13.886 distance: 72 - 73: 10.680 distance: 73 - 74: 15.776 distance: 73 - 76: 12.497 distance: 74 - 75: 15.918 distance: 74 - 77: 9.076 distance: 77 - 78: 6.689 distance: 78 - 79: 4.935 distance: 78 - 81: 20.214 distance: 79 - 80: 11.103 distance: 79 - 86: 4.797 distance: 81 - 82: 23.265 distance: 82 - 83: 17.909 distance: 83 - 84: 19.490 distance: 84 - 85: 21.341 distance: 86 - 87: 7.419 distance: 87 - 88: 10.134 distance: 87 - 90: 3.683 distance: 88 - 89: 13.607 distance: 88 - 95: 13.321 distance: 90 - 91: 15.218 distance: 91 - 92: 6.726 distance: 92 - 93: 6.866 distance: 92 - 94: 9.420 distance: 95 - 96: 8.744 distance: 96 - 97: 17.118 distance: 96 - 99: 7.010 distance: 97 - 98: 16.770 distance: 97 - 103: 18.055 distance: 99 - 100: 13.503 distance: 100 - 101: 14.298 distance: 100 - 102: 6.164 distance: 103 - 104: 12.626 distance: 103 - 109: 19.485 distance: 104 - 105: 3.831 distance: 104 - 107: 11.343 distance: 105 - 106: 25.180 distance: 105 - 110: 6.692 distance: 107 - 108: 9.365 distance: 108 - 109: 16.824 distance: 110 - 111: 6.104 distance: 111 - 112: 9.751 distance: 111 - 114: 5.321 distance: 112 - 113: 16.868 distance: 112 - 118: 19.480 distance: 114 - 115: 6.838 distance: 115 - 116: 10.195 distance: 115 - 117: 7.124 distance: 118 - 119: 8.389 distance: 119 - 120: 11.484 distance: 119 - 122: 8.896 distance: 120 - 121: 13.950 distance: 120 - 126: 19.975 distance: 122 - 123: 6.411 distance: 123 - 124: 9.433 distance: 123 - 125: 3.790 distance: 126 - 127: 20.908 distance: 127 - 128: 10.772 distance: 127 - 130: 27.881 distance: 130 - 131: 15.260 distance: 130 - 132: 14.505 distance: 133 - 134: 16.830 distance: 133 - 139: 9.014 distance: 134 - 135: 12.454 distance: 134 - 137: 11.374 distance: 135 - 136: 18.917 distance: 135 - 140: 12.953 distance: 137 - 138: 11.497 distance: 138 - 139: 14.058 distance: 140 - 141: 6.491 distance: 141 - 142: 8.825 distance: 141 - 144: 11.936 distance: 142 - 143: 12.456 distance: 142 - 147: 7.955 distance: 144 - 145: 11.897 distance: 144 - 146: 5.916