Starting phenix.real_space_refine on Sun Aug 24 05:29:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.map" model { file = "/net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x8l_38148/08_2025/8x8l_38148.cif" } resolution = 2.7 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= 0.004 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: 5 Type Number sf(0) Gaussians S 59 5.16 5 C 5641 2.51 5 N 1531 2.21 5 O 1620 1.98 5 H 8704 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 17555 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 3854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 1 Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 4996 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 200 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "E" Number of atoms: 3385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3385 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 834 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 4286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 4286 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 14, 'TRANS': 257} Chain breaks: 1 Time building chain proxies: 3.36, per 1000 atoms: 0.19 Number of scatterers: 17555 At special positions: 0 Unit cell: (123.6, 93.936, 129.368, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 59 16.00 O 1620 8.00 N 1531 7.00 C 5641 6.00 H 8704 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 5 " - pdb=" SG CYS C 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 112 " - 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: 1.59 Conformation dependent library (CDL) restraints added in 505.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.518A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 51 removed outlier: 3.715A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.625A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 245 removed outlier: 4.506A pdb=" N GLN A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.092A pdb=" N ARG A 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 removed outlier: 3.627A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.608A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 319 removed outlier: 3.792A pdb=" N ILE A 315 " --> pdb=" O GLU A 311 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A 319 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 12 through 30 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 220 through 224 removed outlier: 3.540A pdb=" N VAL E 224 " --> pdb=" O ALA E 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 removed outlier: 3.571A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 43 Processing helix chain 'R' and resid 43 through 67 Processing helix chain 'R' and resid 73 through 91 Processing helix chain 'R' and resid 92 through 102 removed outlier: 3.578A pdb=" N ALA R 102 " --> pdb=" O THR R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 143 removed outlier: 4.346A pdb=" N LEU R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU R 114 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 116 " --> pdb=" O CYS R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 178 Proline residue: R 173 - end of helix Processing helix chain 'R' and resid 180 through 184 removed outlier: 4.438A pdb=" N GLY R 183 " --> pdb=" O VAL R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 210 Processing helix chain 'R' and resid 210 through 235 Processing helix chain 'R' and resid 241 through 274 Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 282 through 304 removed outlier: 4.188A pdb=" N TYR R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N PHE R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN R 296 " --> pdb=" O LEU R 292 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER R 297 " --> pdb=" O SER R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 316 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.662A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARG A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 222 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU A 39 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N ASP A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 57 removed outlier: 6.037A pdb=" N THR B 52 " --> pdb=" O ASN B 345 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 345 " --> pdb=" O THR B 52 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG B 54 " --> pdb=" O ILE B 343 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS B 322 " --> pdb=" O GLY B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 3.644A pdb=" N ILE B 85 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 79 " --> pdb=" O LYS B 83 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU B 84 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA B 97 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.442A 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: 6.618A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE B 128 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG B 139 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.871A pdb=" N THR B 183 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 6.643A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 206 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 214 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.542A pdb=" N MET B 267 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ASP B 259 " --> pdb=" O GLU B 265 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLU B 265 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 4.054A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 8 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.566A pdb=" N SER E 71 " --> pdb=" O PHE E 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.952A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 removed outlier: 3.573A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 194 through 195 removed outlier: 6.519A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY E 225 " --> pdb=" O LEU E 245 " (cutoff:3.500A) 460 hydrogen bonds defined for protein. 1278 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: 4.46 Time building geometry restraints manager: 2.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8678 1.02 - 1.22: 46 1.22 - 1.42: 3825 1.42 - 1.62: 5112 1.62 - 1.82: 84 Bond restraints: 17745 Sorted by residual: bond pdb=" SG CYS R 260 " pdb=" HG CYS R 260 " ideal model delta sigma weight residual 1.200 1.339 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" ND2 ASN R 310 " pdb="HD22 ASN R 310 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" ND2 ASN R 310 " pdb="HD21 ASN R 310 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 bond pdb=" NE ARG R 312 " pdb=" HE ARG R 312 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" NE ARG A 309 " pdb=" HE ARG A 309 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 17740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.78: 31897 7.78 - 15.56: 4 15.56 - 23.33: 0 23.33 - 31.11: 1 31.11 - 38.89: 2 Bond angle restraints: 31904 Sorted by residual: angle pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 70.11 38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" N PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 110.00 74.57 35.43 3.00e+00 1.11e-01 1.39e+02 angle pdb=" CB PRO G 54 " pdb=" CA PRO G 54 " pdb=" HA PRO G 54 " ideal model delta sigma weight residual 109.00 78.81 30.19 3.00e+00 1.11e-01 1.01e+02 angle pdb=" N VAL R 207 " pdb=" CA VAL R 207 " pdb=" C VAL R 207 " ideal model delta sigma weight residual 110.30 117.07 -6.77 9.70e-01 1.06e+00 4.87e+01 angle pdb=" N SER A 228 " pdb=" CA SER A 228 " pdb=" C SER A 228 " ideal model delta sigma weight residual 111.82 119.15 -7.33 1.16e+00 7.43e-01 3.99e+01 ... (remaining 31899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 7798 17.74 - 35.49: 395 35.49 - 53.23: 168 53.23 - 70.97: 47 70.97 - 88.72: 9 Dihedral angle restraints: 8417 sinusoidal: 4475 harmonic: 3942 Sorted by residual: dihedral pdb=" CB CYS R 112 " pdb=" SG CYS R 112 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual -86.00 -137.94 51.94 1 1.00e+01 1.00e-02 3.68e+01 dihedral pdb=" C PHE R 211 " pdb=" N PHE R 211 " pdb=" CA PHE R 211 " pdb=" CB PHE R 211 " ideal model delta harmonic sigma weight residual -122.60 -134.21 11.61 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CA PRO G 54 " pdb=" CB PRO G 54 " ideal model delta harmonic sigma weight residual 115.10 124.31 -9.21 0 2.50e+00 1.60e-01 1.36e+01 ... (remaining 8414 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1299 0.095 - 0.190: 87 0.190 - 0.286: 7 0.286 - 0.381: 1 0.381 - 0.476: 3 Chirality restraints: 1397 Sorted by residual: chirality pdb=" CA PRO G 54 " pdb=" N PRO G 54 " pdb=" C PRO G 54 " pdb=" CB PRO G 54 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA PHE R 211 " pdb=" N PHE R 211 " pdb=" C PHE R 211 " pdb=" CB PHE R 211 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA CYS R 260 " pdb=" N CYS R 260 " pdb=" C CYS R 260 " pdb=" CB CYS R 260 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1394 not shown) Planarity restraints: 2649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN R 313 " -0.112 2.00e-02 2.50e+03 1.24e-01 2.31e+02 pdb=" CD GLN R 313 " 0.005 2.00e-02 2.50e+03 pdb=" OE1 GLN R 313 " 0.110 2.00e-02 2.50e+03 pdb=" NE2 GLN R 313 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN R 313 " 0.184 2.00e-02 2.50e+03 pdb="HE22 GLN R 313 " -0.184 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 310 " -0.053 2.00e-02 2.50e+03 5.25e-02 4.14e+01 pdb=" CG ASN R 310 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN R 310 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN R 310 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN R 310 " 0.074 2.00e-02 2.50e+03 pdb="HD22 ASN R 310 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 316 " -0.017 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" N LYS R 317 " 0.056 2.00e-02 2.50e+03 pdb=" CA LYS R 317 " -0.014 2.00e-02 2.50e+03 pdb=" H LYS R 317 " -0.024 2.00e-02 2.50e+03 ... (remaining 2646 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 945 2.19 - 2.79: 35777 2.79 - 3.40: 48855 3.40 - 4.00: 63338 4.00 - 4.60: 97911 Nonbonded interactions: 246826 Sorted by model distance: nonbonded pdb=" O LYS G 19 " pdb="HD21 ASN G 23 " model vdw 1.590 2.450 nonbonded pdb="HH22 ARG A 208 " pdb=" OD1 ASP A 239 " model vdw 1.626 2.450 nonbonded pdb=" OE2 GLU A 8 " pdb=" HH TYR E 175 " model vdw 1.637 2.450 nonbonded pdb=" O ILE E 138 " pdb=" HG1 THR E 238 " model vdw 1.638 2.450 nonbonded pdb="HH12 ARG E 202 " pdb=" OD2 ASP E 223 " model vdw 1.640 2.450 ... (remaining 246821 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: 1.030 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: 0.100 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.550 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 0.068 9045 Z= 0.312 Angle : 0.603 9.479 12277 Z= 0.377 Chirality : 0.050 0.476 1397 Planarity : 0.003 0.034 1557 Dihedral : 9.651 75.047 3215 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.89 % Allowed : 3.68 % Favored : 94.43 % Cbeta Deviations : 0.09 % 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: 2.09 (0.26), residues: 1122 helix: 2.97 (0.27), residues: 385 sheet: 1.24 (0.32), residues: 268 loop : 0.15 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 67 TYR 0.009 0.001 TYR R 89 PHE 0.015 0.001 PHE R 315 TRP 0.029 0.001 TRP R 261 HIS 0.002 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9041) covalent geometry : angle 0.60270 (12269) SS BOND : bond 0.00211 ( 4) SS BOND : angle 0.84928 ( 8) hydrogen bonds : bond 0.20308 ( 449) hydrogen bonds : angle 6.67040 ( 1278) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 371 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 353 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 104 PHE cc_start: 0.5863 (t80) cc_final: 0.5513 (t80) REVERT: R 288 PHE cc_start: 0.7375 (t80) cc_final: 0.7131 (t80) REVERT: R 315 PHE cc_start: 0.7383 (t80) cc_final: 0.7086 (t80) outliers start: 18 outliers final: 5 residues processed: 363 average time/residue: 1.3713 time to fit residues: 529.2414 Evaluate side-chains 182 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 177 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 300 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 28 GLN A 204 GLN A 234 GLN B 49 GLN B 225 GLN B 264 GLN E 142 GLN R 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.146544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.118973 restraints weight = 38942.914| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.15 r_work: 0.3477 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9045 Z= 0.128 Angle : 0.540 8.945 12277 Z= 0.285 Chirality : 0.043 0.479 1397 Planarity : 0.004 0.061 1557 Dihedral : 4.983 73.211 1249 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.99 % Allowed : 19.33 % Favored : 76.68 % 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: 2.16 (0.26), residues: 1122 helix: 3.17 (0.26), residues: 385 sheet: 0.95 (0.31), residues: 256 loop : 0.30 (0.31), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 247 TYR 0.014 0.001 TYR R 63 PHE 0.010 0.001 PHE E 203 TRP 0.012 0.001 TRP B 302 HIS 0.003 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9041) covalent geometry : angle 0.53440 (12269) SS BOND : bond 0.00640 ( 4) SS BOND : angle 3.07634 ( 8) hydrogen bonds : bond 0.04541 ( 449) hydrogen bonds : angle 5.03393 ( 1278) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 GLU cc_start: 0.8449 (mp0) cc_final: 0.8243 (mm-30) REVERT: B 50 MET cc_start: 0.8307 (mtm) cc_final: 0.8009 (mtm) REVERT: E 87 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.6908 (mtt90) REVERT: R 104 PHE cc_start: 0.6163 (t80) cc_final: 0.5610 (t80) REVERT: R 288 PHE cc_start: 0.7580 (t80) cc_final: 0.7144 (t80) REVERT: R 315 PHE cc_start: 0.7368 (t80) cc_final: 0.7100 (t80) outliers start: 38 outliers final: 15 residues processed: 206 average time/residue: 1.2406 time to fit residues: 274.0646 Evaluate side-chains 174 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 206 SER Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 109 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 180 GLN B 181 GLN B 264 GLN E 77 ASN ** G 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 58 ASN R 100 ASN R 296 ASN R 313 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.139033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110216 restraints weight = 38896.039| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.12 r_work: 0.3350 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9045 Z= 0.153 Angle : 0.540 7.346 12277 Z= 0.290 Chirality : 0.043 0.440 1397 Planarity : 0.004 0.044 1557 Dihedral : 4.688 52.563 1247 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.10 % Allowed : 19.85 % Favored : 76.05 % 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: 1.82 (0.26), residues: 1122 helix: 3.04 (0.26), residues: 386 sheet: 0.75 (0.31), residues: 248 loop : -0.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 149 TYR 0.014 0.002 TYR R 294 PHE 0.020 0.001 PHE R 124 TRP 0.010 0.001 TRP B 302 HIS 0.005 0.001 HIS B 188 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9041) covalent geometry : angle 0.53799 (12269) SS BOND : bond 0.01772 ( 4) SS BOND : angle 1.84522 ( 8) hydrogen bonds : bond 0.04206 ( 449) hydrogen bonds : angle 4.76463 ( 1278) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 198 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8105 (tp) cc_final: 0.7816 (mm) REVERT: B 48 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7806 (mp) REVERT: B 60 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8674 (mt) REVERT: E 18 ARG cc_start: 0.7689 (tpp80) cc_final: 0.7422 (tpt-90) REVERT: E 87 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6819 (mtt90) REVERT: R 315 PHE cc_start: 0.7448 (t80) cc_final: 0.7135 (t80) outliers start: 39 outliers final: 20 residues processed: 186 average time/residue: 1.0814 time to fit residues: 216.8818 Evaluate side-chains 169 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 158 LEU Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 247 THR Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 47 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 100 optimal weight: 0.0770 chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN G 17 GLN G 43 HIS R 100 ASN R 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.139933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.110911 restraints weight = 38910.273| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.15 r_work: 0.3361 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9045 Z= 0.110 Angle : 0.499 7.401 12277 Z= 0.262 Chirality : 0.042 0.447 1397 Planarity : 0.004 0.037 1557 Dihedral : 4.574 51.948 1247 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.84 % Allowed : 20.80 % Favored : 76.37 % 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: 1.86 (0.26), residues: 1122 helix: 3.16 (0.26), residues: 386 sheet: 0.65 (0.32), residues: 248 loop : -0.01 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 224 TYR 0.009 0.001 TYR A 306 PHE 0.010 0.001 PHE A 189 TRP 0.008 0.001 TRP B 174 HIS 0.003 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 9041) covalent geometry : angle 0.49839 (12269) SS BOND : bond 0.01238 ( 4) SS BOND : angle 1.08965 ( 8) hydrogen bonds : bond 0.03689 ( 449) hydrogen bonds : angle 4.60553 ( 1278) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8133 (tp) cc_final: 0.7885 (mm) REVERT: B 48 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7809 (mp) REVERT: B 263 ASP cc_start: 0.7550 (t70) cc_final: 0.7312 (t70) REVERT: E 18 ARG cc_start: 0.7507 (tpp80) cc_final: 0.7260 (tpt-90) REVERT: R 249 MET cc_start: 0.7923 (tpp) cc_final: 0.7526 (tpp) REVERT: R 315 PHE cc_start: 0.7427 (t80) cc_final: 0.7128 (t80) outliers start: 27 outliers final: 16 residues processed: 176 average time/residue: 1.0566 time to fit residues: 200.3390 Evaluate side-chains 165 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 242 ASN Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 36 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 0.0170 chunk 85 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.140732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.111907 restraints weight = 38721.882| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.14 r_work: 0.3377 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9045 Z= 0.095 Angle : 0.482 7.473 12277 Z= 0.252 Chirality : 0.042 0.449 1397 Planarity : 0.003 0.039 1557 Dihedral : 4.335 50.875 1245 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.73 % Allowed : 21.43 % Favored : 75.84 % 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: 1.92 (0.26), residues: 1122 helix: 3.23 (0.25), residues: 386 sheet: 0.67 (0.32), residues: 248 loop : 0.02 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 247 TYR 0.009 0.001 TYR A 230 PHE 0.011 0.001 PHE A 189 TRP 0.008 0.001 TRP B 174 HIS 0.002 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 9041) covalent geometry : angle 0.48203 (12269) SS BOND : bond 0.00957 ( 4) SS BOND : angle 0.93941 ( 8) hydrogen bonds : bond 0.03429 ( 449) hydrogen bonds : angle 4.44638 ( 1278) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 183 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8126 (tp) cc_final: 0.7874 (mm) REVERT: B 48 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7785 (mp) REVERT: B 263 ASP cc_start: 0.7538 (t70) cc_final: 0.7139 (t0) REVERT: B 345 ASN cc_start: 0.7274 (t0) cc_final: 0.7046 (t0) REVERT: R 288 PHE cc_start: 0.7537 (t80) cc_final: 0.7051 (OUTLIER) REVERT: R 315 PHE cc_start: 0.7423 (t80) cc_final: 0.7142 (t80) outliers start: 26 outliers final: 14 residues processed: 176 average time/residue: 1.1535 time to fit residues: 218.2447 Evaluate side-chains 157 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 143 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 250 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain G residue 53 VAL Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 227 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 102 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.136301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106804 restraints weight = 38709.411| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.14 r_work: 0.3296 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9045 Z= 0.183 Angle : 0.544 8.094 12277 Z= 0.290 Chirality : 0.043 0.433 1397 Planarity : 0.004 0.040 1557 Dihedral : 4.622 49.842 1245 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.26 % Allowed : 21.01 % Favored : 75.74 % 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: 1.60 (0.26), residues: 1122 helix: 2.88 (0.25), residues: 387 sheet: 0.49 (0.32), residues: 255 loop : -0.10 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 309 TYR 0.012 0.002 TYR R 294 PHE 0.012 0.001 PHE B 297 TRP 0.011 0.001 TRP A 211 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 9041) covalent geometry : angle 0.54329 (12269) SS BOND : bond 0.01136 ( 4) SS BOND : angle 0.89105 ( 8) hydrogen bonds : bond 0.04090 ( 449) hydrogen bonds : angle 4.62995 ( 1278) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8173 (tp) cc_final: 0.7883 (mm) REVERT: B 48 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.7934 (mp) REVERT: B 50 MET cc_start: 0.8389 (mtm) cc_final: 0.8084 (mtm) REVERT: B 139 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7606 (ppt-90) REVERT: B 263 ASP cc_start: 0.7767 (t70) cc_final: 0.7343 (t0) REVERT: R 125 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8546 (t) REVERT: R 249 MET cc_start: 0.7920 (tpp) cc_final: 0.7589 (tpp) REVERT: R 315 PHE cc_start: 0.7486 (t80) cc_final: 0.7173 (t80) outliers start: 31 outliers final: 14 residues processed: 169 average time/residue: 1.1768 time to fit residues: 213.7406 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 88 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN R 100 ASN R 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.136552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107266 restraints weight = 38981.967| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.14 r_work: 0.3306 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.5806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9045 Z= 0.133 Angle : 0.520 7.596 12277 Z= 0.275 Chirality : 0.043 0.431 1397 Planarity : 0.004 0.043 1557 Dihedral : 4.568 48.522 1244 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.21 % Allowed : 22.37 % Favored : 75.42 % 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: 1.57 (0.26), residues: 1122 helix: 2.94 (0.25), residues: 387 sheet: 0.51 (0.33), residues: 250 loop : -0.23 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.010 0.001 TYR A 230 PHE 0.010 0.001 PHE A 189 TRP 0.009 0.001 TRP A 211 HIS 0.003 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9041) covalent geometry : angle 0.51906 (12269) SS BOND : bond 0.01147 ( 4) SS BOND : angle 1.17329 ( 8) hydrogen bonds : bond 0.03810 ( 449) hydrogen bonds : angle 4.54384 ( 1278) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8205 (tp) cc_final: 0.7913 (mm) REVERT: B 48 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 50 MET cc_start: 0.8372 (mtm) cc_final: 0.8081 (mtm) REVERT: B 263 ASP cc_start: 0.7790 (t70) cc_final: 0.7392 (t0) REVERT: E 18 ARG cc_start: 0.7739 (tpt-90) cc_final: 0.7310 (tpt-90) REVERT: R 125 THR cc_start: 0.8719 (OUTLIER) cc_final: 0.8508 (t) REVERT: R 249 MET cc_start: 0.7959 (tpp) cc_final: 0.7632 (tpp) REVERT: R 315 PHE cc_start: 0.7597 (t80) cc_final: 0.7265 (t80) outliers start: 21 outliers final: 15 residues processed: 162 average time/residue: 1.0998 time to fit residues: 192.5463 Evaluate side-chains 151 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ASN Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 40 CYS Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 105 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.133716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.103972 restraints weight = 38819.808| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.14 r_work: 0.3255 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9045 Z= 0.227 Angle : 0.595 9.970 12277 Z= 0.320 Chirality : 0.045 0.422 1397 Planarity : 0.005 0.042 1557 Dihedral : 4.926 47.828 1244 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.57 % Allowed : 21.01 % Favored : 75.42 % 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: 1.11 (0.25), residues: 1122 helix: 2.43 (0.25), residues: 393 sheet: 0.35 (0.32), residues: 257 loop : -0.48 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 6 TYR 0.015 0.002 TYR R 294 PHE 0.015 0.002 PHE R 287 TRP 0.012 0.002 TRP A 211 HIS 0.007 0.002 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00518 ( 9041) covalent geometry : angle 0.59400 (12269) SS BOND : bond 0.01404 ( 4) SS BOND : angle 1.35683 ( 8) hydrogen bonds : bond 0.04538 ( 449) hydrogen bonds : angle 4.79228 ( 1278) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 169 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 135 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8213 (tp) cc_final: 0.7938 (mm) REVERT: B 48 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8020 (mp) REVERT: B 139 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7666 (ppt-90) REVERT: B 219 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7625 (mtt180) REVERT: B 263 ASP cc_start: 0.7970 (t70) cc_final: 0.7556 (t0) REVERT: B 267 MET cc_start: 0.8262 (ttm) cc_final: 0.8060 (mtp) REVERT: C 8 PHE cc_start: 0.7883 (t80) cc_final: 0.7406 (t80) REVERT: R 125 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8526 (t) REVERT: R 249 MET cc_start: 0.8140 (tpp) cc_final: 0.7775 (tpp) REVERT: R 315 PHE cc_start: 0.7629 (t80) cc_final: 0.7281 (t80) REVERT: R 317 LYS cc_start: 0.4815 (mttt) cc_final: 0.4531 (mtmm) outliers start: 34 outliers final: 19 residues processed: 160 average time/residue: 1.2026 time to fit residues: 206.6186 Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 109 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103419 restraints weight = 39150.877| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.15 r_work: 0.3247 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9045 Z= 0.219 Angle : 0.590 9.417 12277 Z= 0.316 Chirality : 0.045 0.421 1397 Planarity : 0.005 0.047 1557 Dihedral : 5.011 47.166 1244 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.84 % Allowed : 21.95 % Favored : 75.21 % 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: 0.96 (0.25), residues: 1122 helix: 2.31 (0.25), residues: 393 sheet: 0.29 (0.32), residues: 256 loop : -0.58 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 54 TYR 0.013 0.002 TYR A 230 PHE 0.014 0.002 PHE R 287 TRP 0.012 0.002 TRP A 211 HIS 0.005 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 9041) covalent geometry : angle 0.58913 (12269) SS BOND : bond 0.01656 ( 4) SS BOND : angle 1.17118 ( 8) hydrogen bonds : bond 0.04470 ( 449) hydrogen bonds : angle 4.82230 ( 1278) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ILE cc_start: 0.8279 (tp) cc_final: 0.7944 (mm) REVERT: B 48 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 139 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7644 (ppt-90) REVERT: B 263 ASP cc_start: 0.8034 (t70) cc_final: 0.7625 (t0) REVERT: B 306 LYS cc_start: 0.8228 (mmtp) cc_final: 0.8024 (mttm) REVERT: C 8 PHE cc_start: 0.7852 (t80) cc_final: 0.7425 (t80) REVERT: E 87 ARG cc_start: 0.7084 (mtm-85) cc_final: 0.6506 (ptt-90) REVERT: R 125 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8539 (t) REVERT: R 249 MET cc_start: 0.8188 (tpp) cc_final: 0.7836 (tpp) REVERT: R 315 PHE cc_start: 0.7691 (t80) cc_final: 0.7316 (t80) REVERT: R 317 LYS cc_start: 0.4964 (mttt) cc_final: 0.4610 (mtmm) outliers start: 27 outliers final: 18 residues processed: 155 average time/residue: 1.1599 time to fit residues: 193.4641 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain G residue 37 MET Chi-restraints excluded: chain R residue 84 VAL Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 100 ASN R 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105169 restraints weight = 38675.904| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.13 r_work: 0.3275 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.6398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9045 Z= 0.140 Angle : 0.538 8.095 12277 Z= 0.286 Chirality : 0.043 0.424 1397 Planarity : 0.004 0.044 1557 Dihedral : 4.840 46.592 1244 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.21 % Allowed : 23.11 % Favored : 74.68 % 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: 1.20 (0.25), residues: 1122 helix: 2.65 (0.25), residues: 387 sheet: 0.29 (0.33), residues: 255 loop : -0.45 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.012 0.001 TYR R 89 PHE 0.013 0.001 PHE R 287 TRP 0.010 0.001 TRP A 211 HIS 0.003 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 9041) covalent geometry : angle 0.53718 (12269) SS BOND : bond 0.01163 ( 4) SS BOND : angle 1.03143 ( 8) hydrogen bonds : bond 0.04024 ( 449) hydrogen bonds : angle 4.68227 ( 1278) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 224 is missing expected H atoms. Skipping. Residue VAL 268 is missing expected H atoms. Skipping. Residue LEU 12 is missing expected H atoms. Skipping. Residue THR 34 is missing expected H atoms. Skipping. Residue SER 36 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue LYS 76 is missing expected H atoms. Skipping. Residue SER 197 is missing expected H atoms. Skipping. Residue VAL 53 is missing expected H atoms. Skipping. Residue SER 56 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue THR 185 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 348 ASP cc_start: 0.8696 (t70) cc_final: 0.8453 (t0) REVERT: B 38 ILE cc_start: 0.8295 (tp) cc_final: 0.7959 (mm) REVERT: B 48 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 263 ASP cc_start: 0.7980 (t70) cc_final: 0.7619 (t0) REVERT: C 8 PHE cc_start: 0.7790 (t80) cc_final: 0.7359 (t80) REVERT: E 87 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6466 (ptt-90) REVERT: R 58 ASN cc_start: 0.8455 (m-40) cc_final: 0.8030 (m110) REVERT: R 125 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8532 (t) REVERT: R 249 MET cc_start: 0.8167 (tpp) cc_final: 0.7813 (tpp) REVERT: R 315 PHE cc_start: 0.7655 (t80) cc_final: 0.7290 (t80) REVERT: R 317 LYS cc_start: 0.4982 (mttt) cc_final: 0.4481 (mtmm) outliers start: 21 outliers final: 15 residues processed: 149 average time/residue: 1.0755 time to fit residues: 172.8374 Evaluate side-chains 146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 158 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 125 THR Chi-restraints excluded: chain R residue 204 TYR Chi-restraints excluded: chain R residue 245 LYS Chi-restraints excluded: chain R residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN R 100 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.135383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106099 restraints weight = 38784.895| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.12 r_work: 0.3286 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.6426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9045 Z= 0.126 Angle : 0.524 7.519 12277 Z= 0.276 Chirality : 0.043 0.429 1397 Planarity : 0.004 0.045 1557 Dihedral : 4.702 46.289 1244 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.10 % Allowed : 23.21 % Favored : 74.68 % 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: 1.35 (0.26), residues: 1122 helix: 2.79 (0.25), residues: 387 sheet: 0.39 (0.33), residues: 261 loop : -0.39 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.011 0.001 TYR R 89 PHE 0.015 0.001 PHE R 287 TRP 0.009 0.001 TRP A 211 HIS 0.004 0.001 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9041) covalent geometry : angle 0.52310 (12269) SS BOND : bond 0.01116 ( 4) SS BOND : angle 0.96572 ( 8) hydrogen bonds : bond 0.03823 ( 449) hydrogen bonds : angle 4.57098 ( 1278) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7594.48 seconds wall clock time: 129 minutes 9.04 seconds (7749.04 seconds total)