Starting phenix.real_space_refine on Tue Jun 24 22:43:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.map" model { file = "/net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x30_38024/06_2025/8x30_38024.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.012 sd= 0.431 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9562 atoms to isotropic. 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 P 290 5.49 5 S 41 5.16 5 C 12780 2.51 5 N 3827 2.21 5 O 4641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21579 Number of models: 1 Model: "" Number of chains: 17 Chain: "K" Number of atoms: 2304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2304 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "M" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1485 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 6, 'TRANS': 173} Chain breaks: 1 Chain: "N" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 576 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain breaks: 1 Chain: "O" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2380 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 12, 'TRANS': 269} Chain: "P" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 283 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "Q" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1777 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain breaks: 1 Chain: "R" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 813 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain breaks: 1 Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2990 Classifications: {'DNA': 146} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 145} Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "B" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 679 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 750 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 11.62, per 1000 atoms: 0.54 Number of scatterers: 21579 At special positions: 0 Unit cell: (139.36, 184.08, 151.84, 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 41 16.00 P 290 15.00 O 4641 8.00 N 3827 7.00 C 12780 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.80 Conformation dependent library (CDL) restraints added in 2.1 seconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3652 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 55.2% alpha, 2.0% beta 144 base pairs and 240 stacking pairs defined. Time for finding SS restraints: 7.91 Creating SS restraints... Processing helix chain 'K' and resid 187 through 192 Processing helix chain 'K' and resid 244 through 259 removed outlier: 3.981A pdb=" N ASN K 250 " --> pdb=" O THR K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 315 through 330 Processing helix chain 'K' and resid 344 through 362 Processing helix chain 'K' and resid 369 through 374 removed outlier: 3.553A pdb=" N ILE K 373 " --> pdb=" O THR K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 383 through 391 removed outlier: 4.148A pdb=" N LEU K 391 " --> pdb=" O THR K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 416 removed outlier: 3.662A pdb=" N LEU K 416 " --> pdb=" O TYR K 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 157 Processing helix chain 'M' and resid 165 through 177 removed outlier: 4.283A pdb=" N GLU M 169 " --> pdb=" O ASP M 165 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN M 175 " --> pdb=" O PHE M 171 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL M 176 " --> pdb=" O LEU M 172 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN M 177 " --> pdb=" O ASN M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 193 removed outlier: 3.833A pdb=" N CYS M 193 " --> pdb=" O PHE M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 204 Processing helix chain 'M' and resid 216 through 220 removed outlier: 3.521A pdb=" N LEU M 220 " --> pdb=" O PHE M 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 231 through 239 removed outlier: 3.679A pdb=" N LEU M 238 " --> pdb=" O LEU M 234 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN M 239 " --> pdb=" O ARG M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 269 Processing helix chain 'M' and resid 271 through 287 removed outlier: 5.043A pdb=" N GLU M 281 " --> pdb=" O ASP M 277 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG M 282 " --> pdb=" O TYR M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 337 through 356 Processing helix chain 'N' and resid 11 through 16 Processing helix chain 'N' and resid 16 through 40 removed outlier: 3.722A pdb=" N GLU N 20 " --> pdb=" O ASN N 16 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU N 27 " --> pdb=" O TYR N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 112 removed outlier: 4.061A pdb=" N GLU N 85 " --> pdb=" O SER N 81 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LYS N 86 " --> pdb=" O LEU N 82 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS N 87 " --> pdb=" O GLN N 83 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL N 88 " --> pdb=" O ARG N 84 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ILE N 97 " --> pdb=" O ALA N 93 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N HIS N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU N 112 " --> pdb=" O ILE N 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 192 Processing helix chain 'O' and resid 210 through 218 Processing helix chain 'O' and resid 245 through 258 Processing helix chain 'O' and resid 308 through 312 removed outlier: 3.647A pdb=" N TYR O 311 " --> pdb=" O LEU O 308 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN O 312 " --> pdb=" O PRO O 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 308 through 312' Processing helix chain 'O' and resid 316 through 329 Processing helix chain 'O' and resid 345 through 361 Processing helix chain 'O' and resid 370 through 375 removed outlier: 4.068A pdb=" N SER O 375 " --> pdb=" O ASP O 371 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 removed outlier: 4.556A pdb=" N HIS O 386 " --> pdb=" O THR O 382 " (cutoff:3.500A) Processing helix chain 'P' and resid 15 through 25 removed outlier: 5.164A pdb=" N ARG P 22 " --> pdb=" O SER P 18 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ARG P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 34 Processing helix chain 'P' and resid 34 through 40 Processing helix chain 'Q' and resid 132 through 137 removed outlier: 3.675A pdb=" N TYR Q 137 " --> pdb=" O TYR Q 133 " (cutoff:3.500A) Processing helix chain 'Q' and resid 153 through 157 removed outlier: 3.561A pdb=" N CYS Q 157 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 165 through 175 removed outlier: 4.226A pdb=" N GLU Q 169 " --> pdb=" O ASP Q 165 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU Q 172 " --> pdb=" O ASP Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 203 removed outlier: 3.550A pdb=" N ILE Q 191 " --> pdb=" O ASP Q 187 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER Q 194 " --> pdb=" O GLU Q 190 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE Q 196 " --> pdb=" O LEU Q 192 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS Q 201 " --> pdb=" O GLU Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 221 through 226 removed outlier: 4.075A pdb=" N LYS Q 226 " --> pdb=" O PRO Q 222 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 242 removed outlier: 3.671A pdb=" N ASN Q 239 " --> pdb=" O ARG Q 235 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU Q 241 " --> pdb=" O GLN Q 237 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 286 removed outlier: 3.700A pdb=" N LEU Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER Q 273 " --> pdb=" O GLU Q 269 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS Q 274 " --> pdb=" O LYS Q 270 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU Q 281 " --> pdb=" O ASP Q 277 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Q 282 " --> pdb=" O TYR Q 278 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LYS Q 283 " --> pdb=" O TRP Q 279 " (cutoff:3.500A) Processing helix chain 'Q' and resid 331 through 367 removed outlier: 5.123A pdb=" N GLU Q 340 " --> pdb=" O ALA Q 336 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU Q 341 " --> pdb=" O LEU Q 337 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 15 removed outlier: 5.470A pdb=" N GLN R 12 " --> pdb=" O GLU R 8 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASP R 13 " --> pdb=" O GLN R 9 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 24 removed outlier: 4.256A pdb=" N SER R 19 " --> pdb=" O SER R 15 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 51 removed outlier: 4.989A pdb=" N GLN R 44 " --> pdb=" O LYS R 40 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LYS R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU R 46 " --> pdb=" O TYR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 113 removed outlier: 4.367A pdb=" N GLU R 85 " --> pdb=" O SER R 81 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.507A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.588A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.908A pdb=" N ARG C 33 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 80 through 87 removed outlier: 4.230A pdb=" N LEU C 85 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.867A pdb=" N ASP C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 60 through 87 removed outlier: 3.727A pdb=" N ILE D 64 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 104 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.617A pdb=" N SER D 125 " --> pdb=" O VAL D 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.639A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.040A pdb=" N ALA E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.519A pdb=" N ILE E 124 " --> pdb=" O GLN E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 38 Processing helix chain 'F' and resid 50 through 77 removed outlier: 4.019A pdb=" N ASP F 68 " --> pdb=" O SER F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 27 through 39 Processing helix chain 'G' and resid 49 through 75 removed outlier: 3.967A pdb=" N LEU G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA G 55 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N GLU G 63 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLU G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS G 73 " --> pdb=" O GLY G 69 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 91 through 96 removed outlier: 4.134A pdb=" N ASP G 96 " --> pdb=" O ASP G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 99 No H-bonds generated for 'chain 'G' and resid 97 through 99' Processing helix chain 'H' and resid 40 through 52 removed outlier: 3.654A pdb=" N ILE H 44 " --> pdb=" O TYR H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 87 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 106 through 126 Processing sheet with id=AA1, first strand: chain 'K' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'K' and resid 226 through 230 removed outlier: 5.050A pdb=" N GLU K 227 " --> pdb=" O GLU K 238 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU K 238 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 170 through 172 Processing sheet with id=AA4, first strand: chain 'O' and resid 229 through 230 removed outlier: 5.999A pdb=" N ARG O 278 " --> pdb=" O LEU O 286 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LEU O 286 " --> pdb=" O ARG O 278 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 2052 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 240 stacking parallelities Total time for adding SS restraints: 7.63 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3330 1.32 - 1.44: 7502 1.44 - 1.57: 11106 1.57 - 1.69: 580 1.69 - 1.81: 62 Bond restraints: 22580 Sorted by residual: bond pdb=" C LEU G 109 " pdb=" N PRO G 110 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.01e-02 9.80e+03 1.03e+01 bond pdb=" CG GLN E 93 " pdb=" CD GLN E 93 " ideal model delta sigma weight residual 1.516 1.441 0.075 2.50e-02 1.60e+03 9.12e+00 bond pdb=" C ILE K 177 " pdb=" N GLU K 178 " ideal model delta sigma weight residual 1.331 1.252 0.079 2.83e-02 1.25e+03 7.74e+00 bond pdb=" CZ ARG E 63 " pdb=" NH2 ARG E 63 " ideal model delta sigma weight residual 1.330 1.295 0.035 1.30e-02 5.92e+03 7.21e+00 bond pdb=" CA ASP H 54 " pdb=" CB ASP H 54 " ideal model delta sigma weight residual 1.527 1.461 0.066 2.48e-02 1.63e+03 7.18e+00 ... (remaining 22575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 30601 3.42 - 6.85: 958 6.85 - 10.27: 124 10.27 - 13.70: 21 13.70 - 17.12: 3 Bond angle restraints: 31707 Sorted by residual: angle pdb=" CA TYR G 34 " pdb=" CB TYR G 34 " pdb=" CG TYR G 34 " ideal model delta sigma weight residual 113.90 125.99 -12.09 1.80e+00 3.09e-01 4.51e+01 angle pdb=" C THR B 71 " pdb=" N TYR B 72 " pdb=" CA TYR B 72 " ideal model delta sigma weight residual 122.06 110.69 11.37 1.86e+00 2.89e-01 3.74e+01 angle pdb=" C LEU A 103 " pdb=" N PHE A 104 " pdb=" CA PHE A 104 " ideal model delta sigma weight residual 122.38 111.57 10.81 1.81e+00 3.05e-01 3.56e+01 angle pdb=" C LYS D 111 " pdb=" N HIS D 112 " pdb=" CA HIS D 112 " ideal model delta sigma weight residual 121.14 111.52 9.62 1.75e+00 3.27e-01 3.02e+01 angle pdb=" N VAL Q 286 " pdb=" CA VAL Q 286 " pdb=" C VAL Q 286 " ideal model delta sigma weight residual 112.83 107.45 5.38 9.90e-01 1.02e+00 2.96e+01 ... (remaining 31702 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.01: 10004 23.01 - 46.02: 2017 46.02 - 69.04: 924 69.04 - 92.05: 54 92.05 - 115.06: 3 Dihedral angle restraints: 13002 sinusoidal: 7376 harmonic: 5626 Sorted by residual: dihedral pdb=" CA LEU K 391 " pdb=" C LEU K 391 " pdb=" N ASN K 392 " pdb=" CA ASN K 392 " ideal model delta harmonic sigma weight residual -180.00 -119.53 -60.47 0 5.00e+00 4.00e-02 1.46e+02 dihedral pdb=" CA TYR G 59 " pdb=" C TYR G 59 " pdb=" N LEU G 60 " pdb=" CA LEU G 60 " ideal model delta harmonic sigma weight residual 180.00 123.32 56.68 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA ASP K 269 " pdb=" C ASP K 269 " pdb=" N PRO K 270 " pdb=" CA PRO K 270 " ideal model delta harmonic sigma weight residual -180.00 -133.72 -46.28 0 5.00e+00 4.00e-02 8.57e+01 ... (remaining 12999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 3046 0.111 - 0.222: 468 0.222 - 0.333: 38 0.333 - 0.443: 2 0.443 - 0.554: 2 Chirality restraints: 3556 Sorted by residual: chirality pdb=" CG LEU G 60 " pdb=" CB LEU G 60 " pdb=" CD1 LEU G 60 " pdb=" CD2 LEU G 60 " both_signs ideal model delta sigma weight residual False -2.59 -2.04 -0.55 2.00e-01 2.50e+01 7.68e+00 chirality pdb=" CB ILE E 62 " pdb=" CA ILE E 62 " pdb=" CG1 ILE E 62 " pdb=" CG2 ILE E 62 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.51e+00 chirality pdb=" CB ILE K 171 " pdb=" CA ILE K 171 " pdb=" CG1 ILE K 171 " pdb=" CG2 ILE K 171 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.43 2.00e-01 2.50e+01 4.59e+00 ... (remaining 3553 not shown) Planarity restraints: 3001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE H 73 " -0.046 2.00e-02 2.50e+03 2.92e-02 1.50e+01 pdb=" CG PHE H 73 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE H 73 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE H 73 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE H 73 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE H 73 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 73 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 353 " 0.037 2.00e-02 2.50e+03 2.43e-02 1.48e+01 pdb=" CG TRP O 353 " -0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP O 353 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP O 353 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP O 353 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 353 " 0.019 2.00e-02 2.50e+03 pdb=" CE3 TRP O 353 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 353 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 353 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP O 353 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 19 " 0.053 2.00e-02 2.50e+03 2.28e-02 1.42e+01 pdb=" N9 DA I 19 " -0.034 2.00e-02 2.50e+03 pdb=" C8 DA I 19 " -0.012 2.00e-02 2.50e+03 pdb=" N7 DA I 19 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DA I 19 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 19 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA I 19 " 0.036 2.00e-02 2.50e+03 pdb=" N1 DA I 19 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 19 " -0.010 2.00e-02 2.50e+03 pdb=" N3 DA I 19 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 19 " -0.007 2.00e-02 2.50e+03 ... (remaining 2998 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 2084 2.71 - 3.26: 21315 3.26 - 3.80: 44995 3.80 - 4.35: 51482 4.35 - 4.90: 71280 Nonbonded interactions: 191156 Sorted by model distance: nonbonded pdb=" OH TYR B 72 " pdb=" O ASP B 85 " model vdw 2.160 3.040 nonbonded pdb=" O ILE D 64 " pdb=" OH TYR F 98 " model vdw 2.180 3.040 nonbonded pdb=" OG SER O 235 " pdb=" OG1 THR O 277 " model vdw 2.188 3.040 nonbonded pdb=" O LEU M 215 " pdb=" OH TYR M 276 " model vdw 2.196 3.040 nonbonded pdb=" O HIS K 386 " pdb=" OG1 THR K 390 " model vdw 2.205 3.040 ... (remaining 191151 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 113) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 36 through 128) } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = (chain 'O' and resid 160 through 431) } 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 group one per residue 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.010 Extract box with map and model: 0.840 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 50.690 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.100 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.012 0.096 22580 Z= 0.544 Angle : 1.443 17.120 31707 Z= 0.795 Chirality : 0.080 0.554 3556 Planarity : 0.009 0.067 3001 Dihedral : 25.514 115.061 9350 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 13.34 % Favored : 86.55 % Rotamer: Outliers : 3.38 % Allowed : 13.99 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 1.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.37 (0.15), residues: 1866 helix: -3.41 (0.11), residues: 972 sheet: -3.98 (0.59), residues: 40 loop : -3.70 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.006 TRP O 353 HIS 0.028 0.004 HIS B 75 PHE 0.046 0.005 PHE H 73 TYR 0.059 0.006 TYR G 59 ARG 0.050 0.003 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.15100 ( 1048) hydrogen bonds : angle 7.13046 ( 2748) covalent geometry : bond 0.01183 (22580) covalent geometry : angle 1.44279 (31707) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 544 time to evaluate : 1.790 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: 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: 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: K 209 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8598 (mmmt) REVERT: K 243 LYS cc_start: 0.8902 (mptt) cc_final: 0.8440 (mptt) REVERT: K 284 HIS cc_start: 0.7625 (m-70) cc_final: 0.7012 (m-70) REVERT: K 302 VAL cc_start: 0.8850 (t) cc_final: 0.8148 (t) REVERT: K 311 TYR cc_start: 0.7022 (t80) cc_final: 0.6619 (t80) REVERT: K 319 LEU cc_start: 0.7952 (tp) cc_final: 0.7692 (pt) REVERT: K 327 LEU cc_start: 0.9202 (mt) cc_final: 0.8923 (pp) REVERT: K 356 THR cc_start: 0.8006 (p) cc_final: 0.7744 (p) REVERT: K 357 LEU cc_start: 0.8979 (tm) cc_final: 0.8744 (mt) REVERT: K 408 ASP cc_start: 0.7498 (t70) cc_final: 0.6603 (m-30) REVERT: M 156 ASP cc_start: 0.6693 (t70) cc_final: 0.6344 (p0) REVERT: M 214 ILE cc_start: 0.4806 (tt) cc_final: 0.4182 (tt) REVERT: M 215 LEU cc_start: 0.8125 (OUTLIER) cc_final: 0.7705 (pt) REVERT: M 232 PHE cc_start: 0.8753 (p90) cc_final: 0.8084 (p90) REVERT: M 234 LEU cc_start: 0.9041 (mp) cc_final: 0.8780 (mp) REVERT: M 259 MET cc_start: 0.8207 (mpm) cc_final: 0.7982 (mpm) REVERT: M 278 TYR cc_start: 0.8616 (t80) cc_final: 0.8242 (t80) REVERT: O 200 PHE cc_start: 0.6820 (m-80) cc_final: 0.6552 (m-80) REVERT: O 230 ARG cc_start: 0.8128 (tmt170) cc_final: 0.7826 (ttp-170) REVERT: O 271 PHE cc_start: 0.8098 (p90) cc_final: 0.7355 (p90) REVERT: O 275 CYS cc_start: 0.8051 (t) cc_final: 0.7473 (t) REVERT: O 325 TYR cc_start: 0.8131 (m-10) cc_final: 0.7823 (m-80) REVERT: O 326 GLU cc_start: 0.8663 (tm-30) cc_final: 0.7634 (tm-30) REVERT: P 43 TYR cc_start: 0.8559 (m-80) cc_final: 0.8056 (m-10) REVERT: Q 133 TYR cc_start: 0.7360 (t80) cc_final: 0.7113 (t80) REVERT: Q 201 HIS cc_start: 0.9296 (m90) cc_final: 0.9043 (m-70) REVERT: Q 229 MET cc_start: 0.6912 (mmp) cc_final: 0.6185 (mmt) REVERT: R 102 ASN cc_start: 0.9057 (m-40) cc_final: 0.8736 (m-40) REVERT: A 50 GLU cc_start: 0.7769 (pt0) cc_final: 0.6978 (tp30) REVERT: A 54 PHE cc_start: 0.6801 (p90) cc_final: 0.6389 (p90) REVERT: A 58 THR cc_start: 0.7882 (p) cc_final: 0.7426 (t) REVERT: A 70 LEU cc_start: 0.8484 (pp) cc_final: 0.8199 (pp) REVERT: A 113 HIS cc_start: 0.6513 (t70) cc_final: 0.6215 (t70) REVERT: A 119 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8323 (mm) REVERT: B 25 ASN cc_start: 0.7381 (t0) cc_final: 0.7015 (t0) REVERT: B 27 GLN cc_start: 0.8170 (pm20) cc_final: 0.7595 (pm20) REVERT: B 34 ILE cc_start: 0.8727 (pp) cc_final: 0.8444 (tp) REVERT: B 59 LYS cc_start: 0.8306 (mptt) cc_final: 0.8098 (mmtt) REVERT: B 74 GLU cc_start: 0.8414 (tp30) cc_final: 0.7723 (tp30) REVERT: C 21 ARG cc_start: 0.7434 (tmt-80) cc_final: 0.6852 (tpt90) REVERT: C 32 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8451 (tppt) REVERT: C 51 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7635 (tp) REVERT: C 59 TYR cc_start: 0.7309 (p90) cc_final: 0.7063 (p90) REVERT: C 70 ASN cc_start: 0.8100 (p0) cc_final: 0.7886 (p0) REVERT: C 74 ASP cc_start: 0.6896 (p0) cc_final: 0.6384 (p0) REVERT: C 86 GLN cc_start: 0.7333 (mt0) cc_final: 0.6925 (mt0) REVERT: C 103 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8799 (pp) REVERT: D 65 LEU cc_start: 0.9036 (mt) cc_final: 0.8788 (mt) REVERT: D 68 PHE cc_start: 0.8183 (p90) cc_final: 0.7955 (p90) REVERT: D 72 ILE cc_start: 0.8925 (pt) cc_final: 0.8618 (pt) REVERT: D 79 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7139 (pp20) REVERT: D 87 ASN cc_start: 0.9046 (p0) cc_final: 0.8630 (p0) REVERT: D 89 LYS cc_start: 0.8595 (tmtp) cc_final: 0.8254 (tmtt) REVERT: D 111 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7459 (pmmt) REVERT: D 124 TYR cc_start: 0.8315 (t80) cc_final: 0.8110 (t80) REVERT: E 41 TYR cc_start: 0.5758 (p90) cc_final: 0.5418 (p90) REVERT: E 64 LYS cc_start: 0.8072 (mppt) cc_final: 0.7706 (mmtm) REVERT: E 72 ARG cc_start: 0.6851 (mmt180) cc_final: 0.6378 (mmt180) REVERT: E 73 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7543 (mm-30) REVERT: E 94 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7392 (tt0) REVERT: E 120 GLN cc_start: 0.6643 (pp30) cc_final: 0.6180 (pp30) REVERT: E 130 LEU cc_start: 0.8636 (pp) cc_final: 0.8382 (pp) REVERT: F 50 ILE cc_start: 0.8280 (pp) cc_final: 0.7775 (mm) REVERT: F 61 PHE cc_start: 0.8303 (t80) cc_final: 0.8085 (t80) REVERT: F 71 THR cc_start: 0.8486 (m) cc_final: 0.7808 (m) REVERT: F 98 TYR cc_start: 0.6931 (t80) cc_final: 0.6402 (t80) REVERT: G 38 HIS cc_start: 0.8157 (p-80) cc_final: 0.7888 (p90) REVERT: G 52 TYR cc_start: 0.7512 (t80) cc_final: 0.7049 (t80) REVERT: G 53 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8585 (mp) REVERT: G 89 ILE cc_start: 0.8703 (mp) cc_final: 0.8326 (pt) REVERT: G 103 ILE cc_start: 0.6662 (pp) cc_final: 0.6242 (mp) REVERT: H 62 MET cc_start: 0.7821 (mmm) cc_final: 0.7595 (mmm) REVERT: H 66 ASN cc_start: 0.7744 (p0) cc_final: 0.7431 (p0) REVERT: H 68 PHE cc_start: 0.8178 (t80) cc_final: 0.7852 (t80) REVERT: H 74 GLU cc_start: 0.7776 (tp30) cc_final: 0.7360 (tp30) REVERT: H 86 TYR cc_start: 0.7113 (p90) cc_final: 0.6699 (p90) REVERT: H 96 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6724 (tm-30) outliers start: 58 outliers final: 7 residues processed: 567 average time/residue: 0.4266 time to fit residues: 339.2237 Evaluate side-chains 461 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 447 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 261 HIS M 175 GLN M 204 GLN M 240 HIS ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN ** O 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 285 HIS O 364 HIS Q 198 HIS Q 204 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 339 GLN R 9 GLN R 31 ASN A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN E 55 GLN E 68 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 GLN H 112 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.119430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.094136 restraints weight = 86411.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.097293 restraints weight = 48526.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.099352 restraints weight = 31340.557| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22580 Z= 0.208 Angle : 0.917 13.878 31707 Z= 0.503 Chirality : 0.049 0.248 3556 Planarity : 0.009 0.268 3001 Dihedral : 29.246 124.755 5372 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 0.76 % Allowed : 7.40 % Favored : 91.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.16), residues: 1866 helix: -2.31 (0.14), residues: 1000 sheet: -2.97 (0.72), residues: 33 loop : -3.43 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP O 353 HIS 0.032 0.002 HIS C 84 PHE 0.063 0.003 PHE H 73 TYR 0.042 0.003 TYR G 59 ARG 0.010 0.001 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.06001 ( 1048) hydrogen bonds : angle 5.51469 ( 2748) covalent geometry : bond 0.00451 (22580) covalent geometry : angle 0.91655 (31707) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 525 time to evaluate : 1.798 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: 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: 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: K 209 LYS cc_start: 0.8783 (mmpt) cc_final: 0.8518 (mmpt) REVERT: K 243 LYS cc_start: 0.8756 (mptt) cc_final: 0.8234 (mptt) REVERT: K 284 HIS cc_start: 0.7659 (m-70) cc_final: 0.7174 (m-70) REVERT: K 310 GLN cc_start: 0.8172 (pm20) cc_final: 0.7896 (pm20) REVERT: K 311 TYR cc_start: 0.6995 (t80) cc_final: 0.6489 (t80) REVERT: K 325 TYR cc_start: 0.8336 (m-10) cc_final: 0.8121 (m-10) REVERT: K 327 LEU cc_start: 0.9301 (mt) cc_final: 0.9005 (pp) REVERT: M 234 LEU cc_start: 0.9140 (mp) cc_final: 0.8816 (pp) REVERT: M 238 LEU cc_start: 0.8847 (tp) cc_final: 0.8561 (tt) REVERT: M 278 TYR cc_start: 0.8706 (t80) cc_final: 0.8325 (t80) REVERT: N 16 ASN cc_start: 0.7480 (p0) cc_final: 0.7226 (p0) REVERT: O 271 PHE cc_start: 0.8083 (p90) cc_final: 0.7386 (p90) REVERT: O 272 LEU cc_start: 0.7619 (mt) cc_final: 0.7399 (tt) REVERT: O 275 CYS cc_start: 0.8616 (t) cc_final: 0.8127 (t) REVERT: O 325 TYR cc_start: 0.8338 (m-10) cc_final: 0.8058 (m-80) REVERT: P 43 TYR cc_start: 0.8736 (m-80) cc_final: 0.8119 (m-10) REVERT: Q 201 HIS cc_start: 0.9235 (m90) cc_final: 0.8973 (m-70) REVERT: Q 229 MET cc_start: 0.6497 (mmp) cc_final: 0.5393 (mmp) REVERT: A 51 ILE cc_start: 0.8748 (mm) cc_final: 0.8127 (mm) REVERT: A 59 GLU cc_start: 0.8831 (pm20) cc_final: 0.8225 (pm20) REVERT: A 82 LEU cc_start: 0.8325 (pt) cc_final: 0.8106 (mt) REVERT: A 100 LEU cc_start: 0.8580 (pp) cc_final: 0.8248 (mm) REVERT: A 119 ILE cc_start: 0.8486 (pt) cc_final: 0.8215 (mm) REVERT: A 121 LYS cc_start: 0.8882 (tttm) cc_final: 0.8645 (tppt) REVERT: B 25 ASN cc_start: 0.7513 (t0) cc_final: 0.7212 (t0) REVERT: B 58 LEU cc_start: 0.8614 (mm) cc_final: 0.8364 (mm) REVERT: B 62 LEU cc_start: 0.8133 (mm) cc_final: 0.7915 (mm) REVERT: B 74 GLU cc_start: 0.8471 (tp30) cc_final: 0.7867 (tp30) REVERT: C 21 ARG cc_start: 0.7419 (tmt-80) cc_final: 0.6970 (tpt90) REVERT: C 31 ILE cc_start: 0.9257 (mm) cc_final: 0.8804 (pt) REVERT: C 32 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8576 (tptt) REVERT: C 33 ARG cc_start: 0.8419 (pmt170) cc_final: 0.8057 (ptt-90) REVERT: C 54 THR cc_start: 0.7904 (m) cc_final: 0.7679 (m) REVERT: C 57 LEU cc_start: 0.8129 (mt) cc_final: 0.7904 (mt) REVERT: C 74 ASP cc_start: 0.7482 (p0) cc_final: 0.7271 (p0) REVERT: C 75 LEU cc_start: 0.8904 (mp) cc_final: 0.8691 (mt) REVERT: C 84 HIS cc_start: 0.7673 (p90) cc_final: 0.6780 (p-80) REVERT: C 89 ILE cc_start: 0.8496 (mm) cc_final: 0.8121 (mm) REVERT: D 47 VAL cc_start: 0.8691 (t) cc_final: 0.7747 (t) REVERT: D 51 THR cc_start: 0.8677 (p) cc_final: 0.8435 (p) REVERT: D 65 LEU cc_start: 0.9064 (mt) cc_final: 0.8669 (mt) REVERT: D 71 ASP cc_start: 0.8268 (p0) cc_final: 0.7982 (p0) REVERT: D 103 LEU cc_start: 0.8226 (pp) cc_final: 0.8012 (pp) REVERT: D 124 TYR cc_start: 0.8068 (t80) cc_final: 0.7773 (t80) REVERT: E 41 TYR cc_start: 0.6324 (p90) cc_final: 0.5756 (p90) REVERT: E 64 LYS cc_start: 0.8194 (mppt) cc_final: 0.7943 (mmtm) REVERT: E 72 ARG cc_start: 0.7587 (mmt180) cc_final: 0.6963 (mmt180) REVERT: E 74 ILE cc_start: 0.8687 (pt) cc_final: 0.8421 (pt) REVERT: E 115 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8732 (ptpp) REVERT: E 125 LYS cc_start: 0.8625 (mtmm) cc_final: 0.8198 (mtmm) REVERT: F 50 ILE cc_start: 0.8316 (pt) cc_final: 0.8008 (mm) REVERT: F 61 PHE cc_start: 0.8461 (t80) cc_final: 0.7811 (t80) REVERT: F 67 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7852 (mtm-85) REVERT: F 77 LYS cc_start: 0.8372 (mptt) cc_final: 0.7970 (mmtp) REVERT: G 31 ILE cc_start: 0.8315 (pt) cc_final: 0.7787 (tt) REVERT: G 34 TYR cc_start: 0.7896 (p90) cc_final: 0.7638 (p90) REVERT: G 52 TYR cc_start: 0.7571 (t80) cc_final: 0.7351 (t80) REVERT: G 86 GLN cc_start: 0.7373 (mp10) cc_final: 0.6987 (mp10) REVERT: G 96 ASP cc_start: 0.8668 (p0) cc_final: 0.8426 (p0) REVERT: H 52 HIS cc_start: 0.7326 (t70) cc_final: 0.7096 (t70) REVERT: H 62 MET cc_start: 0.7927 (mmm) cc_final: 0.7678 (mmm) REVERT: H 66 ASN cc_start: 0.7691 (p0) cc_final: 0.7361 (p0) REVERT: H 68 PHE cc_start: 0.8094 (t80) cc_final: 0.7873 (t80) REVERT: H 82 LYS cc_start: 0.9013 (tmmt) cc_final: 0.8719 (ptmm) REVERT: H 86 TYR cc_start: 0.7333 (p90) cc_final: 0.6860 (p90) REVERT: H 88 LYS cc_start: 0.9298 (ptpp) cc_final: 0.9070 (ptmm) REVERT: H 101 VAL cc_start: 0.8721 (p) cc_final: 0.8484 (m) REVERT: H 102 ARG cc_start: 0.8365 (ttm110) cc_final: 0.8083 (ptp-170) REVERT: H 105 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8551 (pp) REVERT: H 108 GLU cc_start: 0.8175 (pm20) cc_final: 0.7839 (pm20) REVERT: H 112 HIS cc_start: 0.7476 (m90) cc_final: 0.6634 (m90) outliers start: 13 outliers final: 1 residues processed: 531 average time/residue: 0.4121 time to fit residues: 310.6138 Evaluate side-chains 466 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 464 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 132 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 170 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 42 optimal weight: 0.0370 chunk 11 optimal weight: 4.9990 chunk 171 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 301 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 34 GLN ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.121686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096539 restraints weight = 86714.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.099726 restraints weight = 48853.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.101836 restraints weight = 31468.120| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22580 Z= 0.187 Angle : 0.852 12.545 31707 Z= 0.466 Chirality : 0.047 0.226 3556 Planarity : 0.006 0.085 3001 Dihedral : 28.854 121.015 5372 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 0.29 % Allowed : 6.88 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.77 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.18), residues: 1866 helix: -1.63 (0.15), residues: 975 sheet: -2.90 (0.74), residues: 35 loop : -3.06 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP O 353 HIS 0.014 0.002 HIS C 84 PHE 0.049 0.002 PHE H 73 TYR 0.051 0.003 TYR C 59 ARG 0.017 0.001 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.05489 ( 1048) hydrogen bonds : angle 5.19328 ( 2748) covalent geometry : bond 0.00401 (22580) covalent geometry : angle 0.85239 (31707) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 526 time to evaluate : 1.824 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: 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: 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: symmetry clash REVERT: K 212 GLU cc_start: 0.8058 (mp0) cc_final: 0.7793 (mp0) REVERT: K 273 PHE cc_start: 0.8346 (m-10) cc_final: 0.8119 (m-80) REVERT: K 284 HIS cc_start: 0.7539 (m-70) cc_final: 0.7160 (m-70) REVERT: K 302 VAL cc_start: 0.8542 (t) cc_final: 0.7072 (t) REVERT: K 319 LEU cc_start: 0.8033 (tp) cc_final: 0.7765 (pt) REVERT: K 327 LEU cc_start: 0.9255 (mt) cc_final: 0.9016 (pp) REVERT: K 343 ASP cc_start: 0.8929 (p0) cc_final: 0.8426 (p0) REVERT: K 376 MET cc_start: 0.8641 (pmm) cc_final: 0.8389 (pmm) REVERT: M 234 LEU cc_start: 0.9152 (mp) cc_final: 0.8794 (pp) REVERT: M 237 GLN cc_start: 0.8991 (tp-100) cc_final: 0.8726 (tp-100) REVERT: M 238 LEU cc_start: 0.8739 (tp) cc_final: 0.8467 (tt) REVERT: M 260 ASN cc_start: 0.6893 (OUTLIER) cc_final: 0.6630 (t160) REVERT: M 278 TYR cc_start: 0.8702 (t80) cc_final: 0.8416 (t80) REVERT: M 279 TRP cc_start: 0.8430 (t60) cc_final: 0.8170 (t60) REVERT: O 271 PHE cc_start: 0.8027 (p90) cc_final: 0.7385 (p90) REVERT: O 275 CYS cc_start: 0.8540 (t) cc_final: 0.8153 (t) REVERT: O 353 TRP cc_start: 0.7126 (p90) cc_final: 0.6515 (p90) REVERT: P 43 TYR cc_start: 0.8696 (m-80) cc_final: 0.8127 (m-10) REVERT: Q 201 HIS cc_start: 0.9273 (m90) cc_final: 0.8912 (m-70) REVERT: Q 229 MET cc_start: 0.6356 (mmp) cc_final: 0.3742 (mmt) REVERT: Q 236 ASN cc_start: 0.8347 (t0) cc_final: 0.7855 (t0) REVERT: Q 237 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 51 ILE cc_start: 0.8791 (mm) cc_final: 0.8525 (mm) REVERT: A 59 GLU cc_start: 0.8786 (pm20) cc_final: 0.8093 (pm20) REVERT: A 64 LYS cc_start: 0.9195 (mppt) cc_final: 0.8281 (mmtm) REVERT: A 71 VAL cc_start: 0.8985 (m) cc_final: 0.8778 (m) REVERT: A 73 GLU cc_start: 0.8102 (tt0) cc_final: 0.7807 (tt0) REVERT: A 82 LEU cc_start: 0.8438 (pt) cc_final: 0.8174 (mt) REVERT: A 85 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7849 (tm-30) REVERT: A 100 LEU cc_start: 0.8676 (pp) cc_final: 0.8338 (mm) REVERT: A 122 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8320 (ptmm) REVERT: A 123 ASP cc_start: 0.7821 (m-30) cc_final: 0.7412 (m-30) REVERT: B 27 GLN cc_start: 0.7658 (pm20) cc_final: 0.7359 (pm20) REVERT: B 36 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.8204 (ptp90) REVERT: B 58 LEU cc_start: 0.8545 (mm) cc_final: 0.8329 (mm) REVERT: B 62 LEU cc_start: 0.8058 (mm) cc_final: 0.7853 (mm) REVERT: B 74 GLU cc_start: 0.8403 (tp30) cc_final: 0.7852 (tp30) REVERT: C 31 ILE cc_start: 0.9240 (mm) cc_final: 0.8896 (pt) REVERT: C 34 TYR cc_start: 0.8311 (m-80) cc_final: 0.8108 (m-80) REVERT: C 57 LEU cc_start: 0.8400 (mt) cc_final: 0.8106 (mt) REVERT: C 83 ARG cc_start: 0.7516 (ptm-80) cc_final: 0.6914 (ptm-80) REVERT: D 49 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8166 (mttt) REVERT: D 114 VAL cc_start: 0.8320 (m) cc_final: 0.8086 (p) REVERT: E 41 TYR cc_start: 0.6451 (p90) cc_final: 0.5883 (p90) REVERT: E 56 LYS cc_start: 0.8747 (tmtt) cc_final: 0.8526 (tmtt) REVERT: E 58 THR cc_start: 0.7056 (t) cc_final: 0.6834 (t) REVERT: E 81 ASP cc_start: 0.8384 (p0) cc_final: 0.8180 (p0) REVERT: E 94 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7076 (tt0) REVERT: E 115 LYS cc_start: 0.9128 (ptpp) cc_final: 0.8793 (ptpp) REVERT: E 125 LYS cc_start: 0.8707 (mtmm) cc_final: 0.8456 (mtmm) REVERT: F 50 ILE cc_start: 0.8385 (pt) cc_final: 0.8067 (mm) REVERT: F 58 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7911 (pt) REVERT: F 82 THR cc_start: 0.7611 (p) cc_final: 0.7264 (p) REVERT: F 91 LYS cc_start: 0.8494 (pttp) cc_final: 0.8220 (pttm) REVERT: G 34 TYR cc_start: 0.7905 (p90) cc_final: 0.7649 (p90) REVERT: G 52 TYR cc_start: 0.7273 (t80) cc_final: 0.6825 (t80) REVERT: G 59 TYR cc_start: 0.7244 (p90) cc_final: 0.6630 (p90) REVERT: G 60 LEU cc_start: 0.8670 (pp) cc_final: 0.8274 (pp) REVERT: G 96 ASP cc_start: 0.8401 (p0) cc_final: 0.8067 (p0) REVERT: H 52 HIS cc_start: 0.7462 (t70) cc_final: 0.7121 (t70) REVERT: H 66 ASN cc_start: 0.7801 (p0) cc_final: 0.7499 (p0) REVERT: H 72 ILE cc_start: 0.7753 (tp) cc_final: 0.7438 (tt) REVERT: H 82 LYS cc_start: 0.8928 (tmmt) cc_final: 0.8575 (tmtt) REVERT: H 86 TYR cc_start: 0.7153 (p90) cc_final: 0.6781 (p90) REVERT: H 88 LYS cc_start: 0.9339 (ptpp) cc_final: 0.9102 (ptmm) REVERT: H 102 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8144 (ttp-110) REVERT: H 105 LEU cc_start: 0.9084 (pp) cc_final: 0.8846 (pp) REVERT: H 111 LYS cc_start: 0.8408 (pptt) cc_final: 0.8169 (pptt) REVERT: H 112 HIS cc_start: 0.7696 (m90) cc_final: 0.6652 (m90) REVERT: H 116 GLU cc_start: 0.7990 (mp0) cc_final: 0.7588 (mp0) REVERT: H 119 ARG cc_start: 0.8065 (ttp-110) cc_final: 0.7344 (mtm110) outliers start: 5 outliers final: 2 residues processed: 529 average time/residue: 0.4209 time to fit residues: 315.0949 Evaluate side-chains 465 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 461 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 chunk 173 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 50 optimal weight: 0.0970 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 204 GLN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.121092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095575 restraints weight = 89242.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.098764 restraints weight = 50539.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100843 restraints weight = 32659.456| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.4912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 22580 Z= 0.201 Angle : 0.840 10.256 31707 Z= 0.461 Chirality : 0.047 0.327 3556 Planarity : 0.007 0.095 3001 Dihedral : 28.545 122.066 5372 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.18), residues: 1866 helix: -1.29 (0.16), residues: 975 sheet: -2.72 (0.74), residues: 35 loop : -3.11 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP O 353 HIS 0.012 0.002 HIS C 84 PHE 0.035 0.003 PHE H 73 TYR 0.028 0.002 TYR F 98 ARG 0.009 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.05542 ( 1048) hydrogen bonds : angle 5.07357 ( 2748) covalent geometry : bond 0.00436 (22580) covalent geometry : angle 0.83976 (31707) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 533 time to evaluate : 1.895 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 212 GLU cc_start: 0.8187 (mp0) cc_final: 0.7967 (mp0) REVERT: K 284 HIS cc_start: 0.7688 (m-70) cc_final: 0.7310 (m-70) REVERT: K 327 LEU cc_start: 0.9232 (mt) cc_final: 0.8992 (pp) REVERT: K 343 ASP cc_start: 0.9086 (p0) cc_final: 0.8764 (p0) REVERT: M 204 GLN cc_start: 0.6356 (OUTLIER) cc_final: 0.5707 (pp30) REVERT: M 233 ASN cc_start: 0.7979 (p0) cc_final: 0.7635 (p0) REVERT: M 234 LEU cc_start: 0.9207 (mp) cc_final: 0.8805 (mp) REVERT: M 237 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8695 (tp-100) REVERT: M 280 ARG cc_start: 0.5299 (mmp-170) cc_final: 0.5093 (mmp-170) REVERT: M 339 GLN cc_start: 0.9424 (pt0) cc_final: 0.9152 (pp30) REVERT: O 178 GLU cc_start: 0.7883 (tp30) cc_final: 0.7255 (pm20) REVERT: O 237 PHE cc_start: 0.7109 (m-80) cc_final: 0.6484 (m-80) REVERT: O 271 PHE cc_start: 0.8105 (p90) cc_final: 0.7443 (p90) REVERT: O 275 CYS cc_start: 0.8715 (t) cc_final: 0.8338 (t) REVERT: O 353 TRP cc_start: 0.7132 (p90) cc_final: 0.6553 (p90) REVERT: Q 147 TYR cc_start: 0.6777 (m-10) cc_final: 0.6546 (m-10) REVERT: Q 198 HIS cc_start: 0.9026 (m90) cc_final: 0.8767 (m90) REVERT: R 14 VAL cc_start: 0.7403 (p) cc_final: 0.6794 (p) REVERT: A 59 GLU cc_start: 0.9066 (pm20) cc_final: 0.8594 (pm20) REVERT: A 62 ILE cc_start: 0.9079 (pt) cc_final: 0.8669 (pt) REVERT: A 73 GLU cc_start: 0.8068 (tt0) cc_final: 0.7848 (tt0) REVERT: A 82 LEU cc_start: 0.8777 (pt) cc_final: 0.8571 (pp) REVERT: A 85 GLN cc_start: 0.8207 (tm-30) cc_final: 0.7502 (tm-30) REVERT: A 87 SER cc_start: 0.9202 (t) cc_final: 0.8920 (p) REVERT: A 124 ILE cc_start: 0.8326 (mp) cc_final: 0.7770 (tp) REVERT: B 34 ILE cc_start: 0.9113 (tp) cc_final: 0.8638 (tp) REVERT: B 55 ARG cc_start: 0.7703 (mmp80) cc_final: 0.7494 (tpp-160) REVERT: B 74 GLU cc_start: 0.8458 (tp30) cc_final: 0.7938 (tp30) REVERT: B 80 THR cc_start: 0.5876 (p) cc_final: 0.5597 (p) REVERT: B 83 SER cc_start: 0.8624 (m) cc_final: 0.7943 (m) REVERT: C 25 GLN cc_start: 0.7523 (tp40) cc_final: 0.7311 (tp40) REVERT: C 31 ILE cc_start: 0.9289 (mm) cc_final: 0.8878 (mp) REVERT: C 34 TYR cc_start: 0.8440 (m-80) cc_final: 0.8218 (m-10) REVERT: C 36 LYS cc_start: 0.8723 (mppt) cc_final: 0.8304 (mmmt) REVERT: C 53 LEU cc_start: 0.8584 (mp) cc_final: 0.8162 (tt) REVERT: D 49 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8211 (mttt) REVERT: D 101 VAL cc_start: 0.8340 (m) cc_final: 0.8013 (p) REVERT: E 41 TYR cc_start: 0.6669 (p90) cc_final: 0.6174 (p90) REVERT: E 54 PHE cc_start: 0.6629 (p90) cc_final: 0.6313 (p90) REVERT: E 60 LEU cc_start: 0.9048 (tp) cc_final: 0.8754 (tp) REVERT: E 64 LYS cc_start: 0.8444 (mppt) cc_final: 0.8235 (mmtm) REVERT: E 65 LEU cc_start: 0.8883 (mm) cc_final: 0.8641 (mm) REVERT: E 72 ARG cc_start: 0.8336 (mmt180) cc_final: 0.6884 (mmt180) REVERT: E 104 PHE cc_start: 0.7240 (p90) cc_final: 0.6995 (p90) REVERT: E 108 ASN cc_start: 0.8446 (m110) cc_final: 0.8228 (m-40) REVERT: E 115 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8876 (ptpp) REVERT: E 120 GLN cc_start: 0.7582 (pm20) cc_final: 0.6963 (pm20) REVERT: E 123 ASP cc_start: 0.7750 (m-30) cc_final: 0.7126 (m-30) REVERT: E 125 LYS cc_start: 0.8765 (mtmm) cc_final: 0.8477 (mtmm) REVERT: F 27 GLN cc_start: 0.8378 (mp10) cc_final: 0.7977 (mp10) REVERT: F 36 ARG cc_start: 0.6186 (mpp-170) cc_final: 0.5730 (ptp-170) REVERT: F 50 ILE cc_start: 0.8511 (pt) cc_final: 0.8133 (mm) REVERT: F 57 VAL cc_start: 0.8565 (m) cc_final: 0.8349 (p) REVERT: F 60 SER cc_start: 0.8493 (p) cc_final: 0.7975 (p) REVERT: F 63 GLU cc_start: 0.8465 (pt0) cc_final: 0.8245 (pp20) REVERT: F 82 THR cc_start: 0.7703 (p) cc_final: 0.7053 (p) REVERT: F 91 LYS cc_start: 0.8484 (pttp) cc_final: 0.8042 (pttp) REVERT: F 93 GLN cc_start: 0.8002 (pm20) cc_final: 0.7666 (pp30) REVERT: G 38 HIS cc_start: 0.8008 (p90) cc_final: 0.7683 (p90) REVERT: G 52 TYR cc_start: 0.7360 (t80) cc_final: 0.7069 (t80) REVERT: G 59 TYR cc_start: 0.7349 (p90) cc_final: 0.6916 (p90) REVERT: G 60 LEU cc_start: 0.8866 (pp) cc_final: 0.8619 (pp) REVERT: G 78 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8379 (mtmt) REVERT: G 86 GLN cc_start: 0.7139 (mp10) cc_final: 0.6736 (mp10) REVERT: G 89 ILE cc_start: 0.8926 (mt) cc_final: 0.8699 (mp) REVERT: H 66 ASN cc_start: 0.8102 (p0) cc_final: 0.7678 (p0) REVERT: H 74 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7829 (tp30) REVERT: H 86 TYR cc_start: 0.7181 (p90) cc_final: 0.6785 (p90) REVERT: H 88 LYS cc_start: 0.9352 (ptpp) cc_final: 0.9077 (ptmm) REVERT: H 99 THR cc_start: 0.8775 (m) cc_final: 0.8267 (p) REVERT: H 111 LYS cc_start: 0.8509 (pptt) cc_final: 0.8114 (pptt) REVERT: H 112 HIS cc_start: 0.7760 (m90) cc_final: 0.6610 (m90) REVERT: H 116 GLU cc_start: 0.8154 (mp0) cc_final: 0.7870 (mp0) outliers start: 3 outliers final: 1 residues processed: 536 average time/residue: 0.4157 time to fit residues: 315.9396 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 480 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 135 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 196 optimal weight: 0.0570 chunk 99 optimal weight: 7.9990 chunk 163 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.096356 restraints weight = 89284.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.099504 restraints weight = 51132.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101505 restraints weight = 33356.156| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22580 Z= 0.197 Angle : 0.850 13.824 31707 Z= 0.463 Chirality : 0.047 0.241 3556 Planarity : 0.006 0.136 3001 Dihedral : 28.436 123.666 5372 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 0.12 % Allowed : 4.55 % Favored : 95.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.18), residues: 1866 helix: -1.16 (0.16), residues: 979 sheet: -2.29 (0.79), residues: 35 loop : -3.02 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP O 353 HIS 0.022 0.002 HIS G 84 PHE 0.028 0.002 PHE E 67 TYR 0.031 0.002 TYR D 86 ARG 0.009 0.001 ARG B 67 Details of bonding type rmsd hydrogen bonds : bond 0.05444 ( 1048) hydrogen bonds : angle 5.02961 ( 2748) covalent geometry : bond 0.00428 (22580) covalent geometry : angle 0.85005 (31707) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 525 time to evaluate : 1.960 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 281 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8564 (mm-30) REVERT: K 284 HIS cc_start: 0.7858 (m-70) cc_final: 0.7359 (m-70) REVERT: K 325 TYR cc_start: 0.8157 (m-80) cc_final: 0.7954 (m-80) REVERT: K 327 LEU cc_start: 0.9238 (mt) cc_final: 0.9021 (pp) REVERT: K 404 PHE cc_start: 0.7181 (p90) cc_final: 0.6931 (p90) REVERT: M 164 MET cc_start: -0.0446 (tpt) cc_final: -0.1477 (tpt) REVERT: M 237 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8773 (tm-30) REVERT: M 278 TYR cc_start: 0.8524 (t80) cc_final: 0.8276 (t80) REVERT: M 280 ARG cc_start: 0.5325 (mmp-170) cc_final: 0.4947 (mmp-170) REVERT: O 237 PHE cc_start: 0.6956 (m-80) cc_final: 0.6625 (m-10) REVERT: O 271 PHE cc_start: 0.8123 (p90) cc_final: 0.7418 (p90) REVERT: O 275 CYS cc_start: 0.8646 (t) cc_final: 0.8333 (t) REVERT: O 325 TYR cc_start: 0.8676 (m-80) cc_final: 0.8356 (m-80) REVERT: P 43 TYR cc_start: 0.8771 (m-80) cc_final: 0.8255 (m-10) REVERT: Q 198 HIS cc_start: 0.9049 (m90) cc_final: 0.8759 (m90) REVERT: Q 235 ARG cc_start: 0.6642 (tmm-80) cc_final: 0.6254 (tmm-80) REVERT: R 14 VAL cc_start: 0.7532 (p) cc_final: 0.7228 (p) REVERT: A 51 ILE cc_start: 0.8525 (mm) cc_final: 0.7803 (mm) REVERT: A 70 LEU cc_start: 0.8497 (pp) cc_final: 0.8276 (pp) REVERT: A 73 GLU cc_start: 0.8212 (tt0) cc_final: 0.7898 (tt0) REVERT: A 84 PHE cc_start: 0.7135 (m-10) cc_final: 0.6330 (m-10) REVERT: A 85 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 87 SER cc_start: 0.9181 (t) cc_final: 0.8900 (p) REVERT: A 124 ILE cc_start: 0.8392 (mp) cc_final: 0.7856 (tp) REVERT: B 61 PHE cc_start: 0.8300 (t80) cc_final: 0.8027 (t80) REVERT: B 74 GLU cc_start: 0.8361 (tp30) cc_final: 0.7942 (tp30) REVERT: B 93 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 25 GLN cc_start: 0.7697 (tp40) cc_final: 0.7322 (tp40) REVERT: C 31 ILE cc_start: 0.9197 (mm) cc_final: 0.8903 (mp) REVERT: C 33 ARG cc_start: 0.8489 (pmt170) cc_final: 0.7853 (ptt-90) REVERT: C 53 LEU cc_start: 0.8585 (mp) cc_final: 0.8164 (tt) REVERT: C 78 LYS cc_start: 0.8649 (pttm) cc_final: 0.8424 (pttm) REVERT: C 79 ARG cc_start: 0.7225 (pmt-80) cc_final: 0.6893 (pmt-80) REVERT: C 80 ILE cc_start: 0.8785 (tp) cc_final: 0.8554 (tp) REVERT: C 81 THR cc_start: 0.8528 (p) cc_final: 0.7636 (p) REVERT: C 84 HIS cc_start: 0.7691 (p90) cc_final: 0.7161 (p90) REVERT: D 65 LEU cc_start: 0.9108 (mt) cc_final: 0.8660 (mt) REVERT: D 76 ILE cc_start: 0.9407 (pt) cc_final: 0.9133 (pt) REVERT: D 101 VAL cc_start: 0.8365 (m) cc_final: 0.8072 (p) REVERT: D 109 LEU cc_start: 0.7994 (pt) cc_final: 0.7775 (pt) REVERT: E 41 TYR cc_start: 0.6759 (p90) cc_final: 0.6321 (p90) REVERT: E 60 LEU cc_start: 0.9104 (tp) cc_final: 0.8846 (tp) REVERT: E 64 LYS cc_start: 0.8547 (mppt) cc_final: 0.8070 (mmmm) REVERT: E 69 ARG cc_start: 0.7951 (ptp90) cc_final: 0.7571 (ptp90) REVERT: E 72 ARG cc_start: 0.8319 (mmt180) cc_final: 0.7090 (mmt180) REVERT: E 76 GLN cc_start: 0.8883 (pm20) cc_final: 0.8635 (pm20) REVERT: E 115 LYS cc_start: 0.9173 (ptpp) cc_final: 0.8879 (ptpp) REVERT: E 120 GLN cc_start: 0.7659 (pm20) cc_final: 0.7321 (pm20) REVERT: E 121 LYS cc_start: 0.8608 (tmmt) cc_final: 0.8340 (ptmt) REVERT: F 49 LEU cc_start: 0.8364 (mm) cc_final: 0.7798 (tp) REVERT: F 50 ILE cc_start: 0.8682 (pt) cc_final: 0.8328 (mm) REVERT: F 52 GLU cc_start: 0.7551 (pm20) cc_final: 0.7185 (pm20) REVERT: F 57 VAL cc_start: 0.8739 (m) cc_final: 0.8492 (p) REVERT: F 60 SER cc_start: 0.8542 (p) cc_final: 0.7894 (p) REVERT: F 63 GLU cc_start: 0.8627 (pt0) cc_final: 0.8114 (pp20) REVERT: F 64 SER cc_start: 0.8955 (p) cc_final: 0.8596 (p) REVERT: F 82 THR cc_start: 0.7351 (p) cc_final: 0.6545 (p) REVERT: F 93 GLN cc_start: 0.8233 (pm20) cc_final: 0.7650 (pp30) REVERT: G 34 TYR cc_start: 0.8100 (p90) cc_final: 0.7838 (p90) REVERT: G 52 TYR cc_start: 0.7189 (t80) cc_final: 0.6669 (t80) REVERT: G 59 TYR cc_start: 0.7343 (p90) cc_final: 0.7141 (p90) REVERT: G 60 LEU cc_start: 0.8825 (pp) cc_final: 0.8608 (pp) REVERT: G 73 LYS cc_start: 0.9086 (mptt) cc_final: 0.8857 (mmtp) REVERT: G 74 ASP cc_start: 0.8140 (p0) cc_final: 0.7857 (p0) REVERT: G 89 ILE cc_start: 0.8939 (mt) cc_final: 0.8720 (mm) REVERT: H 62 MET cc_start: 0.8254 (mmp) cc_final: 0.8025 (mmm) REVERT: H 66 ASN cc_start: 0.8034 (p0) cc_final: 0.7708 (p0) REVERT: H 72 ILE cc_start: 0.7749 (tt) cc_final: 0.7483 (tt) REVERT: H 88 LYS cc_start: 0.9353 (ptpp) cc_final: 0.9041 (ptmm) REVERT: H 105 LEU cc_start: 0.9147 (pp) cc_final: 0.8809 (pp) REVERT: H 116 GLU cc_start: 0.8176 (mp0) cc_final: 0.7616 (mp0) outliers start: 2 outliers final: 1 residues processed: 526 average time/residue: 0.4195 time to fit residues: 314.0165 Evaluate side-chains 472 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 471 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 4 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 204 optimal weight: 0.4980 chunk 138 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 158 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 211 optimal weight: 0.0670 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 222 HIS K 400 GLN ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 GLN A 68 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 55 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.123392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.097328 restraints weight = 88305.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.100655 restraints weight = 50436.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.102783 restraints weight = 32746.259| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22580 Z= 0.184 Angle : 0.842 11.578 31707 Z= 0.456 Chirality : 0.047 0.240 3556 Planarity : 0.006 0.097 3001 Dihedral : 28.272 128.899 5372 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 1866 helix: -1.08 (0.16), residues: 978 sheet: -2.07 (0.81), residues: 35 loop : -3.02 (0.20), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP O 353 HIS 0.017 0.002 HIS Q 240 PHE 0.031 0.002 PHE E 67 TYR 0.031 0.002 TYR F 98 ARG 0.014 0.001 ARG F 36 Details of bonding type rmsd hydrogen bonds : bond 0.05119 ( 1048) hydrogen bonds : angle 4.90572 ( 2748) covalent geometry : bond 0.00400 (22580) covalent geometry : angle 0.84215 (31707) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 515 time to evaluate : 1.799 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8574 (mmpt) cc_final: 0.8101 (mmpt) REVERT: K 273 PHE cc_start: 0.8309 (m-10) cc_final: 0.8080 (m-10) REVERT: K 284 HIS cc_start: 0.7984 (m-70) cc_final: 0.7341 (m-70) REVERT: K 318 LYS cc_start: 0.5360 (mmtt) cc_final: 0.4436 (mmpt) REVERT: K 325 TYR cc_start: 0.8148 (m-80) cc_final: 0.7792 (m-80) REVERT: K 404 PHE cc_start: 0.7126 (p90) cc_final: 0.6854 (p90) REVERT: K 415 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7794 (mtm-85) REVERT: M 234 LEU cc_start: 0.9394 (mp) cc_final: 0.9053 (pp) REVERT: M 237 GLN cc_start: 0.8921 (tp-100) cc_final: 0.8708 (tm-30) REVERT: M 278 TYR cc_start: 0.8521 (t80) cc_final: 0.8283 (t80) REVERT: M 280 ARG cc_start: 0.5021 (mmp-170) cc_final: 0.4566 (mmp-170) REVERT: O 237 PHE cc_start: 0.6847 (m-80) cc_final: 0.6326 (m-10) REVERT: O 271 PHE cc_start: 0.8086 (p90) cc_final: 0.7412 (p90) REVERT: O 275 CYS cc_start: 0.8657 (t) cc_final: 0.8371 (t) REVERT: O 329 LYS cc_start: 0.8812 (pptt) cc_final: 0.8491 (ptpp) REVERT: O 353 TRP cc_start: 0.7064 (p90) cc_final: 0.6609 (p90) REVERT: P 43 TYR cc_start: 0.8719 (m-80) cc_final: 0.8259 (m-10) REVERT: Q 196 PHE cc_start: 0.8163 (m-80) cc_final: 0.7948 (m-80) REVERT: Q 198 HIS cc_start: 0.9052 (m90) cc_final: 0.8743 (m-70) REVERT: Q 235 ARG cc_start: 0.6645 (tmm-80) cc_final: 0.6307 (tmm-80) REVERT: R 14 VAL cc_start: 0.7534 (p) cc_final: 0.7275 (p) REVERT: A 69 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.7759 (ptp-170) REVERT: A 71 VAL cc_start: 0.8911 (m) cc_final: 0.8692 (p) REVERT: A 73 GLU cc_start: 0.8009 (tt0) cc_final: 0.7728 (tt0) REVERT: A 84 PHE cc_start: 0.7216 (m-10) cc_final: 0.6968 (m-80) REVERT: A 85 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7764 (tm-30) REVERT: A 87 SER cc_start: 0.9102 (t) cc_final: 0.8861 (p) REVERT: A 113 HIS cc_start: 0.7348 (t-90) cc_final: 0.6391 (t-90) REVERT: B 25 ASN cc_start: 0.7960 (t0) cc_final: 0.7378 (t0) REVERT: B 27 GLN cc_start: 0.8360 (pm20) cc_final: 0.7797 (pm20) REVERT: B 34 ILE cc_start: 0.8996 (tp) cc_final: 0.8394 (tp) REVERT: B 36 ARG cc_start: 0.8299 (ttp-110) cc_final: 0.8048 (ptp90) REVERT: B 61 PHE cc_start: 0.8416 (t80) cc_final: 0.8098 (t80) REVERT: B 62 LEU cc_start: 0.8424 (mm) cc_final: 0.8188 (mm) REVERT: B 70 VAL cc_start: 0.8887 (m) cc_final: 0.8579 (p) REVERT: B 74 GLU cc_start: 0.8383 (tp30) cc_final: 0.8046 (tp30) REVERT: B 93 GLN cc_start: 0.9042 (tm-30) cc_final: 0.8828 (tm-30) REVERT: C 25 GLN cc_start: 0.7590 (tp40) cc_final: 0.7161 (tp40) REVERT: C 31 ILE cc_start: 0.9154 (mm) cc_final: 0.8900 (mp) REVERT: C 33 ARG cc_start: 0.8492 (pmt170) cc_final: 0.8025 (ptt-90) REVERT: C 53 LEU cc_start: 0.8546 (mp) cc_final: 0.8103 (tt) REVERT: C 79 ARG cc_start: 0.7138 (pmt-80) cc_final: 0.6864 (pmt-80) REVERT: C 109 LEU cc_start: 0.8941 (pt) cc_final: 0.8576 (pp) REVERT: C 111 HIS cc_start: 0.7868 (p-80) cc_final: 0.7508 (p-80) REVERT: D 60 LYS cc_start: 0.8470 (ptpp) cc_final: 0.8251 (ptpp) REVERT: D 65 LEU cc_start: 0.9100 (mt) cc_final: 0.8757 (mt) REVERT: D 86 TYR cc_start: 0.7449 (m-10) cc_final: 0.7213 (m-10) REVERT: D 99 THR cc_start: 0.8180 (p) cc_final: 0.7039 (p) REVERT: D 101 VAL cc_start: 0.8447 (m) cc_final: 0.8199 (p) REVERT: D 102 ARG cc_start: 0.7529 (ptt90) cc_final: 0.7241 (ptt90) REVERT: E 41 TYR cc_start: 0.6678 (p90) cc_final: 0.6340 (p90) REVERT: E 64 LYS cc_start: 0.8588 (mppt) cc_final: 0.8232 (mmmm) REVERT: E 69 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7442 (ptp90) REVERT: E 72 ARG cc_start: 0.8220 (mmt180) cc_final: 0.6396 (mmt180) REVERT: E 103 LEU cc_start: 0.8833 (pp) cc_final: 0.8589 (pp) REVERT: E 108 ASN cc_start: 0.8514 (m110) cc_final: 0.8240 (m-40) REVERT: E 115 LYS cc_start: 0.9175 (ptpp) cc_final: 0.8866 (ptpp) REVERT: E 120 GLN cc_start: 0.7501 (pm20) cc_final: 0.7090 (pm20) REVERT: E 123 ASP cc_start: 0.7826 (m-30) cc_final: 0.7474 (m-30) REVERT: F 49 LEU cc_start: 0.8449 (mm) cc_final: 0.8043 (tp) REVERT: F 50 ILE cc_start: 0.8635 (pt) cc_final: 0.8216 (mm) REVERT: F 57 VAL cc_start: 0.8792 (m) cc_final: 0.8546 (p) REVERT: F 60 SER cc_start: 0.8536 (p) cc_final: 0.8089 (p) REVERT: F 63 GLU cc_start: 0.8625 (pt0) cc_final: 0.8307 (pp20) REVERT: F 75 HIS cc_start: 0.7583 (t-90) cc_final: 0.7169 (t70) REVERT: F 91 LYS cc_start: 0.8397 (pttp) cc_final: 0.8110 (pttp) REVERT: F 93 GLN cc_start: 0.8167 (pm20) cc_final: 0.7702 (pp30) REVERT: G 32 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8574 (mmmm) REVERT: G 51 ILE cc_start: 0.8874 (pt) cc_final: 0.8538 (pt) REVERT: G 52 TYR cc_start: 0.7230 (t80) cc_final: 0.6930 (t80) REVERT: G 59 TYR cc_start: 0.7350 (p90) cc_final: 0.6978 (p90) REVERT: G 60 LEU cc_start: 0.8874 (pp) cc_final: 0.8575 (pp) REVERT: G 74 ASP cc_start: 0.8117 (p0) cc_final: 0.7163 (p0) REVERT: G 78 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8217 (mtmt) REVERT: G 86 GLN cc_start: 0.6980 (mp10) cc_final: 0.6657 (mp10) REVERT: G 89 ILE cc_start: 0.8947 (mt) cc_final: 0.8725 (mp) REVERT: H 66 ASN cc_start: 0.8091 (p0) cc_final: 0.7731 (p0) REVERT: H 72 ILE cc_start: 0.7656 (tt) cc_final: 0.7368 (tt) REVERT: H 73 PHE cc_start: 0.7677 (t80) cc_final: 0.7348 (t80) REVERT: H 105 LEU cc_start: 0.9045 (pp) cc_final: 0.8743 (pp) REVERT: H 112 HIS cc_start: 0.7845 (m90) cc_final: 0.7172 (m90) REVERT: H 123 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8727 (ptpp) REVERT: H 124 TYR cc_start: 0.7704 (p90) cc_final: 0.6810 (p90) outliers start: 1 outliers final: 0 residues processed: 516 average time/residue: 0.4290 time to fit residues: 314.4741 Evaluate side-chains 458 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 191 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 208 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** M 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.123771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097634 restraints weight = 88656.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.100990 restraints weight = 50983.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 69)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.103157 restraints weight = 33209.490| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22580 Z= 0.190 Angle : 0.867 12.080 31707 Z= 0.465 Chirality : 0.048 0.353 3556 Planarity : 0.007 0.164 3001 Dihedral : 28.211 130.164 5372 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 22.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.18), residues: 1866 helix: -1.02 (0.16), residues: 973 sheet: -2.24 (0.80), residues: 35 loop : -2.89 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP O 353 HIS 0.014 0.001 HIS C 84 PHE 0.036 0.003 PHE E 67 TYR 0.027 0.002 TYR K 311 ARG 0.013 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.05198 ( 1048) hydrogen bonds : angle 4.99901 ( 2748) covalent geometry : bond 0.00419 (22580) covalent geometry : angle 0.86746 (31707) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 509 time to evaluate : 2.008 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: 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: 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: K 209 LYS cc_start: 0.8543 (mmpt) cc_final: 0.8020 (mmpt) REVERT: K 273 PHE cc_start: 0.8338 (m-10) cc_final: 0.8043 (m-10) REVERT: K 284 HIS cc_start: 0.7846 (m-70) cc_final: 0.7376 (m-70) REVERT: K 325 TYR cc_start: 0.8173 (m-80) cc_final: 0.7814 (m-80) REVERT: K 404 PHE cc_start: 0.7182 (p90) cc_final: 0.6883 (p90) REVERT: M 234 LEU cc_start: 0.9402 (mp) cc_final: 0.9056 (pp) REVERT: M 235 ARG cc_start: 0.8688 (ptt90) cc_final: 0.8273 (ptt90) REVERT: M 278 TYR cc_start: 0.8407 (t80) cc_final: 0.8166 (t80) REVERT: O 237 PHE cc_start: 0.6882 (m-80) cc_final: 0.6314 (m-80) REVERT: O 265 TYR cc_start: 0.7138 (p90) cc_final: 0.6763 (p90) REVERT: O 271 PHE cc_start: 0.8099 (p90) cc_final: 0.7415 (p90) REVERT: O 275 CYS cc_start: 0.8735 (t) cc_final: 0.8340 (t) REVERT: O 325 TYR cc_start: 0.8696 (m-80) cc_final: 0.8492 (m-80) REVERT: O 329 LYS cc_start: 0.8689 (pptt) cc_final: 0.8465 (ptpp) REVERT: O 353 TRP cc_start: 0.6945 (p90) cc_final: 0.6470 (p90) REVERT: P 43 TYR cc_start: 0.8724 (m-80) cc_final: 0.8280 (m-10) REVERT: Q 164 MET cc_start: 0.6457 (mtt) cc_final: 0.5841 (mtt) REVERT: Q 196 PHE cc_start: 0.8088 (m-80) cc_final: 0.7817 (m-80) REVERT: Q 198 HIS cc_start: 0.9066 (m90) cc_final: 0.8774 (m-70) REVERT: Q 235 ARG cc_start: 0.6519 (tmm-80) cc_final: 0.6034 (tmm-80) REVERT: R 14 VAL cc_start: 0.7385 (p) cc_final: 0.7104 (p) REVERT: A 70 LEU cc_start: 0.8438 (pp) cc_final: 0.7962 (pp) REVERT: A 71 VAL cc_start: 0.9050 (m) cc_final: 0.8832 (p) REVERT: A 73 GLU cc_start: 0.8009 (tt0) cc_final: 0.7764 (tt0) REVERT: A 84 PHE cc_start: 0.7423 (m-10) cc_final: 0.7151 (m-80) REVERT: A 87 SER cc_start: 0.9158 (t) cc_final: 0.8814 (p) REVERT: A 107 THR cc_start: 0.8193 (p) cc_final: 0.7251 (p) REVERT: B 27 GLN cc_start: 0.8568 (pm20) cc_final: 0.7514 (pm20) REVERT: B 44 LYS cc_start: 0.8917 (pptt) cc_final: 0.7973 (tppt) REVERT: B 61 PHE cc_start: 0.8364 (t80) cc_final: 0.7983 (t80) REVERT: B 70 VAL cc_start: 0.8926 (m) cc_final: 0.8633 (p) REVERT: B 74 GLU cc_start: 0.8328 (tp30) cc_final: 0.8037 (tp30) REVERT: C 44 ARG cc_start: 0.6670 (ptt180) cc_final: 0.5949 (ptt180) REVERT: C 79 ARG cc_start: 0.7185 (pmt-80) cc_final: 0.6921 (pmt-80) REVERT: C 80 ILE cc_start: 0.8778 (tp) cc_final: 0.8264 (tp) REVERT: C 81 THR cc_start: 0.8249 (p) cc_final: 0.7634 (p) REVERT: C 84 HIS cc_start: 0.7142 (p90) cc_final: 0.6013 (p90) REVERT: D 45 TYR cc_start: 0.7422 (t80) cc_final: 0.7036 (t80) REVERT: D 47 VAL cc_start: 0.8822 (t) cc_final: 0.8128 (t) REVERT: D 51 THR cc_start: 0.8979 (p) cc_final: 0.8477 (p) REVERT: D 60 LYS cc_start: 0.8510 (ptpp) cc_final: 0.8203 (ptpp) REVERT: D 65 LEU cc_start: 0.9070 (mt) cc_final: 0.8825 (mt) REVERT: D 76 ILE cc_start: 0.9333 (pt) cc_final: 0.8388 (pt) REVERT: D 79 GLU cc_start: 0.8287 (pt0) cc_final: 0.7854 (pp20) REVERT: D 99 THR cc_start: 0.8272 (p) cc_final: 0.7281 (p) REVERT: D 101 VAL cc_start: 0.8403 (m) cc_final: 0.8039 (p) REVERT: D 102 ARG cc_start: 0.7537 (ptt90) cc_final: 0.7105 (ppt90) REVERT: D 114 VAL cc_start: 0.8529 (m) cc_final: 0.8267 (p) REVERT: E 41 TYR cc_start: 0.6706 (p90) cc_final: 0.6313 (p90) REVERT: E 54 PHE cc_start: 0.6930 (p90) cc_final: 0.6331 (p90) REVERT: E 64 LYS cc_start: 0.8604 (mppt) cc_final: 0.8261 (mmmm) REVERT: E 104 PHE cc_start: 0.7338 (p90) cc_final: 0.7069 (p90) REVERT: E 108 ASN cc_start: 0.8460 (m110) cc_final: 0.8242 (m-40) REVERT: E 115 LYS cc_start: 0.9138 (ptpp) cc_final: 0.8826 (ptpp) REVERT: E 123 ASP cc_start: 0.8276 (m-30) cc_final: 0.7950 (m-30) REVERT: F 27 GLN cc_start: 0.6647 (mt0) cc_final: 0.6095 (mt0) REVERT: F 30 THR cc_start: 0.8534 (p) cc_final: 0.8185 (p) REVERT: F 49 LEU cc_start: 0.8450 (mm) cc_final: 0.7921 (tp) REVERT: F 50 ILE cc_start: 0.8767 (pt) cc_final: 0.8336 (mm) REVERT: F 52 GLU cc_start: 0.7583 (pm20) cc_final: 0.7312 (pm20) REVERT: F 55 ARG cc_start: 0.8197 (ttm-80) cc_final: 0.7687 (mmt90) REVERT: F 57 VAL cc_start: 0.8838 (m) cc_final: 0.8633 (p) REVERT: F 60 SER cc_start: 0.8529 (p) cc_final: 0.8126 (p) REVERT: F 63 GLU cc_start: 0.8613 (pt0) cc_final: 0.8355 (pp20) REVERT: F 75 HIS cc_start: 0.7551 (t-90) cc_final: 0.7285 (t70) REVERT: F 87 VAL cc_start: 0.8572 (t) cc_final: 0.8371 (t) REVERT: F 91 LYS cc_start: 0.8421 (pttp) cc_final: 0.7889 (pttm) REVERT: F 93 GLN cc_start: 0.8198 (pm20) cc_final: 0.7678 (pp30) REVERT: G 34 TYR cc_start: 0.8238 (p90) cc_final: 0.7797 (p90) REVERT: G 51 ILE cc_start: 0.8790 (pt) cc_final: 0.8429 (pt) REVERT: G 52 TYR cc_start: 0.7100 (t80) cc_final: 0.6696 (t80) REVERT: G 59 TYR cc_start: 0.7273 (p90) cc_final: 0.6937 (p90) REVERT: G 74 ASP cc_start: 0.8142 (p0) cc_final: 0.7755 (p0) REVERT: G 78 LYS cc_start: 0.8449 (mtmt) cc_final: 0.7839 (mtmt) REVERT: G 86 GLN cc_start: 0.7201 (mp10) cc_final: 0.6829 (mp10) REVERT: G 89 ILE cc_start: 0.8943 (mt) cc_final: 0.8694 (mp) REVERT: H 49 LYS cc_start: 0.8618 (pttm) cc_final: 0.8389 (pttp) REVERT: H 66 ASN cc_start: 0.8086 (p0) cc_final: 0.7742 (p0) REVERT: H 72 ILE cc_start: 0.7736 (tt) cc_final: 0.6995 (tt) REVERT: H 79 GLU cc_start: 0.7523 (pm20) cc_final: 0.7259 (pm20) REVERT: H 88 LYS cc_start: 0.9158 (ptmm) cc_final: 0.8793 (ptmm) REVERT: H 112 HIS cc_start: 0.7630 (m90) cc_final: 0.7158 (m90) REVERT: H 116 GLU cc_start: 0.8144 (mp0) cc_final: 0.7873 (mp0) REVERT: H 124 TYR cc_start: 0.7635 (p90) cc_final: 0.6684 (p90) outliers start: 0 outliers final: 0 residues processed: 509 average time/residue: 0.4214 time to fit residues: 305.0020 Evaluate side-chains 454 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 170 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.119776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.093695 restraints weight = 88340.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 66)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.096901 restraints weight = 51160.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.098969 restraints weight = 33654.389| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22580 Z= 0.248 Angle : 0.901 12.551 31707 Z= 0.487 Chirality : 0.049 0.321 3556 Planarity : 0.008 0.143 3001 Dihedral : 28.255 127.880 5372 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.15 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.18), residues: 1866 helix: -1.06 (0.16), residues: 982 sheet: -2.15 (0.78), residues: 33 loop : -2.98 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 353 HIS 0.023 0.002 HIS Q 240 PHE 0.042 0.003 PHE E 67 TYR 0.031 0.003 TYR O 325 ARG 0.016 0.001 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.06018 ( 1048) hydrogen bonds : angle 5.13858 ( 2748) covalent geometry : bond 0.00547 (22580) covalent geometry : angle 0.90138 (31707) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.839 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 209 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8208 (mmpt) REVERT: K 273 PHE cc_start: 0.8414 (m-10) cc_final: 0.8034 (m-10) REVERT: K 284 HIS cc_start: 0.8012 (m-70) cc_final: 0.7518 (m-70) REVERT: K 314 MET cc_start: -0.0053 (ptt) cc_final: -0.1370 (ptp) REVERT: K 325 TYR cc_start: 0.8243 (m-80) cc_final: 0.7954 (m-80) REVERT: K 376 MET cc_start: 0.8606 (pmm) cc_final: 0.8380 (pmm) REVERT: K 404 PHE cc_start: 0.7375 (p90) cc_final: 0.7103 (p90) REVERT: M 234 LEU cc_start: 0.9434 (mp) cc_final: 0.9038 (mt) REVERT: M 237 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8334 (tm-30) REVERT: M 278 TYR cc_start: 0.8464 (t80) cc_final: 0.8209 (t80) REVERT: O 237 PHE cc_start: 0.7173 (m-80) cc_final: 0.6580 (m-80) REVERT: O 265 TYR cc_start: 0.7250 (p90) cc_final: 0.6852 (p90) REVERT: O 271 PHE cc_start: 0.8150 (p90) cc_final: 0.7554 (p90) REVERT: O 275 CYS cc_start: 0.8808 (t) cc_final: 0.8450 (t) REVERT: O 325 TYR cc_start: 0.8662 (m-80) cc_final: 0.8004 (m-80) REVERT: O 329 LYS cc_start: 0.8834 (pptt) cc_final: 0.8569 (pttm) REVERT: O 353 TRP cc_start: 0.6990 (p90) cc_final: 0.6477 (p90) REVERT: P 43 TYR cc_start: 0.8763 (m-80) cc_final: 0.8367 (m-10) REVERT: Q 147 TYR cc_start: 0.6885 (m-80) cc_final: 0.6590 (m-10) REVERT: Q 196 PHE cc_start: 0.8176 (m-80) cc_final: 0.7955 (m-80) REVERT: Q 198 HIS cc_start: 0.9046 (m90) cc_final: 0.8777 (m90) REVERT: R 14 VAL cc_start: 0.7468 (p) cc_final: 0.7159 (p) REVERT: R 100 HIS cc_start: 0.8484 (t70) cc_final: 0.8279 (t70) REVERT: A 71 VAL cc_start: 0.9090 (m) cc_final: 0.8849 (p) REVERT: A 84 PHE cc_start: 0.7539 (m-10) cc_final: 0.7098 (m-80) REVERT: A 87 SER cc_start: 0.9106 (t) cc_final: 0.8750 (p) REVERT: A 119 ILE cc_start: 0.8498 (mp) cc_final: 0.8223 (tp) REVERT: B 25 ASN cc_start: 0.8136 (t0) cc_final: 0.7903 (t0) REVERT: B 61 PHE cc_start: 0.8570 (t80) cc_final: 0.8047 (t80) REVERT: B 62 LEU cc_start: 0.8404 (mm) cc_final: 0.8140 (mm) REVERT: B 63 GLU cc_start: 0.8376 (pt0) cc_final: 0.7959 (pp20) REVERT: B 70 VAL cc_start: 0.8978 (m) cc_final: 0.8736 (p) REVERT: B 74 GLU cc_start: 0.8407 (tp30) cc_final: 0.7998 (tp30) REVERT: B 88 TYR cc_start: 0.7805 (m-10) cc_final: 0.7584 (m-10) REVERT: C 25 GLN cc_start: 0.7893 (tp40) cc_final: 0.7553 (tp40) REVERT: C 32 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8501 (mmtt) REVERT: C 35 LEU cc_start: 0.8402 (mm) cc_final: 0.8079 (mt) REVERT: C 36 LYS cc_start: 0.8752 (mptt) cc_final: 0.8324 (mmmt) REVERT: C 44 ARG cc_start: 0.7066 (ptt180) cc_final: 0.6436 (ptt180) REVERT: C 53 LEU cc_start: 0.8731 (mp) cc_final: 0.8322 (tt) REVERT: C 54 THR cc_start: 0.8361 (m) cc_final: 0.8042 (p) REVERT: C 80 ILE cc_start: 0.8840 (tp) cc_final: 0.8351 (tp) REVERT: C 84 HIS cc_start: 0.7433 (p90) cc_final: 0.6276 (p90) REVERT: C 103 ILE cc_start: 0.8327 (tt) cc_final: 0.7991 (tp) REVERT: D 51 THR cc_start: 0.9075 (p) cc_final: 0.8759 (p) REVERT: D 62 MET cc_start: 0.8072 (pmm) cc_final: 0.7741 (pmm) REVERT: D 64 ILE cc_start: 0.8620 (mm) cc_final: 0.7990 (tp) REVERT: D 65 LEU cc_start: 0.9061 (mt) cc_final: 0.8635 (mt) REVERT: D 92 ILE cc_start: 0.8376 (pt) cc_final: 0.7967 (pt) REVERT: D 99 THR cc_start: 0.8463 (p) cc_final: 0.7250 (p) REVERT: D 102 ARG cc_start: 0.7669 (ptt90) cc_final: 0.7326 (ptt90) REVERT: E 41 TYR cc_start: 0.6861 (p90) cc_final: 0.6464 (p90) REVERT: E 49 ARG cc_start: 0.8515 (pmt-80) cc_final: 0.8004 (pmt-80) REVERT: E 51 ILE cc_start: 0.8517 (mm) cc_final: 0.8061 (mm) REVERT: E 54 PHE cc_start: 0.7073 (p90) cc_final: 0.6530 (p90) REVERT: E 56 LYS cc_start: 0.9053 (tmtt) cc_final: 0.8739 (tmtt) REVERT: E 60 LEU cc_start: 0.8996 (tp) cc_final: 0.8749 (tp) REVERT: E 64 LYS cc_start: 0.8692 (mppt) cc_final: 0.8308 (mmmm) REVERT: E 79 LYS cc_start: 0.8534 (tmtt) cc_final: 0.8222 (tmtt) REVERT: E 115 LYS cc_start: 0.9193 (ptpp) cc_final: 0.8904 (ptpp) REVERT: E 125 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8877 (mmmm) REVERT: F 30 THR cc_start: 0.8614 (p) cc_final: 0.8265 (p) REVERT: F 46 ILE cc_start: 0.8743 (pt) cc_final: 0.8402 (pt) REVERT: F 49 LEU cc_start: 0.8592 (mm) cc_final: 0.7962 (tp) REVERT: F 50 ILE cc_start: 0.8620 (pt) cc_final: 0.8270 (mm) REVERT: F 57 VAL cc_start: 0.8911 (m) cc_final: 0.8683 (p) REVERT: F 59 LYS cc_start: 0.8642 (ptpp) cc_final: 0.8407 (pttm) REVERT: F 60 SER cc_start: 0.8517 (p) cc_final: 0.8087 (p) REVERT: F 63 GLU cc_start: 0.8592 (pt0) cc_final: 0.8386 (pp20) REVERT: F 87 VAL cc_start: 0.8598 (t) cc_final: 0.8306 (t) REVERT: F 91 LYS cc_start: 0.8552 (pttp) cc_final: 0.8201 (pttm) REVERT: F 93 GLN cc_start: 0.8290 (pm20) cc_final: 0.7875 (pp30) REVERT: G 32 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8056 (mmmm) REVERT: G 34 TYR cc_start: 0.8407 (p90) cc_final: 0.6985 (p90) REVERT: G 52 TYR cc_start: 0.7312 (t80) cc_final: 0.6697 (t80) REVERT: G 86 GLN cc_start: 0.7325 (mp10) cc_final: 0.6773 (mp10) REVERT: H 49 LYS cc_start: 0.8778 (pttm) cc_final: 0.8446 (pttp) REVERT: H 64 ILE cc_start: 0.8848 (pt) cc_final: 0.8646 (pt) REVERT: H 66 ASN cc_start: 0.8181 (p0) cc_final: 0.7752 (p0) REVERT: H 71 ASP cc_start: 0.7882 (p0) cc_final: 0.7617 (p0) REVERT: H 73 PHE cc_start: 0.7689 (t80) cc_final: 0.6823 (t80) REVERT: H 86 TYR cc_start: 0.6939 (p90) cc_final: 0.6037 (p90) REVERT: H 105 LEU cc_start: 0.9082 (pp) cc_final: 0.8855 (pp) REVERT: H 112 HIS cc_start: 0.7568 (m90) cc_final: 0.7120 (m90) REVERT: H 116 GLU cc_start: 0.8102 (mp0) cc_final: 0.7641 (mp0) REVERT: H 124 TYR cc_start: 0.7674 (p90) cc_final: 0.6967 (p90) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.4240 time to fit residues: 311.5128 Evaluate side-chains 461 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 96 optimal weight: 3.9990 chunk 175 optimal weight: 0.2980 chunk 141 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 182 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 192 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 55 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.123863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.097799 restraints weight = 88972.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.101155 restraints weight = 51255.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103329 restraints weight = 33386.333| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22580 Z= 0.185 Angle : 0.893 14.405 31707 Z= 0.476 Chirality : 0.048 0.300 3556 Planarity : 0.006 0.088 3001 Dihedral : 28.234 132.914 5372 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.18), residues: 1866 helix: -0.93 (0.16), residues: 953 sheet: -2.16 (0.79), residues: 35 loop : -2.78 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP O 353 HIS 0.019 0.002 HIS Q 240 PHE 0.037 0.002 PHE A 104 TYR 0.038 0.003 TYR F 72 ARG 0.012 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.05217 ( 1048) hydrogen bonds : angle 5.02287 ( 2748) covalent geometry : bond 0.00403 (22580) covalent geometry : angle 0.89257 (31707) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 512 time to evaluate : 1.882 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 249 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8133 (mtt-85) REVERT: K 273 PHE cc_start: 0.8311 (m-10) cc_final: 0.7971 (m-10) REVERT: K 281 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8451 (mm-30) REVERT: K 284 HIS cc_start: 0.7893 (m-70) cc_final: 0.7345 (m-70) REVERT: K 310 GLN cc_start: 0.7312 (pm20) cc_final: 0.6723 (pm20) REVERT: K 325 TYR cc_start: 0.8294 (m-80) cc_final: 0.7944 (m-80) REVERT: K 404 PHE cc_start: 0.7207 (p90) cc_final: 0.6940 (p90) REVERT: M 234 LEU cc_start: 0.9428 (mp) cc_final: 0.9030 (mt) REVERT: M 235 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8349 (ptt90) REVERT: M 237 GLN cc_start: 0.8834 (tm-30) cc_final: 0.8477 (tm-30) REVERT: M 278 TYR cc_start: 0.8424 (t80) cc_final: 0.8161 (t80) REVERT: O 237 PHE cc_start: 0.6956 (m-80) cc_final: 0.6678 (m-80) REVERT: O 265 TYR cc_start: 0.7198 (p90) cc_final: 0.6820 (p90) REVERT: O 271 PHE cc_start: 0.8228 (p90) cc_final: 0.7580 (p90) REVERT: O 275 CYS cc_start: 0.8714 (t) cc_final: 0.8361 (t) REVERT: O 328 SER cc_start: 0.6759 (m) cc_final: 0.6492 (p) REVERT: O 329 LYS cc_start: 0.8597 (pptt) cc_final: 0.8354 (pttm) REVERT: O 353 TRP cc_start: 0.6868 (p90) cc_final: 0.6418 (p90) REVERT: P 43 TYR cc_start: 0.8688 (m-80) cc_final: 0.8304 (m-10) REVERT: Q 147 TYR cc_start: 0.6805 (m-80) cc_final: 0.6579 (m-10) REVERT: Q 196 PHE cc_start: 0.8111 (m-80) cc_final: 0.7909 (m-80) REVERT: Q 198 HIS cc_start: 0.9057 (m90) cc_final: 0.8760 (m-70) REVERT: Q 235 ARG cc_start: 0.6707 (tmm-80) cc_final: 0.6252 (tmm-80) REVERT: R 14 VAL cc_start: 0.7515 (p) cc_final: 0.7254 (p) REVERT: A 67 PHE cc_start: 0.8066 (t80) cc_final: 0.7794 (t80) REVERT: A 69 ARG cc_start: 0.8653 (mtm-85) cc_final: 0.7800 (ptp-170) REVERT: A 70 LEU cc_start: 0.8441 (pp) cc_final: 0.8053 (pp) REVERT: A 71 VAL cc_start: 0.9110 (m) cc_final: 0.8849 (p) REVERT: A 84 PHE cc_start: 0.7480 (m-10) cc_final: 0.7073 (m-80) REVERT: A 87 SER cc_start: 0.9086 (t) cc_final: 0.8758 (p) REVERT: A 107 THR cc_start: 0.8280 (p) cc_final: 0.7722 (p) REVERT: A 115 LYS cc_start: 0.9433 (ptpp) cc_final: 0.9202 (ptpp) REVERT: A 119 ILE cc_start: 0.8130 (mp) cc_final: 0.7695 (mt) REVERT: B 25 ASN cc_start: 0.8275 (t0) cc_final: 0.7555 (t0) REVERT: B 61 PHE cc_start: 0.8503 (t80) cc_final: 0.7978 (t80) REVERT: B 62 LEU cc_start: 0.8393 (mm) cc_final: 0.8113 (mm) REVERT: B 70 VAL cc_start: 0.8958 (m) cc_final: 0.8724 (p) REVERT: B 74 GLU cc_start: 0.8359 (tp30) cc_final: 0.8041 (tp30) REVERT: B 88 TYR cc_start: 0.7499 (m-10) cc_final: 0.7202 (m-80) REVERT: C 25 GLN cc_start: 0.7647 (tp40) cc_final: 0.7262 (tp40) REVERT: C 36 LYS cc_start: 0.8770 (mptt) cc_final: 0.8401 (mmmt) REVERT: C 44 ARG cc_start: 0.6599 (ptt180) cc_final: 0.5805 (ptt180) REVERT: C 53 LEU cc_start: 0.8583 (mp) cc_final: 0.8215 (tt) REVERT: C 79 ARG cc_start: 0.7533 (tmm160) cc_final: 0.6863 (ttp80) REVERT: C 80 ILE cc_start: 0.8835 (tp) cc_final: 0.8214 (tp) REVERT: C 81 THR cc_start: 0.8342 (p) cc_final: 0.7833 (p) REVERT: C 84 HIS cc_start: 0.7219 (p90) cc_final: 0.6702 (p90) REVERT: D 47 VAL cc_start: 0.8815 (t) cc_final: 0.8424 (t) REVERT: D 51 THR cc_start: 0.8989 (p) cc_final: 0.8719 (p) REVERT: D 76 ILE cc_start: 0.9377 (pt) cc_final: 0.8492 (pt) REVERT: D 79 GLU cc_start: 0.8281 (pt0) cc_final: 0.7643 (pp20) REVERT: D 99 THR cc_start: 0.8252 (p) cc_final: 0.6987 (p) REVERT: D 102 ARG cc_start: 0.7425 (ptt90) cc_final: 0.7098 (ptt90) REVERT: E 41 TYR cc_start: 0.6724 (p90) cc_final: 0.6292 (p90) REVERT: E 49 ARG cc_start: 0.8468 (pmt-80) cc_final: 0.8054 (pmt-80) REVERT: E 56 LYS cc_start: 0.9044 (tmtt) cc_final: 0.8791 (tmtt) REVERT: E 60 LEU cc_start: 0.8667 (tp) cc_final: 0.8425 (tp) REVERT: E 64 LYS cc_start: 0.8683 (mppt) cc_final: 0.8320 (mmmm) REVERT: E 108 ASN cc_start: 0.8934 (t0) cc_final: 0.8521 (t0) REVERT: E 112 ILE cc_start: 0.8841 (mm) cc_final: 0.8622 (mm) REVERT: E 115 LYS cc_start: 0.9159 (ptpp) cc_final: 0.8863 (ptpp) REVERT: E 123 ASP cc_start: 0.8321 (m-30) cc_final: 0.8090 (m-30) REVERT: E 125 LYS cc_start: 0.9130 (mmmm) cc_final: 0.8885 (mmmm) REVERT: F 49 LEU cc_start: 0.8407 (mm) cc_final: 0.8163 (tp) REVERT: F 50 ILE cc_start: 0.8620 (pt) cc_final: 0.8190 (mm) REVERT: F 60 SER cc_start: 0.8549 (p) cc_final: 0.8128 (p) REVERT: F 63 GLU cc_start: 0.8695 (pt0) cc_final: 0.8473 (pp20) REVERT: F 87 VAL cc_start: 0.8606 (t) cc_final: 0.8310 (t) REVERT: F 91 LYS cc_start: 0.8525 (pttp) cc_final: 0.8061 (pttm) REVERT: F 93 GLN cc_start: 0.8209 (pm20) cc_final: 0.7687 (pp30) REVERT: G 34 TYR cc_start: 0.8311 (p90) cc_final: 0.7282 (p90) REVERT: G 51 ILE cc_start: 0.8560 (pt) cc_final: 0.8331 (pt) REVERT: G 52 TYR cc_start: 0.7200 (t80) cc_final: 0.6742 (t80) REVERT: G 59 TYR cc_start: 0.7652 (p90) cc_final: 0.7068 (p90) REVERT: G 74 ASP cc_start: 0.8074 (p0) cc_final: 0.7687 (p0) REVERT: G 86 GLN cc_start: 0.7270 (mp10) cc_final: 0.6774 (mp10) REVERT: H 49 LYS cc_start: 0.8701 (pttm) cc_final: 0.8395 (pttp) REVERT: H 64 ILE cc_start: 0.8905 (pt) cc_final: 0.8695 (pt) REVERT: H 66 ASN cc_start: 0.8167 (p0) cc_final: 0.7813 (p0) REVERT: H 72 ILE cc_start: 0.7696 (tp) cc_final: 0.7380 (tt) REVERT: H 73 PHE cc_start: 0.7462 (t80) cc_final: 0.7151 (t80) REVERT: H 74 GLU cc_start: 0.7951 (tp30) cc_final: 0.7291 (tp30) REVERT: H 76 ILE cc_start: 0.8094 (tp) cc_final: 0.7705 (tp) REVERT: H 86 TYR cc_start: 0.7316 (p90) cc_final: 0.7014 (p90) REVERT: H 112 HIS cc_start: 0.7608 (m90) cc_final: 0.7145 (m90) REVERT: H 124 TYR cc_start: 0.7640 (p90) cc_final: 0.7112 (p90) outliers start: 1 outliers final: 0 residues processed: 512 average time/residue: 0.4694 time to fit residues: 341.3438 Evaluate side-chains 461 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 156 optimal weight: 0.8980 chunk 157 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 0.6980 chunk 146 optimal weight: 0.5980 chunk 144 optimal weight: 0.3980 chunk 37 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.124345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.097994 restraints weight = 88503.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.101319 restraints weight = 51676.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 67)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.103446 restraints weight = 34075.413| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.7424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 22580 Z= 0.185 Angle : 0.889 14.738 31707 Z= 0.474 Chirality : 0.048 0.286 3556 Planarity : 0.006 0.083 3001 Dihedral : 28.185 132.433 5372 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.18), residues: 1866 helix: -0.97 (0.16), residues: 950 sheet: -2.03 (0.81), residues: 35 loop : -2.73 (0.20), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP O 353 HIS 0.019 0.001 HIS Q 240 PHE 0.038 0.002 PHE A 104 TYR 0.028 0.002 TYR F 72 ARG 0.014 0.001 ARG D 119 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 1048) hydrogen bonds : angle 4.97331 ( 2748) covalent geometry : bond 0.00403 (22580) covalent geometry : angle 0.88949 (31707) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 498 time to evaluate : 2.253 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 233 TYR cc_start: 0.7402 (t80) cc_final: 0.6854 (t80) REVERT: K 273 PHE cc_start: 0.8408 (m-10) cc_final: 0.8040 (m-10) REVERT: K 281 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8424 (mm-30) REVERT: K 284 HIS cc_start: 0.7853 (m-70) cc_final: 0.7272 (m-70) REVERT: K 325 TYR cc_start: 0.8306 (m-80) cc_final: 0.7936 (m-80) REVERT: K 368 ILE cc_start: 0.8060 (tp) cc_final: 0.7492 (tp) REVERT: K 404 PHE cc_start: 0.7227 (p90) cc_final: 0.6960 (p90) REVERT: M 234 LEU cc_start: 0.9434 (mp) cc_final: 0.9043 (mt) REVERT: M 235 ARG cc_start: 0.8702 (ptt90) cc_final: 0.8483 (ptt90) REVERT: M 237 GLN cc_start: 0.8915 (tm-30) cc_final: 0.8595 (tm-30) REVERT: M 278 TYR cc_start: 0.8457 (t80) cc_final: 0.8198 (t80) REVERT: O 237 PHE cc_start: 0.7008 (m-80) cc_final: 0.6572 (m-80) REVERT: O 265 TYR cc_start: 0.7146 (p90) cc_final: 0.6779 (p90) REVERT: O 271 PHE cc_start: 0.8193 (p90) cc_final: 0.7579 (p90) REVERT: O 275 CYS cc_start: 0.8679 (t) cc_final: 0.8412 (t) REVERT: O 325 TYR cc_start: 0.8759 (m-80) cc_final: 0.8083 (m-80) REVERT: O 328 SER cc_start: 0.6641 (m) cc_final: 0.6281 (p) REVERT: O 329 LYS cc_start: 0.8756 (pptt) cc_final: 0.8551 (pttm) REVERT: O 353 TRP cc_start: 0.6842 (p90) cc_final: 0.6378 (p90) REVERT: P 43 TYR cc_start: 0.8690 (m-80) cc_final: 0.8293 (m-10) REVERT: Q 147 TYR cc_start: 0.6788 (m-80) cc_final: 0.6499 (m-10) REVERT: Q 150 PHE cc_start: 0.8255 (m-80) cc_final: 0.7869 (m-10) REVERT: Q 198 HIS cc_start: 0.9075 (m90) cc_final: 0.8774 (m90) REVERT: Q 235 ARG cc_start: 0.6792 (tmm-80) cc_final: 0.6305 (tmm-80) REVERT: A 71 VAL cc_start: 0.9121 (m) cc_final: 0.8918 (p) REVERT: A 84 PHE cc_start: 0.7355 (m-10) cc_final: 0.7082 (m-80) REVERT: A 87 SER cc_start: 0.9092 (t) cc_final: 0.8774 (p) REVERT: A 115 LYS cc_start: 0.9411 (ptpp) cc_final: 0.9167 (ptpp) REVERT: A 119 ILE cc_start: 0.8250 (mp) cc_final: 0.8015 (tp) REVERT: B 25 ASN cc_start: 0.8283 (t0) cc_final: 0.8003 (t0) REVERT: B 44 LYS cc_start: 0.8764 (pptt) cc_final: 0.8041 (tptt) REVERT: B 50 ILE cc_start: 0.8246 (tp) cc_final: 0.7866 (tp) REVERT: B 61 PHE cc_start: 0.8494 (t80) cc_final: 0.7983 (t80) REVERT: B 70 VAL cc_start: 0.8990 (m) cc_final: 0.8740 (p) REVERT: B 74 GLU cc_start: 0.8371 (tp30) cc_final: 0.8050 (tp30) REVERT: B 88 TYR cc_start: 0.7376 (m-10) cc_final: 0.7172 (m-80) REVERT: B 96 THR cc_start: 0.7162 (p) cc_final: 0.6734 (p) REVERT: B 98 TYR cc_start: 0.5786 (m-80) cc_final: 0.5582 (m-80) REVERT: C 35 LEU cc_start: 0.8401 (mm) cc_final: 0.8182 (mt) REVERT: C 36 LYS cc_start: 0.8760 (mptt) cc_final: 0.8536 (mmmt) REVERT: C 44 ARG cc_start: 0.6578 (ptt180) cc_final: 0.5906 (ptt180) REVERT: C 53 LEU cc_start: 0.8471 (mp) cc_final: 0.8202 (tt) REVERT: C 75 LEU cc_start: 0.8978 (mt) cc_final: 0.8656 (mt) REVERT: C 79 ARG cc_start: 0.7588 (tmm160) cc_final: 0.6778 (ttp80) REVERT: C 80 ILE cc_start: 0.8751 (tp) cc_final: 0.8128 (tp) REVERT: C 84 HIS cc_start: 0.7197 (p90) cc_final: 0.6744 (p90) REVERT: D 47 VAL cc_start: 0.8851 (t) cc_final: 0.8492 (t) REVERT: D 51 THR cc_start: 0.8954 (p) cc_final: 0.8728 (p) REVERT: D 64 ILE cc_start: 0.8569 (mm) cc_final: 0.8078 (tp) REVERT: D 82 LYS cc_start: 0.8615 (tttm) cc_final: 0.8243 (tmtt) REVERT: D 86 TYR cc_start: 0.7324 (m-80) cc_final: 0.6443 (m-10) REVERT: D 104 ILE cc_start: 0.8309 (tp) cc_final: 0.8066 (mt) REVERT: D 124 TYR cc_start: 0.6897 (t80) cc_final: 0.6516 (t80) REVERT: E 41 TYR cc_start: 0.6770 (p90) cc_final: 0.6324 (p90) REVERT: E 54 PHE cc_start: 0.7214 (p90) cc_final: 0.6598 (p90) REVERT: E 56 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8717 (tmtt) REVERT: E 64 LYS cc_start: 0.8850 (mppt) cc_final: 0.8548 (mmmm) REVERT: E 69 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7535 (ptp90) REVERT: E 70 LEU cc_start: 0.8127 (mm) cc_final: 0.7337 (mm) REVERT: E 108 ASN cc_start: 0.8804 (t0) cc_final: 0.8433 (t0) REVERT: E 115 LYS cc_start: 0.9107 (ptpp) cc_final: 0.8815 (ptpp) REVERT: E 122 LYS cc_start: 0.8772 (mptt) cc_final: 0.8355 (mmmt) REVERT: F 46 ILE cc_start: 0.8742 (pt) cc_final: 0.8467 (pt) REVERT: F 50 ILE cc_start: 0.8675 (pt) cc_final: 0.8151 (mm) REVERT: F 60 SER cc_start: 0.8563 (p) cc_final: 0.8069 (p) REVERT: F 63 GLU cc_start: 0.8743 (pt0) cc_final: 0.8404 (pp20) REVERT: F 93 GLN cc_start: 0.8130 (pm20) cc_final: 0.7379 (pp30) REVERT: G 34 TYR cc_start: 0.8066 (p90) cc_final: 0.7056 (p90) REVERT: G 52 TYR cc_start: 0.6970 (t80) cc_final: 0.6442 (t80) REVERT: G 59 TYR cc_start: 0.7418 (p90) cc_final: 0.6889 (p90) REVERT: G 74 ASP cc_start: 0.8134 (p0) cc_final: 0.7795 (p0) REVERT: G 78 LYS cc_start: 0.8423 (pttm) cc_final: 0.8080 (pttp) REVERT: G 86 GLN cc_start: 0.7129 (mp10) cc_final: 0.6635 (mp10) REVERT: H 49 LYS cc_start: 0.8667 (pttm) cc_final: 0.8329 (pttp) REVERT: H 62 MET cc_start: 0.8329 (mmp) cc_final: 0.8037 (mmp) REVERT: H 64 ILE cc_start: 0.8890 (pt) cc_final: 0.8664 (pt) REVERT: H 66 ASN cc_start: 0.8299 (p0) cc_final: 0.7821 (p0) REVERT: H 72 ILE cc_start: 0.7747 (tp) cc_final: 0.7317 (tt) REVERT: H 73 PHE cc_start: 0.7700 (t80) cc_final: 0.7483 (t80) REVERT: H 76 ILE cc_start: 0.8148 (tp) cc_final: 0.7758 (tp) REVERT: H 112 HIS cc_start: 0.7645 (m90) cc_final: 0.7160 (m90) REVERT: H 124 TYR cc_start: 0.7551 (p90) cc_final: 0.7044 (p90) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.4544 time to fit residues: 324.0018 Evaluate side-chains 457 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 154 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 6 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 90 optimal weight: 0.0870 chunk 195 optimal weight: 0.4980 chunk 163 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 166 ASN ** K 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 260 ASN ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.125662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.099348 restraints weight = 89013.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.102664 restraints weight = 51803.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104820 restraints weight = 34056.871| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.7689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 22580 Z= 0.181 Angle : 0.898 15.701 31707 Z= 0.477 Chirality : 0.048 0.287 3556 Planarity : 0.006 0.174 3001 Dihedral : 28.112 134.045 5372 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.18), residues: 1866 helix: -0.97 (0.16), residues: 954 sheet: -1.89 (0.82), residues: 35 loop : -2.77 (0.20), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.003 TRP O 353 HIS 0.020 0.002 HIS Q 240 PHE 0.037 0.002 PHE A 104 TYR 0.029 0.002 TYR F 72 ARG 0.013 0.001 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.05031 ( 1048) hydrogen bonds : angle 5.00789 ( 2748) covalent geometry : bond 0.00392 (22580) covalent geometry : angle 0.89788 (31707) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9585.41 seconds wall clock time: 168 minutes 22.88 seconds (10102.88 seconds total)