Starting phenix.real_space_refine on Mon Nov 17 21:48:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exd_31371/11_2025/7exd_31371.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 60 5.16 5 C 5574 2.51 5 N 1491 2.21 5 O 1621 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8749 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1766 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2592 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1748 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "R" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2169 Classifications: {'peptide': 272} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'05X': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.18, per 1000 atoms: 0.25 Number of scatterers: 8749 At special positions: 0 Unit cell: (114.48, 128.52, 112.32, 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 60 16.00 F 3 9.00 O 1621 8.00 N 1491 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 232.4 milliseconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 39.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.650A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.621A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.987A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 4.489A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.638A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.576A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.613A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.764A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.626A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'R' and resid 20 through 51 removed outlier: 4.000A pdb=" N VAL R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU R 33 " --> pdb=" O THR R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 58 No H-bonds generated for 'chain 'R' and resid 56 through 58' Processing helix chain 'R' and resid 59 through 76 Processing helix chain 'R' and resid 76 through 86 Processing helix chain 'R' and resid 92 through 127 removed outlier: 3.737A pdb=" N ASP R 97 " --> pdb=" O GLN R 93 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 135 removed outlier: 3.991A pdb=" N LYS R 134 " --> pdb=" O GLU R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 154 Processing helix chain 'R' and resid 156 through 163 removed outlier: 3.707A pdb=" N TRP R 161 " --> pdb=" O PRO R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 178 through 213 removed outlier: 3.559A pdb=" N THR R 182 " --> pdb=" O HIS R 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE R 192 " --> pdb=" O GLY R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 286 through 319 removed outlier: 3.765A pdb=" N LYS R 290 " --> pdb=" O THR R 286 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N PHE R 302 " --> pdb=" O ILE R 298 " (cutoff:3.500A) Proline residue: R 308 - end of helix removed outlier: 3.536A pdb=" N ASN R 317 " --> pdb=" O GLU R 313 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS R 319 " --> pdb=" O VAL R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 347 removed outlier: 3.927A pdb=" N ASN R 339 " --> pdb=" O LEU R 335 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N SER R 340 " --> pdb=" O GLY R 336 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU R 341 " --> pdb=" O TYR R 337 " (cutoff:3.500A) Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 351 through 361 removed outlier: 3.772A pdb=" N GLN R 359 " --> pdb=" O LYS R 355 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS R 360 " --> pdb=" O LYS R 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU R 361 " --> pdb=" O ALA R 357 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.676A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.391A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.001A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.772A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.605A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.561A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.506A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.023A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 289 " --> pdb=" O ASN B 293 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.163A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.163A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.777A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.466A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.466A pdb=" N VAL E 147 " --> pdb=" O GLU E 246 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN E 231 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1409 1.31 - 1.44: 2455 1.44 - 1.57: 4979 1.57 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 8929 Sorted by residual: bond pdb=" C17 05X R 501 " pdb=" N16 05X R 501 " ideal model delta sigma weight residual 1.360 1.457 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C12 05X R 501 " pdb=" N16 05X R 501 " ideal model delta sigma weight residual 1.396 1.455 -0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" N PHE R 310 " pdb=" CA PHE R 310 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.63e+00 bond pdb=" N TYR R 212 " pdb=" CA TYR R 212 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.45e+00 bond pdb=" C5 05X R 501 " pdb=" C8 05X R 501 " ideal model delta sigma weight residual 1.506 1.551 -0.045 2.00e-02 2.50e+03 5.06e+00 ... (remaining 8924 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 11913 1.67 - 3.35: 144 3.35 - 5.02: 34 5.02 - 6.70: 3 6.70 - 8.37: 3 Bond angle restraints: 12097 Sorted by residual: angle pdb=" N ARG R 287 " pdb=" CA ARG R 287 " pdb=" C ARG R 287 " ideal model delta sigma weight residual 113.41 105.04 8.37 1.22e+00 6.72e-01 4.71e+01 angle pdb=" N LYS R 175 " pdb=" CA LYS R 175 " pdb=" C LYS R 175 " ideal model delta sigma weight residual 108.52 102.20 6.32 1.63e+00 3.76e-01 1.50e+01 angle pdb=" N ILE R 104 " pdb=" CA ILE R 104 " pdb=" C ILE R 104 " ideal model delta sigma weight residual 110.42 114.02 -3.60 9.60e-01 1.09e+00 1.40e+01 angle pdb=" CA PHE R 310 " pdb=" C PHE R 310 " pdb=" O PHE R 310 " ideal model delta sigma weight residual 120.42 117.03 3.39 1.06e+00 8.90e-01 1.02e+01 angle pdb=" C ARG R 287 " pdb=" N GLU R 288 " pdb=" CA GLU R 288 " ideal model delta sigma weight residual 120.28 116.35 3.93 1.34e+00 5.57e-01 8.60e+00 ... (remaining 12092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.13: 4802 16.13 - 32.26: 411 32.26 - 48.39: 66 48.39 - 64.52: 21 64.52 - 80.65: 8 Dihedral angle restraints: 5308 sinusoidal: 2060 harmonic: 3248 Sorted by residual: dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N ILE R 179 " pdb=" CA ILE R 179 " ideal model delta harmonic sigma weight residual 180.00 -162.24 -17.76 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE R 153 " pdb=" C PHE R 153 " pdb=" N ILE R 154 " pdb=" CA ILE R 154 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 172 " pdb=" CB CYS R 172 " ideal model delta sinusoidal sigma weight residual 93.00 119.54 -26.54 1 1.00e+01 1.00e-02 1.01e+01 ... (remaining 5305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1085 0.041 - 0.082: 204 0.082 - 0.123: 87 0.123 - 0.164: 6 0.164 - 0.205: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA LYS R 175 " pdb=" N LYS R 175 " pdb=" C LYS R 175 " pdb=" CB LYS R 175 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ARG R 287 " pdb=" N ARG R 287 " pdb=" C ARG R 287 " pdb=" CB ARG R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1381 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 286 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.09e+00 pdb=" C THR R 286 " -0.052 2.00e-02 2.50e+03 pdb=" O THR R 286 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG R 287 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO R 157 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO R 158 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO R 158 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 158 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO G 53 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.024 5.00e-02 4.00e+02 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 162 2.67 - 3.23: 8803 3.23 - 3.79: 13397 3.79 - 4.34: 18287 4.34 - 4.90: 30218 Nonbonded interactions: 70867 Sorted by model distance: nonbonded pdb=" NH1 ARG B 22 " pdb=" OD1 ASP B 258 " model vdw 2.114 3.120 nonbonded pdb=" OH TYR A 290 " pdb=" O SER A 293 " model vdw 2.146 3.040 nonbonded pdb=" NH1 ARG B 96 " pdb=" OE2 GLU B 138 " model vdw 2.184 3.120 nonbonded pdb=" OD1 ASP A 272 " pdb=" N LEU A 273 " model vdw 2.204 3.120 nonbonded pdb=" ND1 HIS G 44 " pdb=" OE2 GLU G 47 " model vdw 2.233 3.120 ... (remaining 70862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.490 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 : 0.003 0.097 8932 Z= 0.157 Angle : 0.518 8.371 12103 Z= 0.296 Chirality : 0.039 0.205 1384 Planarity : 0.003 0.047 1518 Dihedral : 12.790 80.645 3201 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.53 % Allowed : 0.21 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.27), residues: 1100 helix: 2.45 (0.29), residues: 366 sheet: 1.17 (0.31), residues: 277 loop : 0.51 (0.33), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 160 TYR 0.010 0.001 TYR R 191 PHE 0.011 0.001 PHE R 302 TRP 0.008 0.001 TRP R 334 HIS 0.003 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8929) covalent geometry : angle 0.51754 (12097) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.66380 ( 6) hydrogen bonds : bond 0.16693 ( 430) hydrogen bonds : angle 6.53955 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 325 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8294 (tppp) cc_final: 0.7903 (tppp) REVERT: A 191 PHE cc_start: 0.7739 (t80) cc_final: 0.7461 (t80) REVERT: A 222 ILE cc_start: 0.8234 (mt) cc_final: 0.7970 (mt) REVERT: A 271 LYS cc_start: 0.7797 (ptmt) cc_final: 0.7482 (ptmt) REVERT: A 289 GLU cc_start: 0.7970 (mp0) cc_final: 0.7770 (mp0) REVERT: A 308 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7275 (mt-10) REVERT: A 336 PHE cc_start: 0.8204 (t80) cc_final: 0.7693 (t80) REVERT: A 351 CYS cc_start: 0.7512 (t) cc_final: 0.7257 (t) REVERT: B 134 ARG cc_start: 0.7568 (ptt180) cc_final: 0.7322 (ptp90) REVERT: B 153 ASP cc_start: 0.7124 (t0) cc_final: 0.6883 (t70) REVERT: B 188 MET cc_start: 0.6135 (mmp) cc_final: 0.5674 (mmt) REVERT: B 205 ASP cc_start: 0.7284 (p0) cc_final: 0.7055 (p0) REVERT: B 232 ILE cc_start: 0.8430 (tt) cc_final: 0.8230 (tt) REVERT: G 21 MET cc_start: 0.7212 (tmm) cc_final: 0.6739 (tmm) REVERT: E 59 TYR cc_start: 0.7769 (m-80) cc_final: 0.7473 (m-10) REVERT: E 191 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7284 (mmt90) REVERT: R 77 MET cc_start: 0.7414 (mtp) cc_final: 0.7198 (mtp) REVERT: R 126 THR cc_start: 0.7044 (t) cc_final: 0.6805 (t) REVERT: R 176 HIS cc_start: 0.7094 (t70) cc_final: 0.6714 (t70) REVERT: R 290 LYS cc_start: 0.8248 (tmtt) cc_final: 0.7994 (tmtt) outliers start: 5 outliers final: 2 residues processed: 328 average time/residue: 0.1000 time to fit residues: 43.9308 Evaluate side-chains 294 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 292 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 354 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN R 113 HIS ** R 176 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 = 0.3713 r_free = 0.3713 target = 0.129743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114992 restraints weight = 13829.339| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.50 r_work: 0.3383 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8932 Z= 0.229 Angle : 0.617 7.243 12103 Z= 0.326 Chirality : 0.046 0.154 1384 Planarity : 0.005 0.061 1518 Dihedral : 5.322 53.296 1227 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.70 % Allowed : 11.42 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.26), residues: 1100 helix: 1.74 (0.28), residues: 378 sheet: 0.76 (0.31), residues: 279 loop : 0.37 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 98 TYR 0.023 0.002 TYR R 347 PHE 0.021 0.002 PHE R 302 TRP 0.023 0.003 TRP B 211 HIS 0.006 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00494 ( 8929) covalent geometry : angle 0.61634 (12097) SS BOND : bond 0.00457 ( 3) SS BOND : angle 0.91924 ( 6) hydrogen bonds : bond 0.03792 ( 430) hydrogen bonds : angle 4.79942 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8600 (tppp) cc_final: 0.8143 (tppp) REVERT: A 33 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 34 VAL cc_start: 0.8266 (t) cc_final: 0.8045 (t) REVERT: A 219 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 222 ILE cc_start: 0.8667 (mt) cc_final: 0.8462 (mt) REVERT: A 271 LYS cc_start: 0.7834 (ptmt) cc_final: 0.7418 (ptmt) REVERT: A 274 PHE cc_start: 0.7625 (t80) cc_final: 0.7306 (t80) REVERT: A 275 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7331 (mm-30) REVERT: A 297 GLU cc_start: 0.7848 (mp0) cc_final: 0.7597 (mp0) REVERT: A 308 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7514 (mt-10) REVERT: A 336 PHE cc_start: 0.8395 (t80) cc_final: 0.8167 (t80) REVERT: A 342 VAL cc_start: 0.8140 (t) cc_final: 0.7906 (t) REVERT: A 351 CYS cc_start: 0.7936 (t) cc_final: 0.7683 (t) REVERT: B 8 ARG cc_start: 0.8123 (mtm-85) cc_final: 0.7786 (mpp80) REVERT: B 42 ARG cc_start: 0.6585 (tpt170) cc_final: 0.6381 (tpt170) REVERT: B 50 THR cc_start: 0.8167 (m) cc_final: 0.7427 (t) REVERT: B 134 ARG cc_start: 0.8336 (ptt180) cc_final: 0.7875 (ptp90) REVERT: B 155 ASN cc_start: 0.8305 (t0) cc_final: 0.7984 (t0) REVERT: B 170 ASP cc_start: 0.7817 (t0) cc_final: 0.7140 (t0) REVERT: B 188 MET cc_start: 0.7021 (mmp) cc_final: 0.6630 (mmt) REVERT: B 205 ASP cc_start: 0.7567 (p0) cc_final: 0.7346 (p0) REVERT: B 258 ASP cc_start: 0.7323 (t0) cc_final: 0.6622 (t0) REVERT: B 259 GLN cc_start: 0.7734 (pp30) cc_final: 0.7079 (pp30) REVERT: B 298 ASP cc_start: 0.8002 (t0) cc_final: 0.7754 (t0) REVERT: B 325 MET cc_start: 0.8028 (tpp) cc_final: 0.7777 (mmm) REVERT: G 21 MET cc_start: 0.7602 (tmm) cc_final: 0.7151 (tmm) REVERT: G 47 GLU cc_start: 0.8073 (pt0) cc_final: 0.7833 (pt0) REVERT: E 99 SER cc_start: 0.8284 (t) cc_final: 0.7971 (p) REVERT: E 228 TYR cc_start: 0.8317 (m-10) cc_final: 0.8109 (m-10) REVERT: R 77 MET cc_start: 0.8179 (mtp) cc_final: 0.7703 (mtp) REVERT: R 98 ILE cc_start: 0.8244 (tp) cc_final: 0.8022 (tp) REVERT: R 175 LYS cc_start: 0.8174 (tptp) cc_final: 0.7903 (tppp) REVERT: R 176 HIS cc_start: 0.7616 (t70) cc_final: 0.7157 (t70) REVERT: R 290 LYS cc_start: 0.8447 (tmtt) cc_final: 0.8177 (tmtt) outliers start: 35 outliers final: 24 residues processed: 312 average time/residue: 0.1153 time to fit residues: 47.5963 Evaluate side-chains 317 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 292 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 104 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN B 239 ASN G 18 GLN ** R 176 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 = 0.3729 r_free = 0.3729 target = 0.130907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.116185 restraints weight = 13635.136| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 2.52 r_work: 0.3398 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8932 Z= 0.133 Angle : 0.551 6.254 12103 Z= 0.289 Chirality : 0.043 0.165 1384 Planarity : 0.004 0.068 1518 Dihedral : 4.862 53.736 1225 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.38 % Allowed : 15.43 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1100 helix: 1.70 (0.27), residues: 372 sheet: 0.55 (0.30), residues: 275 loop : 0.17 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.022 0.002 TYR E 228 PHE 0.015 0.001 PHE R 190 TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 8929) covalent geometry : angle 0.55081 (12097) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.73323 ( 6) hydrogen bonds : bond 0.03278 ( 430) hydrogen bonds : angle 4.52578 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 291 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8601 (tppp) cc_final: 0.8141 (tppp) REVERT: A 33 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7692 (mt-10) REVERT: A 191 PHE cc_start: 0.7957 (t80) cc_final: 0.7547 (t80) REVERT: A 212 ILE cc_start: 0.8655 (tp) cc_final: 0.8356 (tp) REVERT: A 222 ILE cc_start: 0.8683 (mt) cc_final: 0.8458 (mt) REVERT: A 271 LYS cc_start: 0.7809 (ptmt) cc_final: 0.7424 (ptmt) REVERT: A 274 PHE cc_start: 0.7596 (t80) cc_final: 0.7337 (t80) REVERT: A 275 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 276 GLU cc_start: 0.7745 (pm20) cc_final: 0.7492 (pm20) REVERT: A 297 GLU cc_start: 0.7863 (mp0) cc_final: 0.7545 (mp0) REVERT: A 335 VAL cc_start: 0.8368 (t) cc_final: 0.8152 (t) REVERT: A 351 CYS cc_start: 0.7886 (t) cc_final: 0.7628 (t) REVERT: B 8 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7842 (mpp80) REVERT: B 50 THR cc_start: 0.8178 (m) cc_final: 0.7626 (t) REVERT: B 134 ARG cc_start: 0.8321 (ptt180) cc_final: 0.7862 (ptp90) REVERT: B 155 ASN cc_start: 0.8291 (t0) cc_final: 0.7959 (t0) REVERT: B 170 ASP cc_start: 0.7783 (t0) cc_final: 0.7121 (t0) REVERT: B 188 MET cc_start: 0.7094 (mmp) cc_final: 0.6682 (mmt) REVERT: B 205 ASP cc_start: 0.7526 (p0) cc_final: 0.7280 (p0) REVERT: B 233 CYS cc_start: 0.8343 (t) cc_final: 0.8057 (t) REVERT: B 258 ASP cc_start: 0.7330 (t0) cc_final: 0.6540 (t0) REVERT: B 259 GLN cc_start: 0.7739 (pp30) cc_final: 0.7032 (pp30) REVERT: B 296 VAL cc_start: 0.8388 (t) cc_final: 0.7996 (m) REVERT: B 314 ARG cc_start: 0.7802 (mtp85) cc_final: 0.7600 (ttm170) REVERT: B 325 MET cc_start: 0.8029 (tpp) cc_final: 0.7769 (mmm) REVERT: G 21 MET cc_start: 0.7605 (tmm) cc_final: 0.7264 (tmm) REVERT: G 47 GLU cc_start: 0.8072 (pt0) cc_final: 0.7871 (pt0) REVERT: E 99 SER cc_start: 0.8212 (t) cc_final: 0.7936 (p) REVERT: E 173 TYR cc_start: 0.8490 (m-80) cc_final: 0.7984 (m-80) REVERT: E 191 ARG cc_start: 0.7778 (mmt90) cc_final: 0.7533 (mmt90) REVERT: E 228 TYR cc_start: 0.8332 (m-10) cc_final: 0.8066 (m-80) REVERT: R 77 MET cc_start: 0.8170 (mtp) cc_final: 0.7578 (mtp) REVERT: R 81 ILE cc_start: 0.8151 (mt) cc_final: 0.7892 (mp) REVERT: R 91 MET cc_start: 0.7097 (mpp) cc_final: 0.6566 (mpp) REVERT: R 126 THR cc_start: 0.7614 (t) cc_final: 0.7414 (t) REVERT: R 143 MET cc_start: 0.8318 (tpp) cc_final: 0.7974 (tpp) REVERT: R 175 LYS cc_start: 0.8214 (tptp) cc_final: 0.7945 (tppp) REVERT: R 186 THR cc_start: 0.7464 (m) cc_final: 0.7264 (m) REVERT: R 290 LYS cc_start: 0.8454 (tmtt) cc_final: 0.8205 (tmtt) outliers start: 32 outliers final: 28 residues processed: 304 average time/residue: 0.1076 time to fit residues: 43.5332 Evaluate side-chains 310 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 304 GLN Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 340 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN E 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.115761 restraints weight = 13840.053| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.54 r_work: 0.3394 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8932 Z= 0.140 Angle : 0.547 6.791 12103 Z= 0.286 Chirality : 0.043 0.167 1384 Planarity : 0.004 0.072 1518 Dihedral : 4.861 54.948 1225 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.17 % Allowed : 18.08 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1100 helix: 1.68 (0.27), residues: 372 sheet: 0.34 (0.30), residues: 277 loop : 0.10 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 180 TYR 0.016 0.002 TYR E 228 PHE 0.020 0.002 PHE A 259 TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8929) covalent geometry : angle 0.54699 (12097) SS BOND : bond 0.00327 ( 3) SS BOND : angle 0.68981 ( 6) hydrogen bonds : bond 0.03131 ( 430) hydrogen bonds : angle 4.35674 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 289 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8626 (tppp) cc_final: 0.8113 (tppp) REVERT: A 212 ILE cc_start: 0.8681 (tp) cc_final: 0.8419 (tp) REVERT: A 219 THR cc_start: 0.8581 (OUTLIER) cc_final: 0.8367 (p) REVERT: A 222 ILE cc_start: 0.8719 (mt) cc_final: 0.8490 (mt) REVERT: A 271 LYS cc_start: 0.7837 (ptmt) cc_final: 0.7415 (ptmt) REVERT: A 275 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 351 CYS cc_start: 0.7874 (t) cc_final: 0.7611 (t) REVERT: B 50 THR cc_start: 0.8263 (m) cc_final: 0.7740 (t) REVERT: B 155 ASN cc_start: 0.8340 (t0) cc_final: 0.7996 (t0) REVERT: B 160 SER cc_start: 0.7817 (m) cc_final: 0.7581 (p) REVERT: B 163 ASP cc_start: 0.7265 (p0) cc_final: 0.7061 (p0) REVERT: B 170 ASP cc_start: 0.7810 (t0) cc_final: 0.7214 (t0) REVERT: B 188 MET cc_start: 0.7170 (mmp) cc_final: 0.6761 (mmt) REVERT: B 205 ASP cc_start: 0.7507 (p0) cc_final: 0.7271 (p0) REVERT: B 233 CYS cc_start: 0.8373 (t) cc_final: 0.8007 (t) REVERT: B 258 ASP cc_start: 0.7383 (t0) cc_final: 0.6520 (t0) REVERT: B 259 GLN cc_start: 0.7729 (pp30) cc_final: 0.7050 (pp30) REVERT: B 296 VAL cc_start: 0.8418 (t) cc_final: 0.8053 (m) REVERT: B 325 MET cc_start: 0.8046 (tpp) cc_final: 0.7799 (mmm) REVERT: G 21 MET cc_start: 0.7626 (tmm) cc_final: 0.7274 (tmm) REVERT: G 47 GLU cc_start: 0.8064 (pt0) cc_final: 0.7858 (pt0) REVERT: E 99 SER cc_start: 0.8199 (t) cc_final: 0.7929 (p) REVERT: E 173 TYR cc_start: 0.8431 (m-80) cc_final: 0.8094 (m-80) REVERT: E 228 TYR cc_start: 0.8331 (m-10) cc_final: 0.8058 (m-80) REVERT: R 77 MET cc_start: 0.8200 (mtp) cc_final: 0.7591 (mtp) REVERT: R 126 THR cc_start: 0.7637 (t) cc_final: 0.7404 (t) REVERT: R 143 MET cc_start: 0.8276 (tpp) cc_final: 0.7982 (tpp) REVERT: R 154 ILE cc_start: 0.8449 (tp) cc_final: 0.8226 (tp) REVERT: R 175 LYS cc_start: 0.8242 (tptp) cc_final: 0.7980 (tppp) REVERT: R 290 LYS cc_start: 0.8518 (tmtt) cc_final: 0.8206 (tmtt) REVERT: R 310 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6919 (t80) REVERT: R 355 LYS cc_start: 0.8355 (mttm) cc_final: 0.7899 (mttm) outliers start: 30 outliers final: 27 residues processed: 301 average time/residue: 0.1119 time to fit residues: 44.5886 Evaluate side-chains 309 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.101374 restraints weight = 14161.641| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.60 r_work: 0.3196 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8932 Z= 0.314 Angle : 0.658 6.890 12103 Z= 0.348 Chirality : 0.048 0.192 1384 Planarity : 0.005 0.076 1518 Dihedral : 5.251 60.093 1222 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.18 % Allowed : 18.18 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.25), residues: 1100 helix: 1.25 (0.27), residues: 380 sheet: -0.04 (0.29), residues: 281 loop : -0.09 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 180 TYR 0.022 0.003 TYR B 111 PHE 0.019 0.003 PHE A 334 TRP 0.023 0.003 TRP B 211 HIS 0.007 0.002 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 8929) covalent geometry : angle 0.65740 (12097) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.93297 ( 6) hydrogen bonds : bond 0.03727 ( 430) hydrogen bonds : angle 4.64869 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 325 time to evaluate : 0.333 Fit side-chains REVERT: A 29 LYS cc_start: 0.8670 (tppp) cc_final: 0.8106 (tppp) REVERT: A 33 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7797 (mt-10) REVERT: A 212 ILE cc_start: 0.8704 (tp) cc_final: 0.8455 (tp) REVERT: A 219 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8284 (p) REVERT: A 222 ILE cc_start: 0.8738 (mt) cc_final: 0.8510 (mt) REVERT: A 271 LYS cc_start: 0.8008 (ptmt) cc_final: 0.7660 (ptmt) REVERT: A 275 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7635 (mt-10) REVERT: A 276 GLU cc_start: 0.8031 (pm20) cc_final: 0.7783 (pm20) REVERT: A 297 GLU cc_start: 0.8031 (mp0) cc_final: 0.7662 (mp0) REVERT: A 308 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7672 (mt-10) REVERT: A 339 VAL cc_start: 0.8602 (t) cc_final: 0.8325 (p) REVERT: A 351 CYS cc_start: 0.7844 (t) cc_final: 0.7618 (t) REVERT: B 49 ARG cc_start: 0.8421 (mmt-90) cc_final: 0.8103 (mpt180) REVERT: B 75 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7775 (mp10) REVERT: B 150 ARG cc_start: 0.7951 (mmt-90) cc_final: 0.7539 (mpt180) REVERT: B 155 ASN cc_start: 0.8591 (t0) cc_final: 0.8169 (t0) REVERT: B 160 SER cc_start: 0.7761 (m) cc_final: 0.7523 (p) REVERT: B 163 ASP cc_start: 0.7409 (p0) cc_final: 0.7098 (p0) REVERT: B 170 ASP cc_start: 0.7855 (t0) cc_final: 0.7139 (t0) REVERT: B 188 MET cc_start: 0.7463 (mmp) cc_final: 0.6965 (mmt) REVERT: B 205 ASP cc_start: 0.7563 (p0) cc_final: 0.7354 (p0) REVERT: B 243 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7494 (t) REVERT: B 251 ARG cc_start: 0.8673 (mtt-85) cc_final: 0.8305 (mtp180) REVERT: B 259 GLN cc_start: 0.7870 (pp30) cc_final: 0.7153 (pp30) REVERT: B 292 PHE cc_start: 0.8042 (m-10) cc_final: 0.7809 (m-80) REVERT: B 296 VAL cc_start: 0.8447 (t) cc_final: 0.8122 (m) REVERT: G 21 MET cc_start: 0.7683 (tmm) cc_final: 0.7276 (tmm) REVERT: G 47 GLU cc_start: 0.8065 (pt0) cc_final: 0.7804 (pt0) REVERT: E 138 ILE cc_start: 0.8539 (mm) cc_final: 0.8165 (mm) REVERT: E 140 MET cc_start: 0.8436 (mmm) cc_final: 0.8189 (mmm) REVERT: R 53 LYS cc_start: 0.8061 (tppp) cc_final: 0.7615 (tppp) REVERT: R 77 MET cc_start: 0.8303 (mtp) cc_final: 0.7709 (mtp) REVERT: R 126 THR cc_start: 0.7783 (t) cc_final: 0.7552 (t) REVERT: R 143 MET cc_start: 0.8128 (tpp) cc_final: 0.7851 (tpp) REVERT: R 175 LYS cc_start: 0.8303 (tptp) cc_final: 0.8051 (tppp) REVERT: R 290 LYS cc_start: 0.8461 (tmtt) cc_final: 0.8009 (tmtt) REVERT: R 294 THR cc_start: 0.8274 (m) cc_final: 0.8046 (m) REVERT: R 310 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6842 (t80) REVERT: R 355 LYS cc_start: 0.8449 (mttm) cc_final: 0.7942 (mttm) outliers start: 49 outliers final: 37 residues processed: 343 average time/residue: 0.1169 time to fit residues: 52.6258 Evaluate side-chains 353 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 312 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 310 PHE Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 230 ASN E 142 GLN ** R 113 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 = 0.3617 r_free = 0.3617 target = 0.123377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107859 restraints weight = 14138.115| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.70 r_work: 0.3237 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8932 Z= 0.138 Angle : 0.581 7.590 12103 Z= 0.303 Chirality : 0.044 0.193 1384 Planarity : 0.004 0.076 1518 Dihedral : 4.902 60.023 1222 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.12 % Allowed : 21.67 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.26), residues: 1100 helix: 1.43 (0.27), residues: 378 sheet: -0.00 (0.29), residues: 281 loop : -0.02 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 98 TYR 0.016 0.002 TYR E 228 PHE 0.025 0.002 PHE R 190 TRP 0.012 0.002 TRP B 211 HIS 0.010 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8929) covalent geometry : angle 0.58120 (12097) SS BOND : bond 0.00395 ( 3) SS BOND : angle 0.77333 ( 6) hydrogen bonds : bond 0.03218 ( 430) hydrogen bonds : angle 4.43206 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 312 time to evaluate : 0.398 Fit side-chains REVERT: A 29 LYS cc_start: 0.8600 (tppp) cc_final: 0.8128 (tppp) REVERT: A 212 ILE cc_start: 0.8633 (tp) cc_final: 0.8366 (tp) REVERT: A 219 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8312 (p) REVERT: A 222 ILE cc_start: 0.8737 (mt) cc_final: 0.8508 (mt) REVERT: A 271 LYS cc_start: 0.7912 (ptmt) cc_final: 0.7579 (ptmt) REVERT: A 275 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7590 (mt-10) REVERT: A 276 GLU cc_start: 0.7948 (pm20) cc_final: 0.7722 (pm20) REVERT: A 297 GLU cc_start: 0.7971 (mp0) cc_final: 0.7607 (mp0) REVERT: A 308 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7489 (mt-10) REVERT: A 351 CYS cc_start: 0.7863 (t) cc_final: 0.7570 (t) REVERT: B 8 ARG cc_start: 0.8198 (mtm-85) cc_final: 0.7676 (mtm110) REVERT: B 50 THR cc_start: 0.8359 (m) cc_final: 0.7966 (t) REVERT: B 75 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: B 150 ARG cc_start: 0.7924 (mmt-90) cc_final: 0.7562 (mpt180) REVERT: B 155 ASN cc_start: 0.8442 (t0) cc_final: 0.8046 (t0) REVERT: B 160 SER cc_start: 0.7805 (m) cc_final: 0.7464 (p) REVERT: B 163 ASP cc_start: 0.7404 (p0) cc_final: 0.7117 (p0) REVERT: B 170 ASP cc_start: 0.7806 (t0) cc_final: 0.7166 (t0) REVERT: B 188 MET cc_start: 0.7498 (mmp) cc_final: 0.6980 (mmp) REVERT: B 205 ASP cc_start: 0.7541 (p0) cc_final: 0.7320 (p0) REVERT: B 214 ARG cc_start: 0.8324 (ptp90) cc_final: 0.8088 (ptp-170) REVERT: B 233 CYS cc_start: 0.8385 (t) cc_final: 0.8004 (t) REVERT: B 239 ASN cc_start: 0.8103 (m-40) cc_final: 0.7895 (m-40) REVERT: B 243 THR cc_start: 0.7923 (OUTLIER) cc_final: 0.7571 (t) REVERT: B 259 GLN cc_start: 0.7864 (pp30) cc_final: 0.7109 (pp30) REVERT: B 292 PHE cc_start: 0.7928 (m-10) cc_final: 0.7716 (m-80) REVERT: B 296 VAL cc_start: 0.8413 (t) cc_final: 0.8128 (m) REVERT: G 21 MET cc_start: 0.7722 (tmm) cc_final: 0.7329 (tmm) REVERT: G 47 GLU cc_start: 0.8150 (pt0) cc_final: 0.7904 (pt0) REVERT: G 58 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7056 (tm-30) REVERT: E 173 TYR cc_start: 0.8706 (m-80) cc_final: 0.8418 (m-80) REVERT: R 77 MET cc_start: 0.8330 (mtp) cc_final: 0.7832 (mtp) REVERT: R 126 THR cc_start: 0.7717 (t) cc_final: 0.7485 (t) REVERT: R 143 MET cc_start: 0.8020 (tpp) cc_final: 0.7742 (tpp) REVERT: R 175 LYS cc_start: 0.8305 (tptp) cc_final: 0.8027 (tppp) REVERT: R 290 LYS cc_start: 0.8469 (tmtt) cc_final: 0.7957 (tmtt) REVERT: R 294 THR cc_start: 0.8147 (m) cc_final: 0.7827 (m) REVERT: R 355 LYS cc_start: 0.8390 (mttm) cc_final: 0.7932 (mttm) outliers start: 39 outliers final: 29 residues processed: 326 average time/residue: 0.1191 time to fit residues: 50.8137 Evaluate side-chains 340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 308 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 25 optimal weight: 0.0270 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 99 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 31 optimal weight: 0.0020 overall best weight: 0.4446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.125342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110058 restraints weight = 14177.841| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.63 r_work: 0.3318 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8932 Z= 0.114 Angle : 0.556 6.815 12103 Z= 0.290 Chirality : 0.042 0.197 1384 Planarity : 0.004 0.076 1518 Dihedral : 4.720 61.868 1222 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.55 % Allowed : 22.41 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1100 helix: 1.57 (0.27), residues: 378 sheet: 0.00 (0.29), residues: 283 loop : 0.03 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 160 TYR 0.012 0.002 TYR B 111 PHE 0.024 0.001 PHE R 190 TRP 0.013 0.001 TRP R 89 HIS 0.007 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 8929) covalent geometry : angle 0.55542 (12097) SS BOND : bond 0.00380 ( 3) SS BOND : angle 0.89392 ( 6) hydrogen bonds : bond 0.02992 ( 430) hydrogen bonds : angle 4.30571 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 304 time to evaluate : 0.335 Fit side-chains REVERT: A 29 LYS cc_start: 0.8604 (tppp) cc_final: 0.8112 (tppp) REVERT: A 210 LYS cc_start: 0.7150 (ttmm) cc_final: 0.6922 (mttm) REVERT: A 212 ILE cc_start: 0.8605 (tp) cc_final: 0.8325 (tp) REVERT: A 222 ILE cc_start: 0.8705 (mt) cc_final: 0.8463 (mt) REVERT: A 271 LYS cc_start: 0.7864 (ptmt) cc_final: 0.7534 (ptmt) REVERT: A 274 PHE cc_start: 0.7591 (t80) cc_final: 0.7338 (t80) REVERT: A 275 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7585 (mt-10) REVERT: A 276 GLU cc_start: 0.7950 (pm20) cc_final: 0.7714 (pm20) REVERT: A 296 TYR cc_start: 0.8203 (t80) cc_final: 0.7503 (t80) REVERT: A 308 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 351 CYS cc_start: 0.7826 (t) cc_final: 0.7514 (t) REVERT: B 8 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7682 (mpp80) REVERT: B 50 THR cc_start: 0.8361 (m) cc_final: 0.7928 (t) REVERT: B 75 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7649 (mp10) REVERT: B 83 ASP cc_start: 0.7607 (t0) cc_final: 0.7186 (t0) REVERT: B 155 ASN cc_start: 0.8352 (t0) cc_final: 0.7992 (t0) REVERT: B 160 SER cc_start: 0.7800 (m) cc_final: 0.7492 (p) REVERT: B 163 ASP cc_start: 0.7331 (p0) cc_final: 0.7098 (p0) REVERT: B 170 ASP cc_start: 0.7798 (t0) cc_final: 0.7130 (t0) REVERT: B 188 MET cc_start: 0.7438 (mmp) cc_final: 0.6879 (mmp) REVERT: B 200 VAL cc_start: 0.8576 (m) cc_final: 0.8143 (p) REVERT: B 205 ASP cc_start: 0.7540 (p0) cc_final: 0.7308 (p0) REVERT: B 233 CYS cc_start: 0.8394 (t) cc_final: 0.8056 (t) REVERT: B 243 THR cc_start: 0.7892 (OUTLIER) cc_final: 0.7567 (t) REVERT: B 292 PHE cc_start: 0.7875 (m-10) cc_final: 0.7669 (m-80) REVERT: B 294 CYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6798 (m) REVERT: B 296 VAL cc_start: 0.8363 (t) cc_final: 0.8101 (m) REVERT: B 325 MET cc_start: 0.8013 (tpp) cc_final: 0.7810 (tpp) REVERT: G 21 MET cc_start: 0.7727 (tmm) cc_final: 0.7335 (tmm) REVERT: G 47 GLU cc_start: 0.8145 (pt0) cc_final: 0.7884 (pt0) REVERT: G 58 GLU cc_start: 0.7285 (tm-30) cc_final: 0.7058 (tm-30) REVERT: E 138 ILE cc_start: 0.8436 (mm) cc_final: 0.8091 (mm) REVERT: E 173 TYR cc_start: 0.8620 (m-80) cc_final: 0.8200 (m-80) REVERT: R 23 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8204 (mmmm) REVERT: R 77 MET cc_start: 0.8227 (mtp) cc_final: 0.7607 (mtp) REVERT: R 126 THR cc_start: 0.7613 (t) cc_final: 0.7378 (t) REVERT: R 143 MET cc_start: 0.8128 (tpp) cc_final: 0.7819 (tpp) REVERT: R 175 LYS cc_start: 0.8271 (tptp) cc_final: 0.8055 (tppp) REVERT: R 190 PHE cc_start: 0.8407 (t80) cc_final: 0.8077 (t80) REVERT: R 287 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7269 (ptm160) REVERT: R 290 LYS cc_start: 0.8511 (tmtt) cc_final: 0.8134 (tmtt) REVERT: R 310 PHE cc_start: 0.7203 (m-80) cc_final: 0.6919 (m-80) REVERT: R 355 LYS cc_start: 0.8352 (mttm) cc_final: 0.7889 (mttm) outliers start: 43 outliers final: 30 residues processed: 323 average time/residue: 0.1112 time to fit residues: 47.6040 Evaluate side-chains 343 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 156 MET Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 53 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.124911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.109793 restraints weight = 14059.413| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.59 r_work: 0.3277 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8932 Z= 0.135 Angle : 0.586 8.176 12103 Z= 0.301 Chirality : 0.043 0.205 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.759 63.408 1222 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.12 % Allowed : 22.94 % Favored : 72.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1100 helix: 1.59 (0.27), residues: 378 sheet: 0.02 (0.29), residues: 281 loop : 0.01 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 160 TYR 0.013 0.002 TYR B 111 PHE 0.022 0.002 PHE A 334 TRP 0.013 0.002 TRP B 211 HIS 0.007 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8929) covalent geometry : angle 0.58621 (12097) SS BOND : bond 0.00404 ( 3) SS BOND : angle 0.83633 ( 6) hydrogen bonds : bond 0.02997 ( 430) hydrogen bonds : angle 4.26473 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 317 time to evaluate : 0.307 Fit side-chains REVERT: A 8 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: A 29 LYS cc_start: 0.8605 (tppp) cc_final: 0.7959 (tppp) REVERT: A 33 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 210 LYS cc_start: 0.7234 (ttmm) cc_final: 0.7009 (mttm) REVERT: A 212 ILE cc_start: 0.8643 (tp) cc_final: 0.8381 (tp) REVERT: A 222 ILE cc_start: 0.8722 (mt) cc_final: 0.8484 (mt) REVERT: A 271 LYS cc_start: 0.7865 (ptmt) cc_final: 0.7524 (ptmt) REVERT: A 274 PHE cc_start: 0.7617 (t80) cc_final: 0.7364 (t80) REVERT: A 275 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7562 (mt-10) REVERT: A 276 GLU cc_start: 0.7939 (pm20) cc_final: 0.7738 (pm20) REVERT: A 296 TYR cc_start: 0.8192 (t80) cc_final: 0.7471 (t80) REVERT: A 297 GLU cc_start: 0.8017 (mp0) cc_final: 0.7655 (mp0) REVERT: A 308 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7469 (mt-10) REVERT: A 351 CYS cc_start: 0.7836 (t) cc_final: 0.7532 (t) REVERT: B 8 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7690 (mpp80) REVERT: B 50 THR cc_start: 0.8338 (m) cc_final: 0.7934 (t) REVERT: B 75 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: B 83 ASP cc_start: 0.7614 (t0) cc_final: 0.7197 (t0) REVERT: B 155 ASN cc_start: 0.8377 (t0) cc_final: 0.8023 (t0) REVERT: B 160 SER cc_start: 0.7774 (m) cc_final: 0.7496 (p) REVERT: B 163 ASP cc_start: 0.7338 (p0) cc_final: 0.7093 (p0) REVERT: B 170 ASP cc_start: 0.7761 (t0) cc_final: 0.7106 (t0) REVERT: B 188 MET cc_start: 0.7516 (mmp) cc_final: 0.6973 (mmp) REVERT: B 205 ASP cc_start: 0.7570 (p0) cc_final: 0.7344 (p0) REVERT: B 233 CYS cc_start: 0.8335 (t) cc_final: 0.7969 (t) REVERT: B 243 THR cc_start: 0.7883 (OUTLIER) cc_final: 0.7558 (t) REVERT: B 292 PHE cc_start: 0.7878 (m-10) cc_final: 0.7666 (m-80) REVERT: B 294 CYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6831 (m) REVERT: B 296 VAL cc_start: 0.8372 (t) cc_final: 0.8110 (m) REVERT: B 325 MET cc_start: 0.8044 (tpp) cc_final: 0.7831 (tpp) REVERT: G 21 MET cc_start: 0.7731 (tmm) cc_final: 0.7346 (tmm) REVERT: G 47 GLU cc_start: 0.8133 (pt0) cc_final: 0.7863 (pt0) REVERT: G 58 GLU cc_start: 0.7342 (tm-30) cc_final: 0.7090 (tm-30) REVERT: E 60 TYR cc_start: 0.8205 (m-80) cc_final: 0.7662 (m-80) REVERT: E 138 ILE cc_start: 0.8499 (mm) cc_final: 0.8154 (mm) REVERT: E 173 TYR cc_start: 0.8601 (m-80) cc_final: 0.7850 (m-80) REVERT: R 77 MET cc_start: 0.8266 (mtp) cc_final: 0.7633 (mtp) REVERT: R 126 THR cc_start: 0.7671 (t) cc_final: 0.7416 (t) REVERT: R 143 MET cc_start: 0.8151 (tpp) cc_final: 0.7857 (tpp) REVERT: R 175 LYS cc_start: 0.8273 (tptp) cc_final: 0.8064 (tppp) REVERT: R 287 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: R 290 LYS cc_start: 0.8507 (tmtt) cc_final: 0.8144 (tmtt) outliers start: 39 outliers final: 31 residues processed: 332 average time/residue: 0.1044 time to fit residues: 46.2614 Evaluate side-chains 353 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 317 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 325 SER Chi-restraints excluded: chain R residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 24 optimal weight: 0.0170 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 75 optimal weight: 0.4980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 317 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.110046 restraints weight = 14135.761| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.63 r_work: 0.3316 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8932 Z= 0.125 Angle : 0.579 7.352 12103 Z= 0.300 Chirality : 0.043 0.212 1384 Planarity : 0.004 0.077 1518 Dihedral : 4.736 64.256 1222 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.44 % Allowed : 23.78 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1100 helix: 1.63 (0.27), residues: 379 sheet: 0.01 (0.30), residues: 271 loop : -0.05 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.012 0.001 TYR A 296 PHE 0.028 0.002 PHE R 190 TRP 0.012 0.001 TRP B 211 HIS 0.006 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 8929) covalent geometry : angle 0.57907 (12097) SS BOND : bond 0.00398 ( 3) SS BOND : angle 0.82221 ( 6) hydrogen bonds : bond 0.02984 ( 430) hydrogen bonds : angle 4.23632 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 318 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: A 29 LYS cc_start: 0.8607 (tppp) cc_final: 0.7947 (tppp) REVERT: A 33 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 210 LYS cc_start: 0.7123 (ttmm) cc_final: 0.6826 (mttm) REVERT: A 212 ILE cc_start: 0.8625 (tp) cc_final: 0.8369 (tp) REVERT: A 222 ILE cc_start: 0.8731 (mt) cc_final: 0.8491 (mt) REVERT: A 271 LYS cc_start: 0.7844 (ptmt) cc_final: 0.7504 (ptmt) REVERT: A 274 PHE cc_start: 0.7618 (t80) cc_final: 0.7358 (t80) REVERT: A 275 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: A 276 GLU cc_start: 0.7884 (pm20) cc_final: 0.7649 (pm20) REVERT: A 296 TYR cc_start: 0.8204 (t80) cc_final: 0.7473 (t80) REVERT: A 308 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7450 (mt-10) REVERT: A 351 CYS cc_start: 0.7838 (t) cc_final: 0.7524 (t) REVERT: B 8 ARG cc_start: 0.8168 (mtm-85) cc_final: 0.7700 (mpp80) REVERT: B 50 THR cc_start: 0.8321 (m) cc_final: 0.7923 (t) REVERT: B 75 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.7609 (mp10) REVERT: B 83 ASP cc_start: 0.7596 (t0) cc_final: 0.7378 (t0) REVERT: B 155 ASN cc_start: 0.8340 (t0) cc_final: 0.7993 (t0) REVERT: B 160 SER cc_start: 0.7753 (m) cc_final: 0.7485 (p) REVERT: B 163 ASP cc_start: 0.7334 (p0) cc_final: 0.7106 (p0) REVERT: B 170 ASP cc_start: 0.7744 (t0) cc_final: 0.7066 (t0) REVERT: B 188 MET cc_start: 0.7533 (mmp) cc_final: 0.6949 (mmp) REVERT: B 205 ASP cc_start: 0.7567 (p0) cc_final: 0.7341 (p0) REVERT: B 233 CYS cc_start: 0.8340 (t) cc_final: 0.7958 (t) REVERT: B 243 THR cc_start: 0.7874 (OUTLIER) cc_final: 0.7358 (t) REVERT: B 256 ARG cc_start: 0.8532 (mtm-85) cc_final: 0.8262 (mtm-85) REVERT: B 294 CYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6794 (m) REVERT: B 296 VAL cc_start: 0.8356 (t) cc_final: 0.8096 (m) REVERT: B 325 MET cc_start: 0.8031 (tpp) cc_final: 0.7815 (tpp) REVERT: G 21 MET cc_start: 0.7769 (tmm) cc_final: 0.7377 (tmm) REVERT: G 47 GLU cc_start: 0.8155 (pt0) cc_final: 0.7877 (pt0) REVERT: G 58 GLU cc_start: 0.7331 (tm-30) cc_final: 0.7077 (tm-30) REVERT: E 93 MET cc_start: 0.7502 (tpp) cc_final: 0.7286 (tpp) REVERT: E 102 TYR cc_start: 0.7856 (p90) cc_final: 0.7624 (p90) REVERT: E 231 GLN cc_start: 0.8064 (pp30) cc_final: 0.7857 (pp30) REVERT: R 23 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8219 (mmmm) REVERT: R 77 MET cc_start: 0.8237 (mtp) cc_final: 0.7596 (mtp) REVERT: R 126 THR cc_start: 0.7617 (t) cc_final: 0.7382 (t) REVERT: R 143 MET cc_start: 0.8133 (tpp) cc_final: 0.7824 (tpp) REVERT: R 175 LYS cc_start: 0.8212 (tptp) cc_final: 0.7989 (tppp) REVERT: R 287 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7309 (ptm160) REVERT: R 290 LYS cc_start: 0.8522 (tmtt) cc_final: 0.8161 (tmtt) REVERT: R 341 LEU cc_start: 0.8374 (tt) cc_final: 0.8121 (tp) outliers start: 42 outliers final: 28 residues processed: 334 average time/residue: 0.1102 time to fit residues: 48.8449 Evaluate side-chains 349 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 68 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** R 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.124277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.109132 restraints weight = 14105.683| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.60 r_work: 0.3275 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8932 Z= 0.146 Angle : 0.592 8.268 12103 Z= 0.308 Chirality : 0.044 0.208 1384 Planarity : 0.004 0.077 1518 Dihedral : 4.805 64.879 1222 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.49 % Allowed : 25.16 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1100 helix: 1.63 (0.27), residues: 379 sheet: 0.04 (0.30), residues: 271 loop : -0.08 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.014 0.002 TYR B 111 PHE 0.025 0.002 PHE R 190 TRP 0.013 0.002 TRP B 82 HIS 0.007 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 8929) covalent geometry : angle 0.59179 (12097) SS BOND : bond 0.00412 ( 3) SS BOND : angle 0.86169 ( 6) hydrogen bonds : bond 0.03048 ( 430) hydrogen bonds : angle 4.31478 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 313 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7521 (pm20) REVERT: A 29 LYS cc_start: 0.8620 (tppp) cc_final: 0.7938 (tppp) REVERT: A 33 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7574 (mp0) REVERT: A 210 LYS cc_start: 0.7232 (ttmm) cc_final: 0.6931 (mttm) REVERT: A 212 ILE cc_start: 0.8666 (tp) cc_final: 0.8412 (tp) REVERT: A 222 ILE cc_start: 0.8728 (mt) cc_final: 0.8492 (mt) REVERT: A 271 LYS cc_start: 0.7866 (ptmt) cc_final: 0.7527 (ptmt) REVERT: A 274 PHE cc_start: 0.7646 (t80) cc_final: 0.7372 (t80) REVERT: A 275 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7591 (mt-10) REVERT: A 276 GLU cc_start: 0.7884 (pm20) cc_final: 0.7659 (pm20) REVERT: A 296 TYR cc_start: 0.8235 (t80) cc_final: 0.7507 (t80) REVERT: A 308 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7543 (mt-10) REVERT: A 351 CYS cc_start: 0.7827 (t) cc_final: 0.7522 (t) REVERT: B 8 ARG cc_start: 0.8197 (mtm-85) cc_final: 0.7724 (mpp80) REVERT: B 50 THR cc_start: 0.8344 (m) cc_final: 0.7219 (t) REVERT: B 52 ARG cc_start: 0.7711 (ptp90) cc_final: 0.7017 (ptp90) REVERT: B 75 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: B 83 ASP cc_start: 0.7652 (t0) cc_final: 0.7438 (t0) REVERT: B 155 ASN cc_start: 0.8395 (t0) cc_final: 0.8020 (t0) REVERT: B 160 SER cc_start: 0.7784 (m) cc_final: 0.7510 (p) REVERT: B 163 ASP cc_start: 0.7332 (p0) cc_final: 0.7096 (p0) REVERT: B 170 ASP cc_start: 0.7736 (t0) cc_final: 0.7052 (t0) REVERT: B 188 MET cc_start: 0.7517 (mmp) cc_final: 0.6964 (mmp) REVERT: B 205 ASP cc_start: 0.7603 (p0) cc_final: 0.7338 (p0) REVERT: B 239 ASN cc_start: 0.7764 (m-40) cc_final: 0.7432 (t0) REVERT: B 294 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6769 (m) REVERT: B 296 VAL cc_start: 0.8376 (t) cc_final: 0.8109 (m) REVERT: B 325 MET cc_start: 0.8071 (tpp) cc_final: 0.7848 (tpp) REVERT: G 21 MET cc_start: 0.7753 (tmm) cc_final: 0.7368 (tmm) REVERT: G 47 GLU cc_start: 0.8144 (pt0) cc_final: 0.7871 (pt0) REVERT: E 93 MET cc_start: 0.7502 (tpp) cc_final: 0.7263 (tpp) REVERT: E 102 TYR cc_start: 0.7885 (p90) cc_final: 0.7677 (p90) REVERT: R 23 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8166 (mmmm) REVERT: R 77 MET cc_start: 0.8228 (mtp) cc_final: 0.8002 (mtp) REVERT: R 126 THR cc_start: 0.7654 (t) cc_final: 0.7424 (t) REVERT: R 143 MET cc_start: 0.8144 (tpp) cc_final: 0.7834 (tpp) REVERT: R 175 LYS cc_start: 0.8178 (tptp) cc_final: 0.7951 (tppp) REVERT: R 287 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7243 (ptm160) REVERT: R 290 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8154 (tmtt) outliers start: 33 outliers final: 27 residues processed: 326 average time/residue: 0.1086 time to fit residues: 47.3481 Evaluate side-chains 342 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 309 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 220 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 287 ARG Chi-restraints excluded: chain R residue 293 THR Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 40 optimal weight: 0.0470 chunk 24 optimal weight: 0.0010 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 313 ASN ** R 56 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 = 0.3646 r_free = 0.3646 target = 0.124656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.109602 restraints weight = 14036.557| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.59 r_work: 0.3281 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8932 Z= 0.143 Angle : 0.591 8.231 12103 Z= 0.307 Chirality : 0.043 0.200 1384 Planarity : 0.004 0.077 1518 Dihedral : 4.820 64.611 1222 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.91 % Allowed : 24.95 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.26), residues: 1100 helix: 1.62 (0.27), residues: 378 sheet: -0.05 (0.29), residues: 282 loop : -0.05 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 160 TYR 0.014 0.002 TYR B 111 PHE 0.026 0.002 PHE R 190 TRP 0.013 0.002 TRP B 82 HIS 0.006 0.001 HIS R 113 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8929) covalent geometry : angle 0.59125 (12097) SS BOND : bond 0.00377 ( 3) SS BOND : angle 0.82005 ( 6) hydrogen bonds : bond 0.03010 ( 430) hydrogen bonds : angle 4.29852 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2112.31 seconds wall clock time: 37 minutes 10.24 seconds (2230.24 seconds total)