Starting phenix.real_space_refine on Sat Dec 28 15:54:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_31371_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_31371.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_31371.map" model { file = "/net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_31371_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7exd_31371/12_2024/7exd_31371_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 5.24, per 1000 atoms: 0.60 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: 2.42 Conformation dependent library (CDL) restraints added in 922.8 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: 1.17 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: 2.67 Time building geometry restraints manager: 2.71 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.630 ------------------------------------------------------------------------------- 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 8929 Z= 0.189 Angle : 0.518 8.371 12097 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 : 6.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (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 TRP 0.008 0.001 TRP R 334 HIS 0.003 0.001 HIS R 113 PHE 0.011 0.001 PHE R 302 TYR 0.010 0.001 TYR R 191 ARG 0.014 0.001 ARG E 160 *********************** 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 : 0.949 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: 0.2365 time to fit residues: 102.6758 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 : 0.972 ------------------------------------------------------------------------------- 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 92 optimal weight: 0.2980 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8929 Z= 0.341 Angle : 0.637 8.287 12097 Z= 0.335 Chirality : 0.047 0.156 1384 Planarity : 0.005 0.066 1518 Dihedral : 5.446 53.750 1227 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.59 % Allowed : 11.21 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.26), residues: 1100 helix: 1.67 (0.28), residues: 378 sheet: 0.67 (0.31), residues: 279 loop : 0.32 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 211 HIS 0.007 0.002 HIS R 113 PHE 0.023 0.002 PHE R 302 TYR 0.024 0.003 TYR R 347 ARG 0.007 0.001 ARG E 98 *********************** 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 341 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 307 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8435 (tppp) cc_final: 0.7962 (tppp) REVERT: A 33 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7283 (mt-10) REVERT: A 34 VAL cc_start: 0.8147 (t) cc_final: 0.7937 (t) REVERT: A 212 ILE cc_start: 0.8626 (tp) cc_final: 0.8288 (tp) REVERT: A 219 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8220 (p) REVERT: A 222 ILE cc_start: 0.8336 (mt) cc_final: 0.8098 (mt) REVERT: A 271 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7406 (ptmt) REVERT: A 272 ASP cc_start: 0.7202 (p0) cc_final: 0.6968 (p0) REVERT: A 274 PHE cc_start: 0.7529 (t80) cc_final: 0.7188 (t80) REVERT: A 275 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7137 (mm-30) REVERT: A 297 GLU cc_start: 0.7627 (mp0) cc_final: 0.7356 (mp0) REVERT: A 308 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 336 PHE cc_start: 0.8303 (t80) cc_final: 0.8098 (t80) REVERT: A 342 VAL cc_start: 0.7884 (t) cc_final: 0.7651 (t) REVERT: A 351 CYS cc_start: 0.7523 (t) cc_final: 0.7302 (t) REVERT: B 50 THR cc_start: 0.8070 (m) cc_final: 0.7218 (t) REVERT: B 52 ARG cc_start: 0.7468 (ptp90) cc_final: 0.7001 (ptp90) REVERT: B 134 ARG cc_start: 0.7536 (ptt180) cc_final: 0.7269 (ptp90) REVERT: B 135 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8342 (p) REVERT: B 155 ASN cc_start: 0.8145 (t0) cc_final: 0.7908 (t0) REVERT: B 170 ASP cc_start: 0.7597 (t0) cc_final: 0.7029 (t0) REVERT: B 186 ASP cc_start: 0.7069 (p0) cc_final: 0.6861 (p0) REVERT: B 188 MET cc_start: 0.6520 (mmp) cc_final: 0.6187 (mmt) REVERT: B 222 PHE cc_start: 0.8441 (m-80) cc_final: 0.8160 (m-80) REVERT: B 258 ASP cc_start: 0.7092 (t0) cc_final: 0.6331 (t0) REVERT: B 259 GLN cc_start: 0.7564 (pp30) cc_final: 0.6882 (pp30) REVERT: B 298 ASP cc_start: 0.7687 (t0) cc_final: 0.7440 (t0) REVERT: B 325 MET cc_start: 0.7405 (tpp) cc_final: 0.7124 (mmm) REVERT: G 21 MET cc_start: 0.7245 (tmm) cc_final: 0.6829 (tmm) REVERT: E 99 SER cc_start: 0.8085 (t) cc_final: 0.7788 (p) REVERT: E 228 TYR cc_start: 0.8053 (m-10) cc_final: 0.7799 (m-10) REVERT: R 53 LYS cc_start: 0.7864 (tppp) cc_final: 0.7537 (tppp) REVERT: R 77 MET cc_start: 0.7648 (mtp) cc_final: 0.7210 (mtp) REVERT: R 98 ILE cc_start: 0.8096 (tp) cc_final: 0.7869 (tp) REVERT: R 143 MET cc_start: 0.7940 (tpp) cc_final: 0.7641 (tpp) REVERT: R 175 LYS cc_start: 0.8033 (tptp) cc_final: 0.7774 (tppp) REVERT: R 186 THR cc_start: 0.7581 (OUTLIER) cc_final: 0.7353 (m) REVERT: R 290 LYS cc_start: 0.8432 (tmtt) cc_final: 0.8193 (tmtt) REVERT: R 297 LEU cc_start: 0.8260 (tp) cc_final: 0.8040 (tt) outliers start: 34 outliers final: 23 residues processed: 320 average time/residue: 0.2388 time to fit residues: 101.0427 Evaluate side-chains 327 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 301 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 304 GLN Chi-restraints excluded: chain B residue 135 VAL 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 186 THR 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 55 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 107 optimal weight: 0.6980 chunk 88 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN G 18 GLN E 186 GLN ** R 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8929 Z= 0.191 Angle : 0.553 6.312 12097 Z= 0.290 Chirality : 0.043 0.146 1384 Planarity : 0.004 0.071 1518 Dihedral : 4.912 54.168 1225 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.59 % Allowed : 16.28 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1100 helix: 1.59 (0.27), residues: 372 sheet: 0.48 (0.30), residues: 277 loop : 0.16 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.015 0.002 PHE A 259 TYR 0.023 0.002 TYR E 228 ARG 0.005 0.000 ARG B 137 *********************** 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 335 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8433 (tppp) cc_final: 0.7971 (tppp) REVERT: A 33 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 212 ILE cc_start: 0.8602 (tp) cc_final: 0.8262 (tp) REVERT: A 222 ILE cc_start: 0.8375 (mt) cc_final: 0.8130 (mt) REVERT: A 271 LYS cc_start: 0.7763 (ptmt) cc_final: 0.7412 (ptmt) REVERT: A 274 PHE cc_start: 0.7487 (t80) cc_final: 0.7214 (t80) REVERT: A 275 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7041 (mm-30) REVERT: A 276 GLU cc_start: 0.7586 (pm20) cc_final: 0.7329 (pm20) REVERT: A 297 GLU cc_start: 0.7629 (mp0) cc_final: 0.7324 (mp0) REVERT: A 308 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7244 (mt-10) REVERT: A 335 VAL cc_start: 0.8257 (t) cc_final: 0.8036 (t) REVERT: A 351 CYS cc_start: 0.7511 (t) cc_final: 0.7279 (t) REVERT: B 50 THR cc_start: 0.8040 (m) cc_final: 0.7699 (t) REVERT: B 134 ARG cc_start: 0.7534 (ptt180) cc_final: 0.7296 (ptp90) REVERT: B 155 ASN cc_start: 0.8102 (t0) cc_final: 0.7786 (t0) REVERT: B 160 SER cc_start: 0.7614 (m) cc_final: 0.7347 (p) REVERT: B 163 ASP cc_start: 0.7077 (p0) cc_final: 0.6859 (p0) REVERT: B 170 ASP cc_start: 0.7531 (t0) cc_final: 0.7015 (t0) REVERT: B 188 MET cc_start: 0.6565 (mmp) cc_final: 0.6133 (mmt) REVERT: B 232 ILE cc_start: 0.8387 (tt) cc_final: 0.8125 (tp) REVERT: B 233 CYS cc_start: 0.7686 (t) cc_final: 0.7354 (t) REVERT: B 247 ASP cc_start: 0.7692 (p0) cc_final: 0.7445 (p0) REVERT: B 249 THR cc_start: 0.8149 (p) cc_final: 0.7915 (p) REVERT: B 258 ASP cc_start: 0.7060 (t0) cc_final: 0.6277 (t0) REVERT: B 259 GLN cc_start: 0.7522 (pp30) cc_final: 0.6817 (pp30) REVERT: B 296 VAL cc_start: 0.8291 (t) cc_final: 0.7881 (m) REVERT: B 325 MET cc_start: 0.7406 (tpp) cc_final: 0.7175 (mmm) REVERT: G 21 MET cc_start: 0.7214 (tmm) cc_final: 0.6932 (tmm) REVERT: E 99 SER cc_start: 0.7970 (t) cc_final: 0.7685 (p) REVERT: E 173 TYR cc_start: 0.8374 (m-80) cc_final: 0.7978 (m-80) REVERT: E 191 ARG cc_start: 0.7688 (mmt90) cc_final: 0.7484 (mmt90) REVERT: E 228 TYR cc_start: 0.8078 (m-10) cc_final: 0.7783 (m-80) REVERT: R 77 MET cc_start: 0.7653 (mtp) cc_final: 0.7037 (mtp) REVERT: R 81 ILE cc_start: 0.8066 (mt) cc_final: 0.7845 (mp) REVERT: R 126 THR cc_start: 0.7285 (t) cc_final: 0.7056 (t) REVERT: R 143 MET cc_start: 0.7850 (tpp) cc_final: 0.7513 (tpp) REVERT: R 175 LYS cc_start: 0.8057 (tptp) cc_final: 0.7789 (tppp) REVERT: R 186 THR cc_start: 0.7626 (m) cc_final: 0.7417 (m) REVERT: R 290 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8247 (tmtt) REVERT: R 355 LYS cc_start: 0.8249 (mttm) cc_final: 0.7796 (mttm) outliers start: 34 outliers final: 24 residues processed: 313 average time/residue: 0.2385 time to fit residues: 98.3761 Evaluate side-chains 308 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 304 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 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 184 SER 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 95 VAL Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 138 LYS 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 310 PHE Chi-restraints excluded: chain R residue 325 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 97 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.0870 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 239 ASN B 313 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8929 Z= 0.194 Angle : 0.554 7.206 12097 Z= 0.288 Chirality : 0.043 0.165 1384 Planarity : 0.004 0.073 1518 Dihedral : 4.872 55.431 1225 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.12 % Allowed : 18.50 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1100 helix: 1.63 (0.27), residues: 371 sheet: 0.31 (0.30), residues: 279 loop : 0.11 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.013 0.001 PHE A 259 TYR 0.016 0.002 TYR E 228 ARG 0.004 0.000 ARG E 160 *********************** 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 337 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8446 (tppp) cc_final: 0.7940 (tppp) REVERT: A 212 ILE cc_start: 0.8614 (tp) cc_final: 0.8251 (tp) REVERT: A 222 ILE cc_start: 0.8370 (mt) cc_final: 0.8143 (mt) REVERT: A 271 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7368 (ptmt) REVERT: A 274 PHE cc_start: 0.7493 (t80) cc_final: 0.7234 (t80) REVERT: A 275 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 336 PHE cc_start: 0.8450 (t80) cc_final: 0.8172 (t80) REVERT: A 351 CYS cc_start: 0.7509 (t) cc_final: 0.7260 (t) REVERT: B 50 THR cc_start: 0.8071 (m) cc_final: 0.7704 (t) REVERT: B 155 ASN cc_start: 0.8112 (t0) cc_final: 0.7822 (t0) REVERT: B 160 SER cc_start: 0.7583 (m) cc_final: 0.7353 (p) REVERT: B 170 ASP cc_start: 0.7552 (t0) cc_final: 0.7081 (t0) REVERT: B 188 MET cc_start: 0.6616 (mmp) cc_final: 0.6186 (mmt) REVERT: B 232 ILE cc_start: 0.8390 (tt) cc_final: 0.8129 (tp) REVERT: B 233 CYS cc_start: 0.7699 (t) cc_final: 0.7281 (t) REVERT: B 239 ASN cc_start: 0.7895 (m-40) cc_final: 0.7678 (m-40) REVERT: B 247 ASP cc_start: 0.7655 (p0) cc_final: 0.7343 (p0) REVERT: B 249 THR cc_start: 0.8128 (p) cc_final: 0.7873 (p) REVERT: B 259 GLN cc_start: 0.7507 (pp30) cc_final: 0.6811 (pp30) REVERT: B 296 VAL cc_start: 0.8301 (t) cc_final: 0.7911 (m) REVERT: B 298 ASP cc_start: 0.7706 (t0) cc_final: 0.7419 (t0) REVERT: B 325 MET cc_start: 0.7410 (tpp) cc_final: 0.7183 (mmm) REVERT: G 21 MET cc_start: 0.7206 (tmm) cc_final: 0.6910 (tmm) REVERT: E 99 SER cc_start: 0.7979 (t) cc_final: 0.7729 (p) REVERT: E 173 TYR cc_start: 0.8335 (m-80) cc_final: 0.8056 (m-80) REVERT: E 228 TYR cc_start: 0.8073 (m-10) cc_final: 0.7794 (m-80) REVERT: R 77 MET cc_start: 0.7768 (mtp) cc_final: 0.7403 (mtp) REVERT: R 98 ILE cc_start: 0.8115 (tp) cc_final: 0.7913 (tp) REVERT: R 126 THR cc_start: 0.7280 (t) cc_final: 0.7033 (t) REVERT: R 143 MET cc_start: 0.7792 (tpp) cc_final: 0.7503 (tpp) REVERT: R 175 LYS cc_start: 0.8049 (tptp) cc_final: 0.7804 (tppp) REVERT: R 186 THR cc_start: 0.7731 (OUTLIER) cc_final: 0.7514 (m) REVERT: R 290 LYS cc_start: 0.8526 (tmtt) cc_final: 0.8253 (tmtt) REVERT: R 355 LYS cc_start: 0.8252 (mttm) cc_final: 0.7810 (mttm) outliers start: 39 outliers final: 27 residues processed: 314 average time/residue: 0.2363 time to fit residues: 98.1842 Evaluate side-chains 320 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 292 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 344 ILE 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 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 B residue 331 SER Chi-restraints excluded: chain E residue 2 VAL 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 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 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 186 THR Chi-restraints excluded: chain R residue 187 PHE 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 59 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8929 Z= 0.227 Angle : 0.565 6.292 12097 Z= 0.294 Chirality : 0.043 0.188 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.685 57.514 1222 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.55 % Allowed : 19.98 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1100 helix: 1.64 (0.27), residues: 372 sheet: 0.20 (0.30), residues: 278 loop : -0.01 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.013 0.002 PHE R 302 TYR 0.016 0.002 TYR E 101 ARG 0.004 0.000 ARG E 180 *********************** 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 345 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 302 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8396 (tppp) cc_final: 0.7933 (tppp) REVERT: A 212 ILE cc_start: 0.8601 (tp) cc_final: 0.8308 (tp) REVERT: A 222 ILE cc_start: 0.8390 (mt) cc_final: 0.8127 (mt) REVERT: A 271 LYS cc_start: 0.7736 (ptmt) cc_final: 0.7507 (ptmt) REVERT: A 274 PHE cc_start: 0.7487 (t80) cc_final: 0.7187 (t80) REVERT: A 276 GLU cc_start: 0.7678 (pm20) cc_final: 0.7469 (pm20) REVERT: A 308 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 351 CYS cc_start: 0.7520 (t) cc_final: 0.7256 (t) REVERT: B 50 THR cc_start: 0.8127 (m) cc_final: 0.7743 (t) REVERT: B 75 GLN cc_start: 0.8496 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: B 83 ASP cc_start: 0.7319 (t0) cc_final: 0.6968 (t0) REVERT: B 155 ASN cc_start: 0.8171 (t0) cc_final: 0.7829 (t0) REVERT: B 160 SER cc_start: 0.7615 (m) cc_final: 0.7374 (p) REVERT: B 163 ASP cc_start: 0.7151 (p0) cc_final: 0.6920 (p0) REVERT: B 170 ASP cc_start: 0.7568 (t0) cc_final: 0.7204 (t0) REVERT: B 186 ASP cc_start: 0.7151 (p0) cc_final: 0.6899 (p0) REVERT: B 188 MET cc_start: 0.6777 (mmp) cc_final: 0.6301 (mmt) REVERT: B 232 ILE cc_start: 0.8396 (tt) cc_final: 0.8179 (tp) REVERT: B 239 ASN cc_start: 0.7985 (m-40) cc_final: 0.7636 (m-40) REVERT: B 243 THR cc_start: 0.7729 (OUTLIER) cc_final: 0.7182 (t) REVERT: B 296 VAL cc_start: 0.8315 (t) cc_final: 0.7950 (m) REVERT: B 298 ASP cc_start: 0.7714 (t0) cc_final: 0.7378 (t0) REVERT: B 325 MET cc_start: 0.7436 (tpp) cc_final: 0.7197 (mmm) REVERT: G 21 MET cc_start: 0.7195 (tmm) cc_final: 0.6880 (tmm) REVERT: E 228 TYR cc_start: 0.8074 (m-10) cc_final: 0.7811 (m-80) REVERT: R 72 VAL cc_start: 0.7582 (OUTLIER) cc_final: 0.7274 (t) REVERT: R 77 MET cc_start: 0.7765 (mtp) cc_final: 0.7445 (mtp) REVERT: R 98 ILE cc_start: 0.8129 (tp) cc_final: 0.7907 (tp) REVERT: R 126 THR cc_start: 0.7334 (t) cc_final: 0.7087 (t) REVERT: R 143 MET cc_start: 0.7771 (tpp) cc_final: 0.7471 (tpp) REVERT: R 186 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7550 (m) REVERT: R 290 LYS cc_start: 0.8517 (tmtt) cc_final: 0.8246 (tmtt) REVERT: R 355 LYS cc_start: 0.8311 (mttm) cc_final: 0.7863 (mttm) outliers start: 43 outliers final: 28 residues processed: 320 average time/residue: 0.2396 time to fit residues: 101.5196 Evaluate side-chains 324 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 292 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN 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 228 ASP Chi-restraints excluded: chain B residue 243 THR 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 B residue 331 SER 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 219 LEU 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 95 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 186 THR 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 94 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8929 Z= 0.196 Angle : 0.556 5.933 12097 Z= 0.290 Chirality : 0.043 0.192 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.660 58.475 1222 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.23 % Allowed : 21.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1100 helix: 1.67 (0.27), residues: 372 sheet: 0.14 (0.30), residues: 278 loop : -0.02 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.010 0.001 PHE B 235 TYR 0.014 0.002 TYR A 296 ARG 0.005 0.000 ARG E 160 *********************** 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 340 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 300 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8400 (tppp) cc_final: 0.7942 (tppp) REVERT: A 212 ILE cc_start: 0.8600 (tp) cc_final: 0.8310 (tp) REVERT: A 222 ILE cc_start: 0.8394 (mt) cc_final: 0.8136 (mt) REVERT: A 271 LYS cc_start: 0.7777 (ptmt) cc_final: 0.7492 (ptmt) REVERT: A 274 PHE cc_start: 0.7471 (t80) cc_final: 0.7198 (t80) REVERT: A 276 GLU cc_start: 0.7675 (pm20) cc_final: 0.7466 (pm20) REVERT: A 296 TYR cc_start: 0.7991 (t80) cc_final: 0.7104 (t80) REVERT: A 297 GLU cc_start: 0.7698 (mp0) cc_final: 0.7358 (mp0) REVERT: A 351 CYS cc_start: 0.7510 (t) cc_final: 0.7237 (t) REVERT: B 50 THR cc_start: 0.8121 (m) cc_final: 0.7676 (t) REVERT: B 52 ARG cc_start: 0.7579 (ptp-110) cc_final: 0.7131 (ptp90) REVERT: B 75 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7421 (mp10) REVERT: B 83 ASP cc_start: 0.7290 (t0) cc_final: 0.6961 (t0) REVERT: B 155 ASN cc_start: 0.8179 (t0) cc_final: 0.7822 (t0) REVERT: B 160 SER cc_start: 0.7616 (m) cc_final: 0.7375 (p) REVERT: B 170 ASP cc_start: 0.7547 (t0) cc_final: 0.7146 (t0) REVERT: B 188 MET cc_start: 0.6758 (mmp) cc_final: 0.6301 (mmt) REVERT: B 232 ILE cc_start: 0.8396 (tt) cc_final: 0.8152 (tp) REVERT: B 233 CYS cc_start: 0.7694 (t) cc_final: 0.7334 (t) REVERT: B 239 ASN cc_start: 0.7850 (m-40) cc_final: 0.7561 (m-40) REVERT: B 243 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7112 (t) REVERT: B 249 THR cc_start: 0.8113 (p) cc_final: 0.7891 (p) REVERT: B 296 VAL cc_start: 0.8306 (t) cc_final: 0.7976 (m) REVERT: B 325 MET cc_start: 0.7439 (tpp) cc_final: 0.7195 (mmm) REVERT: G 21 MET cc_start: 0.7192 (tmm) cc_final: 0.6892 (tmm) REVERT: E 111 TRP cc_start: 0.8089 (m100) cc_final: 0.7576 (m-10) REVERT: E 228 TYR cc_start: 0.8084 (m-10) cc_final: 0.7855 (m-80) REVERT: R 77 MET cc_start: 0.7730 (mtp) cc_final: 0.7414 (mtp) REVERT: R 98 ILE cc_start: 0.8130 (tp) cc_final: 0.7915 (tp) REVERT: R 126 THR cc_start: 0.7345 (t) cc_final: 0.7092 (t) REVERT: R 143 MET cc_start: 0.7773 (tpp) cc_final: 0.7484 (tpp) REVERT: R 290 LYS cc_start: 0.8561 (tmtt) cc_final: 0.8284 (tmtt) REVERT: R 355 LYS cc_start: 0.8315 (mttm) cc_final: 0.7871 (mttm) outliers start: 40 outliers final: 29 residues processed: 317 average time/residue: 0.2432 time to fit residues: 101.9804 Evaluate side-chains 324 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE 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 228 ASP Chi-restraints excluded: chain B residue 243 THR 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 R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 82 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 159 LEU Chi-restraints excluded: chain R residue 187 PHE Chi-restraints excluded: chain R residue 200 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 0.0770 overall best weight: 0.7542 ------------------------------------------------------------------------------- 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 313 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8929 Z= 0.198 Angle : 0.562 8.141 12097 Z= 0.290 Chirality : 0.043 0.202 1384 Planarity : 0.004 0.076 1518 Dihedral : 4.673 59.876 1222 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.91 % Allowed : 22.41 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1100 helix: 1.68 (0.27), residues: 371 sheet: 0.08 (0.29), residues: 288 loop : 0.03 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.017 0.001 PHE A 334 TYR 0.015 0.002 TYR E 101 ARG 0.004 0.000 ARG E 160 *********************** 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 342 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8395 (tppp) cc_final: 0.7808 (tppp) REVERT: A 33 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 212 ILE cc_start: 0.8602 (tp) cc_final: 0.8306 (tp) REVERT: A 222 ILE cc_start: 0.8436 (mt) cc_final: 0.8163 (mt) REVERT: A 271 LYS cc_start: 0.7806 (ptmt) cc_final: 0.7507 (ptmt) REVERT: A 274 PHE cc_start: 0.7494 (t80) cc_final: 0.7242 (t80) REVERT: A 276 GLU cc_start: 0.7666 (pm20) cc_final: 0.7446 (pm20) REVERT: A 296 TYR cc_start: 0.8018 (t80) cc_final: 0.7120 (t80) REVERT: A 308 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7159 (mt-10) REVERT: A 340 THR cc_start: 0.8436 (t) cc_final: 0.8131 (p) REVERT: A 351 CYS cc_start: 0.7511 (t) cc_final: 0.7211 (t) REVERT: B 50 THR cc_start: 0.8141 (m) cc_final: 0.7687 (t) REVERT: B 52 ARG cc_start: 0.7633 (ptp-110) cc_final: 0.7160 (ptp90) REVERT: B 75 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7362 (mp10) REVERT: B 83 ASP cc_start: 0.7277 (t0) cc_final: 0.6721 (t0) REVERT: B 155 ASN cc_start: 0.8166 (t0) cc_final: 0.7819 (t0) REVERT: B 160 SER cc_start: 0.7591 (m) cc_final: 0.7315 (p) REVERT: B 170 ASP cc_start: 0.7519 (t0) cc_final: 0.7122 (t0) REVERT: B 188 MET cc_start: 0.6748 (mmp) cc_final: 0.6286 (mmt) REVERT: B 232 ILE cc_start: 0.8408 (tt) cc_final: 0.8142 (tp) REVERT: B 233 CYS cc_start: 0.7689 (t) cc_final: 0.7311 (t) REVERT: B 239 ASN cc_start: 0.7683 (m-40) cc_final: 0.7469 (m-40) REVERT: B 247 ASP cc_start: 0.7653 (p0) cc_final: 0.7385 (p0) REVERT: B 249 THR cc_start: 0.8171 (p) cc_final: 0.7954 (p) REVERT: B 296 VAL cc_start: 0.8298 (t) cc_final: 0.7971 (m) REVERT: B 325 MET cc_start: 0.7428 (tpp) cc_final: 0.7187 (mmm) REVERT: G 21 MET cc_start: 0.7203 (tmm) cc_final: 0.6874 (tmm) REVERT: E 111 TRP cc_start: 0.8097 (m100) cc_final: 0.7539 (m-10) REVERT: E 173 TYR cc_start: 0.8577 (m-80) cc_final: 0.7535 (m-80) REVERT: E 228 TYR cc_start: 0.8087 (m-10) cc_final: 0.7851 (m-80) REVERT: R 72 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7197 (t) REVERT: R 77 MET cc_start: 0.7724 (mtp) cc_final: 0.7419 (mtp) REVERT: R 98 ILE cc_start: 0.8107 (tp) cc_final: 0.7900 (tp) REVERT: R 126 THR cc_start: 0.7362 (t) cc_final: 0.7095 (t) REVERT: R 143 MET cc_start: 0.7774 (tpp) cc_final: 0.7476 (tpp) REVERT: R 290 LYS cc_start: 0.8565 (tmtt) cc_final: 0.8286 (tmtt) REVERT: R 341 LEU cc_start: 0.8282 (tt) cc_final: 0.8075 (tp) outliers start: 37 outliers final: 29 residues processed: 319 average time/residue: 0.2412 time to fit residues: 101.6271 Evaluate side-chains 331 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 300 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 344 ILE 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 228 ASP 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 213 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 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 159 LEU Chi-restraints excluded: chain R residue 166 THR Chi-restraints excluded: chain R residue 200 LEU 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 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.0370 chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 95 optimal weight: 0.0040 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.5470 ------------------------------------------------------------------------------- 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 313 ASN R 317 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8929 Z= 0.175 Angle : 0.563 7.593 12097 Z= 0.291 Chirality : 0.042 0.199 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.650 61.104 1222 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.38 % Allowed : 23.89 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1100 helix: 1.61 (0.27), residues: 376 sheet: 0.10 (0.30), residues: 274 loop : 0.11 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.021 0.001 PHE A 334 TYR 0.013 0.002 TYR E 102 ARG 0.007 0.001 ARG E 160 *********************** 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 329 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 297 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8399 (tppp) cc_final: 0.7813 (tppp) REVERT: A 33 GLU cc_start: 0.7412 (mt-10) cc_final: 0.7161 (mt-10) REVERT: A 212 ILE cc_start: 0.8599 (tp) cc_final: 0.8290 (tp) REVERT: A 222 ILE cc_start: 0.8442 (mt) cc_final: 0.8156 (mt) REVERT: A 271 LYS cc_start: 0.7801 (ptmt) cc_final: 0.7496 (ptmt) REVERT: A 274 PHE cc_start: 0.7503 (t80) cc_final: 0.7261 (t80) REVERT: A 296 TYR cc_start: 0.7992 (t80) cc_final: 0.7119 (t80) REVERT: A 308 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7156 (mt-10) REVERT: A 340 THR cc_start: 0.8414 (t) cc_final: 0.8128 (p) REVERT: A 351 CYS cc_start: 0.7499 (t) cc_final: 0.7220 (t) REVERT: B 50 THR cc_start: 0.8135 (m) cc_final: 0.7498 (t) REVERT: B 52 ARG cc_start: 0.7580 (ptp-110) cc_final: 0.7044 (ptp90) REVERT: B 75 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: B 83 ASP cc_start: 0.7303 (t0) cc_final: 0.6991 (t0) REVERT: B 155 ASN cc_start: 0.8084 (t0) cc_final: 0.7785 (t0) REVERT: B 160 SER cc_start: 0.7584 (m) cc_final: 0.7307 (p) REVERT: B 170 ASP cc_start: 0.7494 (t0) cc_final: 0.7110 (t0) REVERT: B 188 MET cc_start: 0.6830 (mmp) cc_final: 0.6337 (mmt) REVERT: B 232 ILE cc_start: 0.8423 (tt) cc_final: 0.8178 (tp) REVERT: B 233 CYS cc_start: 0.7692 (t) cc_final: 0.7321 (t) REVERT: B 243 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7163 (t) REVERT: B 296 VAL cc_start: 0.8289 (t) cc_final: 0.7984 (m) REVERT: B 325 MET cc_start: 0.7394 (tpp) cc_final: 0.7154 (mmm) REVERT: G 21 MET cc_start: 0.7200 (tmm) cc_final: 0.6902 (tmm) REVERT: E 60 TYR cc_start: 0.8066 (m-80) cc_final: 0.7627 (m-80) REVERT: E 111 TRP cc_start: 0.8083 (m100) cc_final: 0.7433 (m-10) REVERT: E 138 ILE cc_start: 0.8366 (mm) cc_final: 0.8025 (mm) REVERT: E 228 TYR cc_start: 0.8065 (m-10) cc_final: 0.7827 (m-80) REVERT: R 23 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8308 (mmmm) REVERT: R 77 MET cc_start: 0.7759 (mtp) cc_final: 0.7454 (mtp) REVERT: R 98 ILE cc_start: 0.8098 (tp) cc_final: 0.7897 (tp) REVERT: R 126 THR cc_start: 0.7347 (t) cc_final: 0.7073 (t) REVERT: R 143 MET cc_start: 0.7760 (tpp) cc_final: 0.7481 (tpp) REVERT: R 290 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8291 (tmtt) outliers start: 32 outliers final: 28 residues processed: 310 average time/residue: 0.2375 time to fit residues: 97.1550 Evaluate side-chains 324 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 293 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 LYS 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR 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 213 THR Chi-restraints excluded: chain R residue 23 LYS Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 45 ILE Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 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 200 LEU 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 97 optimal weight: 0.0370 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8929 Z= 0.168 Angle : 0.558 7.063 12097 Z= 0.290 Chirality : 0.042 0.211 1384 Planarity : 0.004 0.076 1518 Dihedral : 4.662 61.862 1222 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 3.28 % Allowed : 24.63 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1100 helix: 1.61 (0.27), residues: 377 sheet: 0.18 (0.30), residues: 272 loop : 0.05 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.019 0.001 PHE A 334 TYR 0.013 0.001 TYR E 173 ARG 0.006 0.000 ARG E 160 *********************** 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 333 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 302 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8387 (tppp) cc_final: 0.7763 (tppp) REVERT: A 33 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7129 (mt-10) REVERT: A 212 ILE cc_start: 0.8589 (tp) cc_final: 0.8265 (tp) REVERT: A 222 ILE cc_start: 0.8433 (mt) cc_final: 0.8171 (mt) REVERT: A 271 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7483 (ptmt) REVERT: A 274 PHE cc_start: 0.7515 (t80) cc_final: 0.7302 (t80) REVERT: A 296 TYR cc_start: 0.7975 (t80) cc_final: 0.7091 (t80) REVERT: A 308 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7178 (mt-10) REVERT: A 340 THR cc_start: 0.8394 (t) cc_final: 0.8141 (p) REVERT: A 351 CYS cc_start: 0.7506 (t) cc_final: 0.7227 (t) REVERT: B 22 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8171 (mtt-85) REVERT: B 50 THR cc_start: 0.8127 (m) cc_final: 0.7502 (t) REVERT: B 52 ARG cc_start: 0.7532 (ptp-110) cc_final: 0.7016 (ptp90) REVERT: B 75 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7342 (mp10) REVERT: B 83 ASP cc_start: 0.7421 (t0) cc_final: 0.6871 (t0) REVERT: B 155 ASN cc_start: 0.8063 (t0) cc_final: 0.7801 (t0) REVERT: B 160 SER cc_start: 0.7567 (m) cc_final: 0.7313 (p) REVERT: B 170 ASP cc_start: 0.7479 (t0) cc_final: 0.7100 (t0) REVERT: B 188 MET cc_start: 0.6856 (mmp) cc_final: 0.6371 (mmt) REVERT: B 232 ILE cc_start: 0.8419 (tt) cc_final: 0.8162 (tp) REVERT: B 233 CYS cc_start: 0.7732 (t) cc_final: 0.7349 (t) REVERT: B 243 THR cc_start: 0.7662 (OUTLIER) cc_final: 0.7169 (t) REVERT: B 246 ASP cc_start: 0.7554 (m-30) cc_final: 0.7339 (m-30) REVERT: B 296 VAL cc_start: 0.8262 (t) cc_final: 0.7993 (m) REVERT: B 325 MET cc_start: 0.7390 (tpp) cc_final: 0.7156 (mmm) REVERT: G 21 MET cc_start: 0.7228 (tmm) cc_final: 0.6915 (tmm) REVERT: E 81 LEU cc_start: 0.7675 (tp) cc_final: 0.7184 (tt) REVERT: E 93 MET cc_start: 0.7052 (tpp) cc_final: 0.6830 (tpp) REVERT: E 111 TRP cc_start: 0.8070 (m100) cc_final: 0.7325 (m-10) REVERT: E 138 ILE cc_start: 0.8385 (mm) cc_final: 0.8025 (mm) REVERT: E 228 TYR cc_start: 0.8050 (m-10) cc_final: 0.7807 (m-80) REVERT: E 231 GLN cc_start: 0.8058 (pp30) cc_final: 0.7821 (pp30) REVERT: R 77 MET cc_start: 0.7744 (mtp) cc_final: 0.7450 (mtp) REVERT: R 98 ILE cc_start: 0.8102 (tp) cc_final: 0.7893 (tp) REVERT: R 126 THR cc_start: 0.7307 (t) cc_final: 0.7032 (t) REVERT: R 143 MET cc_start: 0.7772 (tpp) cc_final: 0.7475 (tpp) REVERT: R 290 LYS cc_start: 0.8544 (tmtt) cc_final: 0.8293 (tmtt) outliers start: 31 outliers final: 24 residues processed: 314 average time/residue: 0.2316 time to fit residues: 96.2668 Evaluate side-chains 326 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 300 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU 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 190 LEU Chi-restraints excluded: chain B residue 220 GLN 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 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 184 SER Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 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 200 LEU 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 49 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0980 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.0040 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8929 Z= 0.164 Angle : 0.564 7.214 12097 Z= 0.292 Chirality : 0.042 0.163 1384 Planarity : 0.004 0.075 1518 Dihedral : 4.658 62.174 1222 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.64 % Allowed : 25.37 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1100 helix: 1.64 (0.27), residues: 376 sheet: 0.07 (0.30), residues: 274 loop : 0.05 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.018 0.001 PHE A 334 TYR 0.012 0.001 TYR A 296 ARG 0.006 0.000 ARG E 160 ********************** 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 328 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 303 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8373 (tppp) cc_final: 0.7746 (tppp) REVERT: A 33 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7118 (mt-10) REVERT: A 212 ILE cc_start: 0.8526 (tp) cc_final: 0.8182 (tp) REVERT: A 222 ILE cc_start: 0.8441 (mt) cc_final: 0.8190 (mt) REVERT: A 271 LYS cc_start: 0.7762 (ptmt) cc_final: 0.7470 (ptmt) REVERT: A 274 PHE cc_start: 0.7532 (t80) cc_final: 0.7323 (t80) REVERT: A 296 TYR cc_start: 0.7959 (t80) cc_final: 0.7047 (t80) REVERT: A 351 CYS cc_start: 0.7518 (t) cc_final: 0.7235 (t) REVERT: B 22 ARG cc_start: 0.8434 (mtt-85) cc_final: 0.8124 (mtt-85) REVERT: B 50 THR cc_start: 0.8111 (m) cc_final: 0.7476 (t) REVERT: B 52 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.6986 (ptp90) REVERT: B 75 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: B 155 ASN cc_start: 0.8044 (t0) cc_final: 0.7766 (t0) REVERT: B 160 SER cc_start: 0.7564 (m) cc_final: 0.7310 (p) REVERT: B 170 ASP cc_start: 0.7360 (t0) cc_final: 0.6918 (t0) REVERT: B 188 MET cc_start: 0.6914 (mmp) cc_final: 0.6388 (mmt) REVERT: B 232 ILE cc_start: 0.8409 (tt) cc_final: 0.8083 (tp) REVERT: B 233 CYS cc_start: 0.7759 (t) cc_final: 0.7420 (t) REVERT: B 243 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7200 (m) REVERT: B 246 ASP cc_start: 0.7315 (m-30) cc_final: 0.7084 (m-30) REVERT: B 294 CYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6444 (m) REVERT: B 296 VAL cc_start: 0.8243 (t) cc_final: 0.7988 (m) REVERT: B 298 ASP cc_start: 0.7626 (t0) cc_final: 0.7034 (t0) REVERT: B 325 MET cc_start: 0.7387 (tpp) cc_final: 0.7147 (mmm) REVERT: G 21 MET cc_start: 0.7225 (tmm) cc_final: 0.6923 (tmm) REVERT: E 81 LEU cc_start: 0.7596 (tp) cc_final: 0.7097 (tt) REVERT: E 93 MET cc_start: 0.7045 (tpp) cc_final: 0.6840 (tpp) REVERT: E 111 TRP cc_start: 0.8058 (m100) cc_final: 0.7136 (m-10) REVERT: E 138 ILE cc_start: 0.8380 (mm) cc_final: 0.8090 (mm) REVERT: E 202 ARG cc_start: 0.8258 (mtm180) cc_final: 0.8052 (mtm-85) REVERT: E 228 TYR cc_start: 0.8042 (m-10) cc_final: 0.7797 (m-80) REVERT: R 23 LYS cc_start: 0.8383 (mmmm) cc_final: 0.8027 (tptm) REVERT: R 77 MET cc_start: 0.7703 (mtp) cc_final: 0.7258 (mtp) REVERT: R 98 ILE cc_start: 0.8086 (tp) cc_final: 0.7878 (tp) REVERT: R 126 THR cc_start: 0.7283 (t) cc_final: 0.7035 (t) REVERT: R 143 MET cc_start: 0.7775 (tpp) cc_final: 0.7483 (tpp) REVERT: R 290 LYS cc_start: 0.8547 (tmtt) cc_final: 0.8305 (tmtt) REVERT: R 349 ILE cc_start: 0.8193 (tp) cc_final: 0.7896 (tp) outliers start: 25 outliers final: 21 residues processed: 312 average time/residue: 0.2319 time to fit residues: 96.0344 Evaluate side-chains 320 residues out of total 961 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 296 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 23 LEU 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 190 LEU Chi-restraints excluded: chain B residue 220 GLN 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 294 CYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain R residue 36 MET Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 82 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 200 LEU 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 79 optimal weight: 0.0980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.125914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.110637 restraints weight = 14086.608| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.66 r_work: 0.3322 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8929 Z= 0.190 Angle : 0.579 7.636 12097 Z= 0.302 Chirality : 0.043 0.179 1384 Planarity : 0.004 0.077 1518 Dihedral : 4.708 63.679 1222 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.85 % Allowed : 26.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1100 helix: 1.66 (0.27), residues: 381 sheet: -0.03 (0.30), residues: 276 loop : 0.11 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS R 213 PHE 0.016 0.001 PHE A 334 TYR 0.014 0.002 TYR E 101 ARG 0.005 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.60 seconds wall clock time: 45 minutes 59.67 seconds (2759.67 seconds total)