Starting phenix.real_space_refine on Wed Apr 30 21:27:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.map" model { file = "/net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k8t_36961/04_2025/8k8t_36961.cif" } resolution = 3.8 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= -0.001 sd= 0.971 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 82 5.16 5 C 6280 2.51 5 N 1706 2.21 5 O 1858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9926 Number of models: 1 Model: "" Number of chains: 4 Chain: "C" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3719 Classifications: {'peptide': 450} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 442} Chain breaks: 7 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3735 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 6, 'TRANS': 445} Chain breaks: 6 Chain: "K" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1236 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 1, 'TRANS': 152} Chain breaks: 1 Chain: "L" Number of atoms: 1236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1236 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 1, 'TRANS': 152} Chain breaks: 1 Time building chain proxies: 7.00, per 1000 atoms: 0.71 Number of scatterers: 9926 At special positions: 0 Unit cell: (138.749, 158.453, 103.446, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 82 16.00 O 1858 8.00 N 1706 7.00 C 6280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.30 Conformation dependent library (CDL) restraints added in 1.0 seconds 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2332 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 4 sheets defined 77.1% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'C' and resid 29 through 46 removed outlier: 3.557A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.760A pdb=" N GLY C 51 " --> pdb=" O ASN C 48 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU C 52 " --> pdb=" O ASN C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 52' Processing helix chain 'C' and resid 53 through 67 Processing helix chain 'C' and resid 69 through 87 removed outlier: 3.511A pdb=" N LEU C 73 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 95 Processing helix chain 'C' and resid 103 through 123 Processing helix chain 'C' and resid 125 through 130 Processing helix chain 'C' and resid 138 through 151 Processing helix chain 'C' and resid 156 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.527A pdb=" N ILE C 183 " --> pdb=" O ASP C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 205 through 225 removed outlier: 3.670A pdb=" N LEU C 225 " --> pdb=" O SER C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 252 Processing helix chain 'C' and resid 256 through 268 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 292 through 304 removed outlier: 3.986A pdb=" N MET C 299 " --> pdb=" O ASP C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 330 removed outlier: 3.963A pdb=" N THR C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N MET C 313 " --> pdb=" O GLY C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 359 removed outlier: 3.763A pdb=" N ILE C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 356 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 378 Processing helix chain 'C' and resid 383 through 397 removed outlier: 3.918A pdb=" N ILE C 392 " --> pdb=" O LEU C 388 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 393 " --> pdb=" O SER C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 422 removed outlier: 3.708A pdb=" N LEU C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 439 removed outlier: 4.097A pdb=" N ARG C 438 " --> pdb=" O GLN C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.537A pdb=" N GLU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS C 452 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE C 455 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 480 removed outlier: 3.796A pdb=" N LYS C 469 " --> pdb=" O GLN C 465 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU C 470 " --> pdb=" O PHE C 466 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N MET C 473 " --> pdb=" O LYS C 469 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE C 474 " --> pdb=" O LEU C 470 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET C 477 " --> pdb=" O MET C 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 46 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.713A pdb=" N GLY D 51 " --> pdb=" O ASN D 48 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LEU D 52 " --> pdb=" O ASN D 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 69 through 87 Processing helix chain 'D' and resid 89 through 95 Processing helix chain 'D' and resid 102 through 123 Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 138 through 151 Processing helix chain 'D' and resid 156 through 174 Processing helix chain 'D' and resid 180 through 193 Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 205 through 225 removed outlier: 3.543A pdb=" N LEU D 225 " --> pdb=" O SER D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 251 Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.678A pdb=" N VAL D 261 " --> pdb=" O GLU D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 271 No H-bonds generated for 'chain 'D' and resid 269 through 271' Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.520A pdb=" N ILE D 276 " --> pdb=" O HIS D 272 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 278 " --> pdb=" O LYS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 304 removed outlier: 3.501A pdb=" N LEU D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N MET D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 330 removed outlier: 3.896A pdb=" N THR D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET D 313 " --> pdb=" O GLY D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 359 removed outlier: 3.998A pdb=" N ILE D 342 " --> pdb=" O PRO D 338 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 355 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 356 " --> pdb=" O PHE D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 381 removed outlier: 4.130A pdb=" N ASN D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 381 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 383 through 397 removed outlier: 3.839A pdb=" N ILE D 392 " --> pdb=" O LEU D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.811A pdb=" N LEU D 418 " --> pdb=" O LYS D 414 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 419 " --> pdb=" O ALA D 415 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 420 " --> pdb=" O MET D 416 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE D 421 " --> pdb=" O VAL D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 442 removed outlier: 3.555A pdb=" N PHE D 428 " --> pdb=" O GLU D 424 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 438 " --> pdb=" O GLN D 434 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR D 442 " --> pdb=" O ARG D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 459 removed outlier: 3.635A pdb=" N GLU D 451 " --> pdb=" O SER D 447 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS D 452 " --> pdb=" O ASP D 448 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE D 455 " --> pdb=" O GLU D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 480 removed outlier: 3.845A pdb=" N LYS D 469 " --> pdb=" O GLN D 465 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LEU D 470 " --> pdb=" O PHE D 466 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET D 473 " --> pdb=" O LYS D 469 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE D 474 " --> pdb=" O LEU D 470 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 47 removed outlier: 4.392A pdb=" N GLN K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 70 removed outlier: 3.917A pdb=" N ALA K 70 " --> pdb=" O LEU K 67 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 80 Processing helix chain 'K' and resid 97 through 111 Processing helix chain 'K' and resid 122 through 131 Processing helix chain 'K' and resid 132 through 146 Processing helix chain 'K' and resid 151 through 163 removed outlier: 3.663A pdb=" N VAL K 155 " --> pdb=" O ASN K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 178 Processing helix chain 'L' and resid 30 through 47 removed outlier: 4.511A pdb=" N GLN L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 71 removed outlier: 3.748A pdb=" N SER L 71 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 80 Processing helix chain 'L' and resid 97 through 111 Processing helix chain 'L' and resid 122 through 131 Processing helix chain 'L' and resid 132 through 146 Processing helix chain 'L' and resid 151 through 163 removed outlier: 3.670A pdb=" N VAL L 155 " --> pdb=" O ASN L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 178 Processing sheet with id=AA1, first strand: chain 'K' and resid 25 through 28 removed outlier: 4.217A pdb=" N ASN K 25 " --> pdb=" O LEU L 115 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU L 115 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 60 through 63 Processing sheet with id=AA3, first strand: chain 'K' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'L' and resid 60 through 63 630 hydrogen bonds defined for protein. 1878 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: 2.73 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.50: 5728 1.50 - 1.78: 4203 1.78 - 2.07: 135 2.07 - 2.35: 0 2.35 - 2.63: 1 Bond restraints: 10067 Sorted by residual: bond pdb=" C LYS C 174 " pdb=" N GLU C 176 " ideal model delta sigma weight residual 1.329 2.633 -1.304 1.40e-02 5.10e+03 8.68e+03 bond pdb=" N ILE K 132 " pdb=" CA ILE K 132 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.30e-03 1.88e+04 2.14e+01 bond pdb=" N VAL L 91 " pdb=" CA VAL L 91 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N VAL C 178 " pdb=" CA VAL C 178 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.07e+01 bond pdb=" N VAL K 96 " pdb=" CA VAL K 96 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 ... (remaining 10062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.43: 13494 6.43 - 12.86: 10 12.86 - 19.29: 0 19.29 - 25.72: 2 25.72 - 32.15: 1 Bond angle restraints: 13507 Sorted by residual: angle pdb=" C LYS C 174 " pdb=" N GLU C 176 " pdb=" CA GLU C 176 " ideal model delta sigma weight residual 121.70 153.85 -32.15 1.80e+00 3.09e-01 3.19e+02 angle pdb=" O LYS C 174 " pdb=" C LYS C 174 " pdb=" N GLU C 176 " ideal model delta sigma weight residual 122.59 99.28 23.31 1.33e+00 5.65e-01 3.07e+02 angle pdb=" CA LYS C 174 " pdb=" C LYS C 174 " pdb=" N GLU C 176 " ideal model delta sigma weight residual 116.84 137.15 -20.31 1.71e+00 3.42e-01 1.41e+02 angle pdb=" N LEU C 380 " pdb=" CA LEU C 380 " pdb=" C LEU C 380 " ideal model delta sigma weight residual 113.19 107.31 5.88 1.19e+00 7.06e-01 2.44e+01 angle pdb=" CA GLU K 169 " pdb=" CB GLU K 169 " pdb=" CG GLU K 169 " ideal model delta sigma weight residual 114.10 122.07 -7.97 2.00e+00 2.50e-01 1.59e+01 ... (remaining 13502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 5114 16.41 - 32.81: 730 32.81 - 49.22: 220 49.22 - 65.62: 98 65.62 - 82.03: 17 Dihedral angle restraints: 6179 sinusoidal: 2610 harmonic: 3569 Sorted by residual: dihedral pdb=" CA GLN L 121 " pdb=" C GLN L 121 " pdb=" N GLU L 122 " pdb=" CA GLU L 122 " ideal model delta harmonic sigma weight residual 180.00 158.72 21.28 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA LYS D 88 " pdb=" C LYS D 88 " pdb=" N VAL D 89 " pdb=" CA VAL D 89 " ideal model delta harmonic sigma weight residual 180.00 163.60 16.40 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLN K 121 " pdb=" C GLN K 121 " pdb=" N GLU K 122 " pdb=" CA GLU K 122 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 6176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 940 0.040 - 0.081: 368 0.081 - 0.121: 140 0.121 - 0.162: 54 0.162 - 0.202: 13 Chirality restraints: 1515 Sorted by residual: chirality pdb=" CA ILE L 93 " pdb=" N ILE L 93 " pdb=" C ILE L 93 " pdb=" CB ILE L 93 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA VAL D 427 " pdb=" N VAL D 427 " pdb=" C VAL D 427 " pdb=" CB VAL D 427 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE K 132 " pdb=" N ILE K 132 " pdb=" C ILE K 132 " pdb=" CB ILE K 132 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.79e-01 ... (remaining 1512 not shown) Planarity restraints: 1726 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 174 " -0.076 2.00e-02 2.50e+03 1.03e-01 1.06e+02 pdb=" C LYS C 174 " 0.177 2.00e-02 2.50e+03 pdb=" O LYS C 174 " -0.062 2.00e-02 2.50e+03 pdb=" N GLU C 176 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 430 " -0.247 9.50e-02 1.11e+02 1.11e-01 7.57e+00 pdb=" NE ARG D 430 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 430 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG D 430 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 430 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 247 " 0.218 9.50e-02 1.11e+02 9.77e-02 5.88e+00 pdb=" NE ARG C 247 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG C 247 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 247 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 247 " 0.007 2.00e-02 2.50e+03 ... (remaining 1723 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 938 2.74 - 3.28: 10831 3.28 - 3.82: 17194 3.82 - 4.36: 19998 4.36 - 4.90: 32396 Nonbonded interactions: 81357 Sorted by model distance: nonbonded pdb=" O GLU D 407 " pdb=" OG1 THR D 410 " model vdw 2.197 3.040 nonbonded pdb=" NH1 ARG D 90 " pdb=" OE1 GLN D 150 " model vdw 2.201 3.120 nonbonded pdb=" OE2 GLU D 206 " pdb=" OG1 THR D 256 " model vdw 2.203 3.040 nonbonded pdb=" N GLU L 150 " pdb=" OE1 GLU L 150 " model vdw 2.226 3.120 nonbonded pdb=" N GLU D 137 " pdb=" OE1 GLU D 137 " model vdw 2.243 3.120 ... (remaining 81352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 14 through 426 or resid 428 or resid 430 through 482)) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.430 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.350 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.014 1.304 10067 Z= 1.016 Angle : 0.972 32.148 13507 Z= 0.638 Chirality : 0.055 0.202 1515 Planarity : 0.007 0.111 1726 Dihedral : 18.585 82.031 3847 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.79 % Allowed : 29.86 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.26), residues: 1171 helix: 0.79 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.005 0.001 HIS C 250 PHE 0.038 0.002 PHE C 224 TYR 0.018 0.002 TYR D 320 ARG 0.005 0.001 ARG D 78 Details of bonding type rmsd hydrogen bonds : bond 0.16639 ( 630) hydrogen bonds : angle 6.55528 ( 1878) covalent geometry : bond 0.01434 (10067) covalent geometry : angle 0.97167 (13507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2342 Ramachandran restraints generated. 1171 Oldfield, 0 Emsley, 1171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 355 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 168 MET cc_start: 0.7565 (mtp) cc_final: 0.7287 (mtt) REVERT: C 246 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6511 (mm-30) REVERT: C 258 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7072 (mm-30) REVERT: C 262 LYS cc_start: 0.7356 (mmtm) cc_final: 0.6739 (mmtm) REVERT: C 267 GLU cc_start: 0.7734 (tp30) cc_final: 0.7362 (tp30) REVERT: C 279 MET cc_start: 0.6129 (mtm) cc_final: 0.5725 (ptt) REVERT: C 315 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6955 (mp0) REVERT: C 317 MET cc_start: 0.7411 (ttp) cc_final: 0.7148 (ptm) REVERT: C 326 LYS cc_start: 0.8131 (tptp) cc_final: 0.7677 (tptp) REVERT: D 78 ARG cc_start: 0.8016 (ttm-80) cc_final: 0.7815 (ttm-80) REVERT: D 128 ARG cc_start: 0.8000 (mmm-85) cc_final: 0.7621 (mmm-85) REVERT: D 167 ASP cc_start: 0.7311 (m-30) cc_final: 0.7073 (m-30) REVERT: D 180 ARG cc_start: 0.8561 (mmm-85) cc_final: 0.8299 (ttm170) REVERT: D 267 GLU cc_start: 0.7942 (tp30) cc_final: 0.7390 (tp30) REVERT: D 315 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7120 (mm-30) REVERT: D 438 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8013 (mmm-85) REVERT: D 450 SER cc_start: 0.8024 (m) cc_final: 0.7740 (p) REVERT: K 27 TYR cc_start: 0.8413 (m-10) cc_final: 0.8048 (m-10) REVERT: K 92 LEU cc_start: 0.7803 (mm) cc_final: 0.7579 (mt) REVERT: L 38 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7354 (mtm-85) REVERT: L 73 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6412 (p0) outliers start: 31 outliers final: 10 residues processed: 368 average time/residue: 0.2598 time to fit residues: 127.7005 Evaluate side-chains 349 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 337 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 222 GLN Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain L residue 73 ASP Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 0.1980 chunk 108 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 188 GLN C 435 HIS D 60 ASN ** D 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.144036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.129786 restraints weight = 18915.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133509 restraints weight = 9141.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.135873 restraints weight = 5213.296| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10067 Z= 0.163 Angle : 0.671 20.663 13507 Z= 0.357 Chirality : 0.041 0.307 1515 Planarity : 0.004 0.038 1726 Dihedral : 5.727 72.433 1346 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.26 % Favored : 95.65 % Rotamer: Outliers : 5.49 % Allowed : 25.63 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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 (0.25), residues: 1173 helix: 1.10 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -0.91 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.003 0.001 HIS D 112 PHE 0.025 0.002 PHE C 377 TYR 0.017 0.002 TYR D 29 ARG 0.006 0.001 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.04576 ( 630) hydrogen bonds : angle 4.82684 ( 1878) covalent geometry : bond 0.00342 (10067) covalent geometry : angle 0.67078 (13507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 343 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 64 MET cc_start: 0.8039 (tpp) cc_final: 0.7688 (tpp) REVERT: C 83 GLU cc_start: 0.7680 (tp30) cc_final: 0.7164 (tp30) REVERT: C 159 ASP cc_start: 0.7119 (t0) cc_final: 0.6572 (t70) REVERT: C 163 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6596 (mp10) REVERT: C 191 MET cc_start: 0.7950 (mtt) cc_final: 0.7721 (mtt) REVERT: C 224 PHE cc_start: 0.7013 (m-80) cc_final: 0.6785 (m-80) REVERT: C 243 GLU cc_start: 0.7604 (tp30) cc_final: 0.7281 (tp30) REVERT: C 246 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6477 (mm-30) REVERT: C 258 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7182 (mm-30) REVERT: C 262 LYS cc_start: 0.7456 (mmtm) cc_final: 0.6884 (mmtm) REVERT: C 315 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: C 326 LYS cc_start: 0.8073 (tptp) cc_final: 0.7666 (tptp) REVERT: C 434 GLN cc_start: 0.7561 (tp40) cc_final: 0.7351 (tp40) REVERT: C 438 ARG cc_start: 0.7755 (mmt90) cc_final: 0.7536 (mmt90) REVERT: D 47 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7974 (mmmt) REVERT: D 62 TYR cc_start: 0.6537 (t80) cc_final: 0.6274 (t80) REVERT: D 64 MET cc_start: 0.7036 (mtp) cc_final: 0.6764 (mtp) REVERT: D 78 ARG cc_start: 0.7963 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: D 83 GLU cc_start: 0.7582 (tp30) cc_final: 0.7291 (tp30) REVERT: D 128 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7585 (mmm-85) REVERT: D 167 ASP cc_start: 0.7454 (m-30) cc_final: 0.7171 (m-30) REVERT: D 203 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6559 (mp0) REVERT: D 267 GLU cc_start: 0.7664 (tp30) cc_final: 0.7132 (tp30) REVERT: D 367 LYS cc_start: 0.8210 (tptt) cc_final: 0.7747 (tptt) REVERT: D 416 MET cc_start: 0.6522 (OUTLIER) cc_final: 0.6232 (mmm) REVERT: D 424 GLU cc_start: 0.7470 (mp0) cc_final: 0.7241 (tp30) REVERT: D 438 ARG cc_start: 0.7882 (mmt90) cc_final: 0.7379 (mmt90) REVERT: D 442 THR cc_start: 0.6921 (OUTLIER) cc_final: 0.6383 (t) REVERT: K 27 TYR cc_start: 0.8350 (m-10) cc_final: 0.8066 (m-10) REVERT: K 92 LEU cc_start: 0.7724 (mm) cc_final: 0.7504 (mt) REVERT: L 73 ASP cc_start: 0.6669 (OUTLIER) cc_final: 0.6461 (p0) REVERT: L 122 GLU cc_start: 0.6914 (pm20) cc_final: 0.6650 (pm20) REVERT: L 169 GLU cc_start: 0.7317 (pp20) cc_final: 0.7016 (pp20) outliers start: 61 outliers final: 27 residues processed: 372 average time/residue: 0.2426 time to fit residues: 119.7743 Evaluate side-chains 361 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 329 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 171 ARG Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 440 LEU Chi-restraints excluded: chain D residue 18 ILE Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 73 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 113 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 100 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126270 restraints weight = 18970.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129993 restraints weight = 9127.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132328 restraints weight = 5209.058| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10067 Z= 0.207 Angle : 0.662 18.921 13507 Z= 0.357 Chirality : 0.043 0.313 1515 Planarity : 0.003 0.032 1726 Dihedral : 4.825 50.097 1329 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 5.94 % Allowed : 27.61 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.80 (0.26), residues: 1173 helix: 1.07 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 146 HIS 0.005 0.001 HIS D 112 PHE 0.018 0.002 PHE C 391 TYR 0.015 0.002 TYR D 29 ARG 0.004 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 630) hydrogen bonds : angle 4.64824 ( 1878) covalent geometry : bond 0.00438 (10067) covalent geometry : angle 0.66218 (13507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 345 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7638 (mm-30) REVERT: C 83 GLU cc_start: 0.7689 (tp30) cc_final: 0.7143 (tp30) REVERT: C 124 MET cc_start: 0.6811 (tmm) cc_final: 0.6579 (tmm) REVERT: C 147 PHE cc_start: 0.7892 (t80) cc_final: 0.7418 (t80) REVERT: C 159 ASP cc_start: 0.7762 (t70) cc_final: 0.7115 (t0) REVERT: C 163 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7191 (mp10) REVERT: C 173 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7780 (mtt180) REVERT: C 213 SER cc_start: 0.8499 (t) cc_final: 0.8086 (p) REVERT: C 218 GLN cc_start: 0.7771 (pp30) cc_final: 0.7382 (pp30) REVERT: C 258 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7194 (mm-30) REVERT: C 262 LYS cc_start: 0.7489 (mmtm) cc_final: 0.7266 (mmtm) REVERT: C 300 TYR cc_start: 0.7886 (t80) cc_final: 0.7686 (t80) REVERT: C 315 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: C 326 LYS cc_start: 0.8099 (tptp) cc_final: 0.7721 (tptp) REVERT: C 438 ARG cc_start: 0.7806 (mmt90) cc_final: 0.7523 (mmm-85) REVERT: D 52 LEU cc_start: 0.8529 (mt) cc_final: 0.8276 (mt) REVERT: D 64 MET cc_start: 0.7359 (mtp) cc_final: 0.6820 (mtp) REVERT: D 78 ARG cc_start: 0.7989 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: D 83 GLU cc_start: 0.7615 (tp30) cc_final: 0.7304 (tp30) REVERT: D 88 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7295 (tppt) REVERT: D 101 PHE cc_start: 0.8278 (t80) cc_final: 0.8031 (t80) REVERT: D 107 GLN cc_start: 0.8435 (tp40) cc_final: 0.8205 (tp40) REVERT: D 124 MET cc_start: 0.6610 (tmm) cc_final: 0.6407 (tmm) REVERT: D 125 TYR cc_start: 0.8047 (t80) cc_final: 0.7637 (t80) REVERT: D 128 ARG cc_start: 0.7916 (mmm-85) cc_final: 0.7574 (mmm-85) REVERT: D 163 GLN cc_start: 0.7921 (mm-40) cc_final: 0.7509 (mm-40) REVERT: D 167 ASP cc_start: 0.7488 (m-30) cc_final: 0.7181 (m-30) REVERT: D 223 LYS cc_start: 0.8092 (tmtt) cc_final: 0.7717 (tmtt) REVERT: D 236 LYS cc_start: 0.7873 (tmmt) cc_final: 0.7665 (tmmt) REVERT: D 267 GLU cc_start: 0.7665 (tp30) cc_final: 0.7147 (tp30) REVERT: D 299 MET cc_start: 0.7545 (tmm) cc_final: 0.7217 (tmm) REVERT: D 323 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6685 (tm-30) REVERT: D 367 LYS cc_start: 0.8203 (tptt) cc_final: 0.7735 (tptt) REVERT: D 416 MET cc_start: 0.6564 (OUTLIER) cc_final: 0.6217 (mmm) REVERT: D 434 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7175 (tm-30) REVERT: D 442 THR cc_start: 0.6876 (OUTLIER) cc_final: 0.6343 (t) REVERT: D 457 LYS cc_start: 0.8363 (mmmt) cc_final: 0.7974 (mmmt) REVERT: K 27 TYR cc_start: 0.8385 (m-10) cc_final: 0.8161 (m-10) REVERT: K 85 GLU cc_start: 0.7238 (tm-30) cc_final: 0.7028 (tm-30) REVERT: L 38 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7568 (mtm-85) REVERT: L 84 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7409 (ttpp) REVERT: L 122 GLU cc_start: 0.6978 (pm20) cc_final: 0.6771 (pm20) outliers start: 66 outliers final: 41 residues processed: 368 average time/residue: 0.2572 time to fit residues: 126.0364 Evaluate side-chains 383 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 337 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 426 ASP Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 84 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.0970 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 82 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 434 GLN C 435 HIS D 106 ASN D 381 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.140932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126676 restraints weight = 18744.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130370 restraints weight = 9033.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132651 restraints weight = 5169.325| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10067 Z= 0.188 Angle : 0.641 18.839 13507 Z= 0.346 Chirality : 0.042 0.299 1515 Planarity : 0.003 0.028 1726 Dihedral : 4.559 53.414 1323 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.38 % Allowed : 29.59 % Favored : 64.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.92 (0.26), residues: 1173 helix: 1.15 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -0.90 (0.40), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.024 0.002 PHE C 21 TYR 0.018 0.002 TYR D 29 ARG 0.005 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 630) hydrogen bonds : angle 4.49025 ( 1878) covalent geometry : bond 0.00397 (10067) covalent geometry : angle 0.64097 (13507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 347 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7650 (mm-30) REVERT: C 62 TYR cc_start: 0.7069 (t80) cc_final: 0.6680 (t80) REVERT: C 83 GLU cc_start: 0.7670 (tp30) cc_final: 0.7108 (tp30) REVERT: C 124 MET cc_start: 0.6756 (tmm) cc_final: 0.6530 (tmm) REVERT: C 125 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7770 (t80) REVERT: C 159 ASP cc_start: 0.7525 (t70) cc_final: 0.7135 (t0) REVERT: C 163 GLN cc_start: 0.7550 (mp-120) cc_final: 0.6988 (mp10) REVERT: C 168 MET cc_start: 0.7569 (mtp) cc_final: 0.7320 (ttm) REVERT: C 173 ARG cc_start: 0.8196 (mtt90) cc_final: 0.7817 (mtt180) REVERT: C 213 SER cc_start: 0.8384 (t) cc_final: 0.8103 (p) REVERT: C 218 GLN cc_start: 0.7655 (pp30) cc_final: 0.7359 (pp30) REVERT: C 315 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: C 326 LYS cc_start: 0.8080 (tptp) cc_final: 0.7712 (tptp) REVERT: C 438 ARG cc_start: 0.7680 (mmt90) cc_final: 0.7473 (mmm-85) REVERT: C 457 LYS cc_start: 0.8183 (mmmt) cc_final: 0.7888 (mmmt) REVERT: D 46 ARG cc_start: 0.7870 (mtp180) cc_final: 0.7646 (mtm110) REVERT: D 64 MET cc_start: 0.7397 (mtp) cc_final: 0.6906 (mtp) REVERT: D 78 ARG cc_start: 0.7986 (ttm-80) cc_final: 0.7747 (ttm-80) REVERT: D 83 GLU cc_start: 0.7670 (tp30) cc_final: 0.7295 (tp30) REVERT: D 88 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7264 (tppt) REVERT: D 101 PHE cc_start: 0.8305 (t80) cc_final: 0.8031 (t80) REVERT: D 124 MET cc_start: 0.6560 (tmm) cc_final: 0.6191 (tmm) REVERT: D 125 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7466 (t80) REVERT: D 163 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7481 (mm-40) REVERT: D 167 ASP cc_start: 0.7515 (m-30) cc_final: 0.7184 (m-30) REVERT: D 203 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6622 (mp0) REVERT: D 212 MET cc_start: 0.7592 (tmm) cc_final: 0.7310 (tmm) REVERT: D 223 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7665 (tmtt) REVERT: D 236 LYS cc_start: 0.8011 (tmmt) cc_final: 0.7753 (pttt) REVERT: D 247 ARG cc_start: 0.7983 (ttm-80) cc_final: 0.7388 (ttm-80) REVERT: D 267 GLU cc_start: 0.7691 (tp30) cc_final: 0.7187 (tp30) REVERT: D 323 GLU cc_start: 0.6935 (tm-30) cc_final: 0.6586 (tm-30) REVERT: D 367 LYS cc_start: 0.8201 (tptt) cc_final: 0.7649 (tptt) REVERT: D 416 MET cc_start: 0.6611 (OUTLIER) cc_final: 0.6275 (mmm) REVERT: D 434 GLN cc_start: 0.7463 (tm-30) cc_final: 0.7162 (tm-30) REVERT: D 442 THR cc_start: 0.6824 (OUTLIER) cc_final: 0.6282 (t) REVERT: D 457 LYS cc_start: 0.8244 (mmmt) cc_final: 0.7902 (mmmt) REVERT: K 27 TYR cc_start: 0.8402 (m-10) cc_final: 0.8190 (m-10) REVERT: K 90 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6933 (mp0) REVERT: K 101 MET cc_start: 0.8273 (mmm) cc_final: 0.7992 (tpt) REVERT: K 105 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7830 (mm) REVERT: K 122 GLU cc_start: 0.6942 (pm20) cc_final: 0.6628 (pm20) REVERT: L 105 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7865 (mm) REVERT: L 122 GLU cc_start: 0.6991 (pm20) cc_final: 0.6679 (pm20) REVERT: L 129 GLN cc_start: 0.8092 (mm110) cc_final: 0.7751 (tp40) REVERT: L 169 GLU cc_start: 0.7372 (pp20) cc_final: 0.7118 (pp20) outliers start: 71 outliers final: 42 residues processed: 374 average time/residue: 0.2725 time to fit residues: 133.6389 Evaluate side-chains 385 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 90 GLU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 105 LEU Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 16 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.141295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.126277 restraints weight = 18564.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130106 restraints weight = 9025.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132489 restraints weight = 5186.614| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10067 Z= 0.185 Angle : 0.645 18.481 13507 Z= 0.346 Chirality : 0.042 0.300 1515 Planarity : 0.003 0.042 1726 Dihedral : 4.548 55.049 1323 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 6.56 % Allowed : 30.40 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1173 helix: 1.20 (0.18), residues: 877 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.033 0.002 PHE D 377 TYR 0.024 0.002 TYR C 125 ARG 0.005 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 630) hydrogen bonds : angle 4.47596 ( 1878) covalent geometry : bond 0.00393 (10067) covalent geometry : angle 0.64476 (13507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 347 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 83 GLU cc_start: 0.7714 (tp30) cc_final: 0.7106 (tp30) REVERT: C 124 MET cc_start: 0.6813 (tmm) cc_final: 0.6392 (tmm) REVERT: C 125 TYR cc_start: 0.8188 (OUTLIER) cc_final: 0.7689 (t80) REVERT: C 159 ASP cc_start: 0.7602 (t70) cc_final: 0.7235 (t70) REVERT: C 163 GLN cc_start: 0.7593 (mp-120) cc_final: 0.7101 (mp10) REVERT: C 173 ARG cc_start: 0.8075 (mtt90) cc_final: 0.7645 (mtt180) REVERT: C 213 SER cc_start: 0.8382 (t) cc_final: 0.8099 (p) REVERT: C 218 GLN cc_start: 0.7707 (pp30) cc_final: 0.7401 (pp30) REVERT: C 262 LYS cc_start: 0.7647 (mmtm) cc_final: 0.7382 (mmtm) REVERT: C 269 ILE cc_start: 0.7224 (pp) cc_final: 0.6901 (pt) REVERT: C 315 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6835 (mp0) REVERT: C 326 LYS cc_start: 0.8074 (tptp) cc_final: 0.7703 (tptp) REVERT: C 382 SER cc_start: 0.7806 (t) cc_final: 0.7488 (p) REVERT: C 383 ARG cc_start: 0.5908 (mmt180) cc_final: 0.5685 (mmm160) REVERT: C 391 PHE cc_start: 0.7847 (t80) cc_final: 0.7622 (t80) REVERT: C 430 ARG cc_start: 0.6179 (ttm170) cc_final: 0.5646 (ttm170) REVERT: C 438 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7473 (mmm-85) REVERT: C 457 LYS cc_start: 0.8275 (mmmt) cc_final: 0.8001 (mmmt) REVERT: D 64 MET cc_start: 0.7425 (mtp) cc_final: 0.7195 (mtp) REVERT: D 78 ARG cc_start: 0.8010 (ttm-80) cc_final: 0.7772 (ttm-80) REVERT: D 83 GLU cc_start: 0.7652 (tp30) cc_final: 0.7222 (tp30) REVERT: D 88 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7308 (tppt) REVERT: D 101 PHE cc_start: 0.8299 (t80) cc_final: 0.8051 (t80) REVERT: D 124 MET cc_start: 0.6566 (tmm) cc_final: 0.6129 (tmm) REVERT: D 125 TYR cc_start: 0.8046 (OUTLIER) cc_final: 0.7457 (t80) REVERT: D 149 ASP cc_start: 0.7148 (t0) cc_final: 0.6809 (t0) REVERT: D 152 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6654 (p) REVERT: D 163 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7373 (mm-40) REVERT: D 167 ASP cc_start: 0.7538 (m-30) cc_final: 0.7206 (m-30) REVERT: D 219 MET cc_start: 0.6801 (tmm) cc_final: 0.6422 (tmm) REVERT: D 223 LYS cc_start: 0.8073 (tmtt) cc_final: 0.7706 (tmtt) REVERT: D 236 LYS cc_start: 0.8136 (tmmt) cc_final: 0.7681 (pttp) REVERT: D 262 LYS cc_start: 0.7296 (mmtm) cc_final: 0.7018 (mmtm) REVERT: D 267 GLU cc_start: 0.7723 (tp30) cc_final: 0.7169 (tp30) REVERT: D 279 MET cc_start: 0.6084 (mtm) cc_final: 0.5732 (ptt) REVERT: D 299 MET cc_start: 0.7707 (tmm) cc_final: 0.7333 (tmm) REVERT: D 315 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6972 (mm-30) REVERT: D 323 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6587 (tm-30) REVERT: D 367 LYS cc_start: 0.8220 (tptt) cc_final: 0.7698 (tptt) REVERT: D 381 ASN cc_start: 0.7262 (t0) cc_final: 0.7033 (t0) REVERT: D 416 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6398 (mmm) REVERT: D 434 GLN cc_start: 0.7467 (tm-30) cc_final: 0.7159 (tm-30) REVERT: D 442 THR cc_start: 0.6864 (OUTLIER) cc_final: 0.6324 (t) REVERT: D 457 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7942 (mmmt) REVERT: K 27 TYR cc_start: 0.8443 (m-10) cc_final: 0.8203 (m-10) REVERT: K 105 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7929 (mp) REVERT: K 125 VAL cc_start: 0.7341 (t) cc_final: 0.7027 (p) REVERT: K 154 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6798 (p0) REVERT: L 38 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7532 (mtm-85) REVERT: L 122 GLU cc_start: 0.6947 (pm20) cc_final: 0.6652 (pm20) REVERT: L 129 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7634 (tp40) REVERT: L 169 GLU cc_start: 0.7394 (pp20) cc_final: 0.7138 (pp20) outliers start: 73 outliers final: 50 residues processed: 370 average time/residue: 0.2605 time to fit residues: 127.1823 Evaluate side-chains 398 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 338 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 356 LEU Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain C residue 477 MET Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 254 LYS Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 70 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 109 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.141254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126247 restraints weight = 18698.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.130077 restraints weight = 9051.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132508 restraints weight = 5172.664| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10067 Z= 0.194 Angle : 0.671 18.244 13507 Z= 0.359 Chirality : 0.042 0.295 1515 Planarity : 0.003 0.036 1726 Dihedral : 4.525 55.819 1321 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.74 % Allowed : 30.85 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.92 (0.26), residues: 1173 helix: 1.17 (0.18), residues: 881 sheet: None (None), residues: 0 loop : -0.97 (0.41), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.028 0.002 PHE C 377 TYR 0.026 0.002 TYR C 125 ARG 0.007 0.000 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 630) hydrogen bonds : angle 4.47272 ( 1878) covalent geometry : bond 0.00416 (10067) covalent geometry : angle 0.67127 (13507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 350 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7457 (m-10) cc_final: 0.7031 (m-10) REVERT: C 43 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7649 (mm-30) REVERT: C 62 TYR cc_start: 0.6834 (t80) cc_final: 0.6570 (t80) REVERT: C 83 GLU cc_start: 0.7699 (tp30) cc_final: 0.7140 (tp30) REVERT: C 90 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7991 (ttt180) REVERT: C 91 GLU cc_start: 0.7482 (pm20) cc_final: 0.7072 (pm20) REVERT: C 124 MET cc_start: 0.6831 (tmm) cc_final: 0.6404 (tmm) REVERT: C 125 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7688 (t80) REVERT: C 159 ASP cc_start: 0.7607 (t70) cc_final: 0.6689 (t70) REVERT: C 163 GLN cc_start: 0.7609 (mp-120) cc_final: 0.6510 (mp10) REVERT: C 173 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7731 (mtt180) REVERT: C 213 SER cc_start: 0.8361 (t) cc_final: 0.8126 (p) REVERT: C 218 GLN cc_start: 0.7707 (pp30) cc_final: 0.7386 (pp30) REVERT: C 223 LYS cc_start: 0.7819 (tptp) cc_final: 0.7370 (ttpp) REVERT: C 236 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7574 (tttm) REVERT: C 262 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7380 (mmtm) REVERT: C 269 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6991 (pt) REVERT: C 315 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: C 326 LYS cc_start: 0.8076 (tptp) cc_final: 0.7718 (tptp) REVERT: C 382 SER cc_start: 0.7923 (t) cc_final: 0.7676 (p) REVERT: C 383 ARG cc_start: 0.5911 (mmt180) cc_final: 0.5586 (mmt180) REVERT: C 430 ARG cc_start: 0.6244 (ttm170) cc_final: 0.5640 (ttm170) REVERT: C 438 ARG cc_start: 0.7769 (mmt90) cc_final: 0.7467 (mmm-85) REVERT: C 457 LYS cc_start: 0.8305 (mmmt) cc_final: 0.8001 (mmmt) REVERT: D 64 MET cc_start: 0.7445 (mtp) cc_final: 0.7228 (mtp) REVERT: D 78 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7766 (ttm-80) REVERT: D 83 GLU cc_start: 0.7680 (tp30) cc_final: 0.7243 (tp30) REVERT: D 88 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7374 (tppt) REVERT: D 124 MET cc_start: 0.6578 (tmm) cc_final: 0.6334 (tmm) REVERT: D 125 TYR cc_start: 0.8056 (OUTLIER) cc_final: 0.7539 (t80) REVERT: D 149 ASP cc_start: 0.7099 (t0) cc_final: 0.6889 (t0) REVERT: D 152 VAL cc_start: 0.7118 (OUTLIER) cc_final: 0.6682 (p) REVERT: D 163 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7319 (mm-40) REVERT: D 167 ASP cc_start: 0.7550 (m-30) cc_final: 0.7185 (m-30) REVERT: D 219 MET cc_start: 0.6788 (tmm) cc_final: 0.6401 (tmm) REVERT: D 223 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7700 (tmtt) REVERT: D 236 LYS cc_start: 0.8201 (tmmt) cc_final: 0.7731 (pttp) REVERT: D 262 LYS cc_start: 0.7323 (mmtm) cc_final: 0.7049 (mmtm) REVERT: D 267 GLU cc_start: 0.7735 (tp30) cc_final: 0.7194 (tp30) REVERT: D 315 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6973 (mm-30) REVERT: D 323 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6572 (tm-30) REVERT: D 367 LYS cc_start: 0.8231 (tptt) cc_final: 0.7680 (tptt) REVERT: D 416 MET cc_start: 0.6747 (OUTLIER) cc_final: 0.6403 (mmm) REVERT: D 434 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7154 (tm-30) REVERT: D 442 THR cc_start: 0.6859 (OUTLIER) cc_final: 0.6316 (t) REVERT: D 457 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7946 (mmmt) REVERT: K 27 TYR cc_start: 0.8427 (m-10) cc_final: 0.8217 (m-10) REVERT: K 154 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6709 (p0) REVERT: K 169 GLU cc_start: 0.7529 (pp20) cc_final: 0.7290 (pp20) REVERT: L 78 MET cc_start: 0.7371 (ttt) cc_final: 0.7110 (ttp) REVERT: L 79 PHE cc_start: 0.7832 (m-10) cc_final: 0.7586 (m-10) REVERT: L 122 GLU cc_start: 0.6922 (pm20) cc_final: 0.6628 (pm20) REVERT: L 129 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7472 (mm110) REVERT: L 169 GLU cc_start: 0.7398 (pp20) cc_final: 0.7137 (pp20) outliers start: 75 outliers final: 53 residues processed: 378 average time/residue: 0.3026 time to fit residues: 151.9836 Evaluate side-chains 400 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 335 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 301 LYS Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 19 optimal weight: 0.2980 chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.139229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.124664 restraints weight = 18665.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.128296 restraints weight = 9125.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130688 restraints weight = 5274.242| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10067 Z= 0.210 Angle : 0.690 18.099 13507 Z= 0.368 Chirality : 0.043 0.290 1515 Planarity : 0.003 0.037 1726 Dihedral : 4.612 56.843 1321 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 7.10 % Allowed : 31.47 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.87 (0.26), residues: 1173 helix: 1.13 (0.18), residues: 882 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.030 0.002 PHE D 377 TYR 0.025 0.002 TYR C 125 ARG 0.006 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04352 ( 630) hydrogen bonds : angle 4.49949 ( 1878) covalent geometry : bond 0.00450 (10067) covalent geometry : angle 0.69017 (13507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 342 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7646 (mm-30) REVERT: C 78 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7718 (ttm-80) REVERT: C 83 GLU cc_start: 0.7691 (tp30) cc_final: 0.7090 (tp30) REVERT: C 90 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.8026 (ttt180) REVERT: C 91 GLU cc_start: 0.7453 (pm20) cc_final: 0.7029 (pm20) REVERT: C 124 MET cc_start: 0.6858 (tmm) cc_final: 0.6404 (tmm) REVERT: C 125 TYR cc_start: 0.8178 (OUTLIER) cc_final: 0.7656 (t80) REVERT: C 159 ASP cc_start: 0.7608 (t70) cc_final: 0.6705 (t70) REVERT: C 163 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.6480 (mp10) REVERT: C 173 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7764 (mtt180) REVERT: C 213 SER cc_start: 0.8371 (t) cc_final: 0.8152 (p) REVERT: C 218 GLN cc_start: 0.7725 (pp30) cc_final: 0.7421 (pp30) REVERT: C 262 LYS cc_start: 0.7718 (mmtm) cc_final: 0.7465 (mmtm) REVERT: C 315 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6845 (mp0) REVERT: C 326 LYS cc_start: 0.8093 (tptp) cc_final: 0.7828 (tptp) REVERT: C 330 SER cc_start: 0.8473 (m) cc_final: 0.8023 (p) REVERT: C 381 ASN cc_start: 0.7142 (t0) cc_final: 0.6680 (t0) REVERT: C 382 SER cc_start: 0.7958 (t) cc_final: 0.7539 (p) REVERT: C 430 ARG cc_start: 0.6274 (ttm170) cc_final: 0.5570 (ttm170) REVERT: C 438 ARG cc_start: 0.7760 (mmt90) cc_final: 0.7494 (mmm-85) REVERT: C 457 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8014 (mmmt) REVERT: D 52 LEU cc_start: 0.8660 (mt) cc_final: 0.8451 (mt) REVERT: D 64 MET cc_start: 0.7426 (mtp) cc_final: 0.7201 (mtp) REVERT: D 78 ARG cc_start: 0.8011 (ttm-80) cc_final: 0.7777 (ttm-80) REVERT: D 83 GLU cc_start: 0.7674 (tp30) cc_final: 0.7192 (tp30) REVERT: D 88 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7319 (tppt) REVERT: D 124 MET cc_start: 0.6642 (tmm) cc_final: 0.6145 (tmm) REVERT: D 125 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7417 (t80) REVERT: D 149 ASP cc_start: 0.7201 (t0) cc_final: 0.6853 (t0) REVERT: D 152 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6632 (p) REVERT: D 163 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7399 (mm-40) REVERT: D 167 ASP cc_start: 0.7543 (m-30) cc_final: 0.7189 (m-30) REVERT: D 219 MET cc_start: 0.6784 (tmm) cc_final: 0.6356 (tmm) REVERT: D 223 LYS cc_start: 0.8047 (tmtt) cc_final: 0.7708 (tmtt) REVERT: D 236 LYS cc_start: 0.8251 (tmmt) cc_final: 0.7910 (ttpp) REVERT: D 240 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7648 (tpp-160) REVERT: D 262 LYS cc_start: 0.7314 (mmtm) cc_final: 0.7046 (mmtm) REVERT: D 267 GLU cc_start: 0.7736 (tp30) cc_final: 0.7147 (tp30) REVERT: D 315 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6975 (mm-30) REVERT: D 323 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6503 (tm-30) REVERT: D 367 LYS cc_start: 0.8236 (tptt) cc_final: 0.7647 (tptt) REVERT: D 416 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6384 (mmm) REVERT: D 424 GLU cc_start: 0.7310 (tp30) cc_final: 0.6848 (tp30) REVERT: D 434 GLN cc_start: 0.7469 (tm-30) cc_final: 0.7149 (tm-30) REVERT: D 442 THR cc_start: 0.6887 (OUTLIER) cc_final: 0.6353 (t) REVERT: D 457 LYS cc_start: 0.8281 (mmmt) cc_final: 0.7938 (mmmt) REVERT: K 92 LEU cc_start: 0.7623 (mm) cc_final: 0.7393 (mp) REVERT: K 125 VAL cc_start: 0.7401 (t) cc_final: 0.7155 (p) REVERT: L 38 ARG cc_start: 0.7796 (mtm-85) cc_final: 0.7585 (mtm-85) REVERT: L 129 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7718 (tp40) REVERT: L 154 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6845 (p0) REVERT: L 169 GLU cc_start: 0.7420 (pp20) cc_final: 0.7137 (pp20) outliers start: 79 outliers final: 56 residues processed: 371 average time/residue: 0.3079 time to fit residues: 151.7250 Evaluate side-chains 399 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 332 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 154 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.141296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.126838 restraints weight = 18648.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.130482 restraints weight = 9081.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132731 restraints weight = 5217.809| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10067 Z= 0.206 Angle : 0.705 18.135 13507 Z= 0.373 Chirality : 0.043 0.285 1515 Planarity : 0.003 0.036 1726 Dihedral : 4.622 55.828 1321 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.83 % Allowed : 32.28 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.87 (0.26), residues: 1173 helix: 1.11 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.026 0.002 PHE C 21 TYR 0.027 0.002 TYR C 125 ARG 0.012 0.001 ARG C 439 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 630) hydrogen bonds : angle 4.51003 ( 1878) covalent geometry : bond 0.00444 (10067) covalent geometry : angle 0.70496 (13507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 354 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 78 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7709 (ttm-80) REVERT: C 83 GLU cc_start: 0.7673 (tp30) cc_final: 0.7069 (tp30) REVERT: C 90 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8019 (ttt180) REVERT: C 91 GLU cc_start: 0.7449 (pm20) cc_final: 0.7028 (pm20) REVERT: C 124 MET cc_start: 0.6849 (tmm) cc_final: 0.6414 (tmm) REVERT: C 125 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7669 (t80) REVERT: C 159 ASP cc_start: 0.7602 (t70) cc_final: 0.6674 (t70) REVERT: C 163 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.6538 (mp10) REVERT: C 173 ARG cc_start: 0.8150 (mtt90) cc_final: 0.7824 (mtt180) REVERT: C 213 SER cc_start: 0.8356 (t) cc_final: 0.8116 (p) REVERT: C 218 GLN cc_start: 0.7728 (pp30) cc_final: 0.7434 (pp30) REVERT: C 262 LYS cc_start: 0.7765 (mmtm) cc_final: 0.7479 (mmtm) REVERT: C 315 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: C 326 LYS cc_start: 0.8080 (tptp) cc_final: 0.7836 (tptp) REVERT: C 330 SER cc_start: 0.8464 (m) cc_final: 0.8032 (p) REVERT: C 381 ASN cc_start: 0.7166 (t0) cc_final: 0.6619 (t0) REVERT: C 382 SER cc_start: 0.7981 (t) cc_final: 0.7672 (p) REVERT: C 430 ARG cc_start: 0.6282 (ttm170) cc_final: 0.5681 (ttm170) REVERT: C 438 ARG cc_start: 0.7732 (mmt90) cc_final: 0.7464 (mmm-85) REVERT: C 457 LYS cc_start: 0.8319 (mmmt) cc_final: 0.8017 (mmmt) REVERT: D 64 MET cc_start: 0.7431 (mtp) cc_final: 0.7194 (mtp) REVERT: D 78 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7754 (ttm-80) REVERT: D 83 GLU cc_start: 0.7648 (tp30) cc_final: 0.7111 (tp30) REVERT: D 88 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7361 (tppt) REVERT: D 124 MET cc_start: 0.6640 (tmm) cc_final: 0.6151 (tmm) REVERT: D 125 TYR cc_start: 0.8038 (OUTLIER) cc_final: 0.7399 (t80) REVERT: D 149 ASP cc_start: 0.7209 (t0) cc_final: 0.6796 (t0) REVERT: D 152 VAL cc_start: 0.7047 (OUTLIER) cc_final: 0.6634 (p) REVERT: D 163 GLN cc_start: 0.7914 (mm-40) cc_final: 0.7314 (mm-40) REVERT: D 167 ASP cc_start: 0.7537 (m-30) cc_final: 0.7182 (m-30) REVERT: D 219 MET cc_start: 0.6787 (tmm) cc_final: 0.6355 (tmm) REVERT: D 223 LYS cc_start: 0.8051 (tmtt) cc_final: 0.7712 (tmtt) REVERT: D 236 LYS cc_start: 0.8278 (tmmt) cc_final: 0.7937 (ttpp) REVERT: D 240 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7577 (tpp-160) REVERT: D 262 LYS cc_start: 0.7312 (mmtm) cc_final: 0.7043 (mmtm) REVERT: D 267 GLU cc_start: 0.7765 (tp30) cc_final: 0.7191 (tp30) REVERT: D 315 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6944 (mm-30) REVERT: D 323 GLU cc_start: 0.6952 (tm-30) cc_final: 0.6451 (tm-30) REVERT: D 367 LYS cc_start: 0.8254 (tptt) cc_final: 0.7664 (tptt) REVERT: D 416 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6441 (mmm) REVERT: D 434 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7158 (tm-30) REVERT: D 442 THR cc_start: 0.6877 (OUTLIER) cc_final: 0.6276 (t) REVERT: D 457 LYS cc_start: 0.8287 (mmmt) cc_final: 0.7933 (mmmt) REVERT: K 92 LEU cc_start: 0.7611 (mm) cc_final: 0.7399 (mp) REVERT: K 101 MET cc_start: 0.8240 (tpp) cc_final: 0.8007 (tpt) REVERT: K 154 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6624 (p0) REVERT: K 169 GLU cc_start: 0.7544 (pp20) cc_final: 0.7249 (pp20) REVERT: L 38 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7506 (mtm-85) REVERT: L 129 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7736 (tp40) REVERT: L 154 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6854 (p0) outliers start: 76 outliers final: 57 residues processed: 379 average time/residue: 0.3010 time to fit residues: 152.1845 Evaluate side-chains 416 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 347 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 91 VAL Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 154 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 11 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 HIS D 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.138888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.124507 restraints weight = 18664.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.128136 restraints weight = 9124.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130331 restraints weight = 5266.407| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10067 Z= 0.217 Angle : 0.725 18.119 13507 Z= 0.383 Chirality : 0.044 0.288 1515 Planarity : 0.003 0.034 1726 Dihedral : 4.693 57.556 1321 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.56 % Allowed : 32.28 % Favored : 61.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 1173 helix: 1.12 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 146 HIS 0.004 0.001 HIS C 112 PHE 0.029 0.002 PHE C 21 TYR 0.027 0.002 TYR C 125 ARG 0.008 0.001 ARG C 439 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 630) hydrogen bonds : angle 4.53987 ( 1878) covalent geometry : bond 0.00468 (10067) covalent geometry : angle 0.72472 (13507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 346 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7645 (mm-30) REVERT: C 78 ARG cc_start: 0.7935 (ttm-80) cc_final: 0.7697 (ttm-80) REVERT: C 83 GLU cc_start: 0.7665 (tp30) cc_final: 0.7084 (tp30) REVERT: C 90 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8068 (ttt180) REVERT: C 91 GLU cc_start: 0.7456 (pm20) cc_final: 0.7025 (pm20) REVERT: C 124 MET cc_start: 0.6876 (tmm) cc_final: 0.6532 (tmm) REVERT: C 125 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.7790 (t80) REVERT: C 159 ASP cc_start: 0.7594 (t70) cc_final: 0.6693 (t70) REVERT: C 163 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6554 (mp10) REVERT: C 218 GLN cc_start: 0.7693 (pp30) cc_final: 0.7386 (pp30) REVERT: C 223 LYS cc_start: 0.7790 (tptp) cc_final: 0.7489 (ttpp) REVERT: C 262 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7471 (mmtm) REVERT: C 315 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: C 326 LYS cc_start: 0.8077 (tptp) cc_final: 0.7832 (tptp) REVERT: C 330 SER cc_start: 0.8467 (m) cc_final: 0.8044 (p) REVERT: C 381 ASN cc_start: 0.7206 (t0) cc_final: 0.6676 (t0) REVERT: C 382 SER cc_start: 0.8076 (t) cc_final: 0.7703 (p) REVERT: C 430 ARG cc_start: 0.6347 (ttm170) cc_final: 0.5713 (ttm170) REVERT: C 438 ARG cc_start: 0.7768 (mmt90) cc_final: 0.7519 (mmm-85) REVERT: C 457 LYS cc_start: 0.8340 (mmmt) cc_final: 0.8033 (mmmt) REVERT: D 64 MET cc_start: 0.7441 (mtp) cc_final: 0.7221 (mtp) REVERT: D 78 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7752 (ttm-80) REVERT: D 83 GLU cc_start: 0.7635 (tp30) cc_final: 0.7087 (tp30) REVERT: D 88 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7366 (tppt) REVERT: D 124 MET cc_start: 0.6632 (tmm) cc_final: 0.6133 (tmm) REVERT: D 125 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7373 (t80) REVERT: D 149 ASP cc_start: 0.7209 (t0) cc_final: 0.6769 (t0) REVERT: D 152 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6641 (p) REVERT: D 163 GLN cc_start: 0.7917 (mm-40) cc_final: 0.6608 (mp10) REVERT: D 167 ASP cc_start: 0.7533 (m-30) cc_final: 0.7213 (m-30) REVERT: D 219 MET cc_start: 0.6822 (tmm) cc_final: 0.6370 (tmm) REVERT: D 223 LYS cc_start: 0.8056 (tmtt) cc_final: 0.7740 (tmtt) REVERT: D 236 LYS cc_start: 0.8333 (tmmt) cc_final: 0.7748 (ttpp) REVERT: D 240 ARG cc_start: 0.8004 (tpp-160) cc_final: 0.7576 (tpp-160) REVERT: D 262 LYS cc_start: 0.7302 (mmtm) cc_final: 0.7061 (mmtm) REVERT: D 267 GLU cc_start: 0.7764 (tp30) cc_final: 0.7391 (tp30) REVERT: D 315 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6946 (mm-30) REVERT: D 323 GLU cc_start: 0.6977 (tm-30) cc_final: 0.6472 (tm-30) REVERT: D 367 LYS cc_start: 0.8247 (tptt) cc_final: 0.7645 (tptt) REVERT: D 416 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6239 (mmm) REVERT: D 442 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6325 (t) REVERT: D 457 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7939 (mmmt) REVERT: K 78 MET cc_start: 0.7844 (ttm) cc_final: 0.6487 (tpp) REVERT: K 85 GLU cc_start: 0.7884 (tt0) cc_final: 0.6420 (tt0) REVERT: K 154 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6671 (p0) REVERT: L 38 ARG cc_start: 0.7770 (mtm-85) cc_final: 0.7499 (mtm-85) REVERT: L 129 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7727 (tp40) REVERT: L 154 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6857 (p0) outliers start: 73 outliers final: 55 residues processed: 370 average time/residue: 0.2651 time to fit residues: 130.1068 Evaluate side-chains 412 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 345 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 154 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 48 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS C 286 HIS D 286 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.123260 restraints weight = 18889.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126935 restraints weight = 9323.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.129303 restraints weight = 5384.512| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10067 Z= 0.238 Angle : 0.758 18.155 13507 Z= 0.401 Chirality : 0.044 0.290 1515 Planarity : 0.004 0.055 1726 Dihedral : 4.753 56.001 1321 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.29 % Allowed : 32.73 % Favored : 60.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.78 (0.26), residues: 1173 helix: 1.05 (0.18), residues: 880 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 146 HIS 0.005 0.001 HIS D 112 PHE 0.030 0.002 PHE C 21 TYR 0.023 0.002 TYR C 125 ARG 0.011 0.001 ARG C 439 Details of bonding type rmsd hydrogen bonds : bond 0.04504 ( 630) hydrogen bonds : angle 4.58349 ( 1878) covalent geometry : bond 0.00511 (10067) covalent geometry : angle 0.75828 (13507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 348 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7643 (mm-30) REVERT: C 78 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: C 83 GLU cc_start: 0.7686 (tp30) cc_final: 0.7097 (tp30) REVERT: C 88 LYS cc_start: 0.8081 (tppt) cc_final: 0.7327 (tppt) REVERT: C 90 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (ttt180) REVERT: C 91 GLU cc_start: 0.7461 (pm20) cc_final: 0.7169 (pm20) REVERT: C 107 GLN cc_start: 0.8306 (tp-100) cc_final: 0.8050 (tp40) REVERT: C 124 MET cc_start: 0.6921 (tmm) cc_final: 0.6427 (tmm) REVERT: C 125 TYR cc_start: 0.8150 (OUTLIER) cc_final: 0.7620 (t80) REVERT: C 159 ASP cc_start: 0.7604 (t70) cc_final: 0.6754 (t70) REVERT: C 163 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.6579 (mp10) REVERT: C 173 ARG cc_start: 0.8219 (mtt90) cc_final: 0.7877 (mtt90) REVERT: C 218 GLN cc_start: 0.7664 (pp30) cc_final: 0.7378 (pp30) REVERT: C 223 LYS cc_start: 0.7856 (tptp) cc_final: 0.7554 (ttpp) REVERT: C 236 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7737 (pttp) REVERT: C 262 LYS cc_start: 0.7758 (mmtm) cc_final: 0.7466 (mmtm) REVERT: C 315 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: C 326 LYS cc_start: 0.8115 (tptp) cc_final: 0.7881 (tptp) REVERT: C 330 SER cc_start: 0.8478 (m) cc_final: 0.8017 (p) REVERT: C 381 ASN cc_start: 0.7247 (t0) cc_final: 0.6755 (t0) REVERT: C 382 SER cc_start: 0.8078 (t) cc_final: 0.7661 (p) REVERT: C 430 ARG cc_start: 0.6304 (ttm170) cc_final: 0.5264 (ttm-80) REVERT: C 438 ARG cc_start: 0.7722 (mmt90) cc_final: 0.7441 (mmm-85) REVERT: C 457 LYS cc_start: 0.8353 (mmmt) cc_final: 0.8044 (mmmt) REVERT: D 52 LEU cc_start: 0.8647 (mt) cc_final: 0.8418 (mt) REVERT: D 64 MET cc_start: 0.7472 (mtp) cc_final: 0.7238 (mtp) REVERT: D 78 ARG cc_start: 0.7995 (ttm-80) cc_final: 0.7770 (ttm-80) REVERT: D 83 GLU cc_start: 0.7644 (tp30) cc_final: 0.7088 (tp30) REVERT: D 88 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7425 (tppt) REVERT: D 124 MET cc_start: 0.6674 (tmm) cc_final: 0.6135 (tmm) REVERT: D 125 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7396 (t80) REVERT: D 149 ASP cc_start: 0.7225 (t0) cc_final: 0.6781 (t0) REVERT: D 152 VAL cc_start: 0.7105 (OUTLIER) cc_final: 0.6702 (p) REVERT: D 162 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8380 (ttp80) REVERT: D 163 GLN cc_start: 0.7913 (mm-40) cc_final: 0.6594 (mp10) REVERT: D 167 ASP cc_start: 0.7531 (m-30) cc_final: 0.7191 (m-30) REVERT: D 168 MET cc_start: 0.7541 (mtm) cc_final: 0.7314 (ttm) REVERT: D 219 MET cc_start: 0.6832 (tmm) cc_final: 0.6372 (tmm) REVERT: D 223 LYS cc_start: 0.8085 (tmtt) cc_final: 0.7762 (tmtt) REVERT: D 236 LYS cc_start: 0.8383 (tmmt) cc_final: 0.7902 (ttpp) REVERT: D 240 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7740 (tpp-160) REVERT: D 262 LYS cc_start: 0.7296 (mmtm) cc_final: 0.7047 (mmtm) REVERT: D 267 GLU cc_start: 0.7823 (tp30) cc_final: 0.7428 (tp30) REVERT: D 294 GLU cc_start: 0.6984 (tt0) cc_final: 0.6688 (tt0) REVERT: D 299 MET cc_start: 0.7691 (tmm) cc_final: 0.7455 (tmm) REVERT: D 315 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6964 (mm-30) REVERT: D 323 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6528 (tm-30) REVERT: D 367 LYS cc_start: 0.8258 (tptt) cc_final: 0.7672 (tptt) REVERT: D 416 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6447 (mmm) REVERT: D 442 THR cc_start: 0.6916 (OUTLIER) cc_final: 0.6345 (t) REVERT: D 457 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7957 (mmmt) REVERT: K 78 MET cc_start: 0.7885 (ttm) cc_final: 0.6343 (tpp) REVERT: K 79 PHE cc_start: 0.8046 (m-10) cc_final: 0.7715 (m-80) REVERT: K 85 GLU cc_start: 0.7988 (tt0) cc_final: 0.6472 (tt0) REVERT: K 101 MET cc_start: 0.8244 (tpp) cc_final: 0.7983 (tpt) REVERT: K 125 VAL cc_start: 0.7746 (t) cc_final: 0.7441 (p) REVERT: K 154 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6692 (p0) REVERT: L 38 ARG cc_start: 0.7801 (mtm-85) cc_final: 0.7512 (mtm-85) REVERT: L 92 LEU cc_start: 0.7881 (mt) cc_final: 0.7670 (mt) REVERT: L 129 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7690 (tp40) REVERT: L 154 ASP cc_start: 0.7261 (OUTLIER) cc_final: 0.6872 (p0) outliers start: 70 outliers final: 56 residues processed: 372 average time/residue: 0.2618 time to fit residues: 127.6209 Evaluate side-chains 415 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 346 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 237 VAL Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 308 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 352 PHE Chi-restraints excluded: chain C residue 355 PHE Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 471 GLU Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 29 TYR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 118 MET Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 125 TYR Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 273 MET Chi-restraints excluded: chain D residue 284 LEU Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 ARG Chi-restraints excluded: chain D residue 308 ASN Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 THR Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 471 GLU Chi-restraints excluded: chain D residue 477 MET Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 GLU Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 136 ILE Chi-restraints excluded: chain K residue 154 ASP Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 158 LEU Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain L residue 37 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 129 GLN Chi-restraints excluded: chain L residue 136 ILE Chi-restraints excluded: chain L residue 154 ASP Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 chunk 82 optimal weight: 0.0470 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 188 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.139800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125615 restraints weight = 18645.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.129257 restraints weight = 9122.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.131499 restraints weight = 5247.778| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10067 Z= 0.185 Angle : 0.738 17.771 13507 Z= 0.385 Chirality : 0.043 0.287 1515 Planarity : 0.003 0.043 1726 Dihedral : 4.649 56.489 1321 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 6.29 % Allowed : 32.82 % Favored : 60.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.08 % 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: 0.89 (0.26), residues: 1173 helix: 1.13 (0.18), residues: 886 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 146 HIS 0.003 0.001 HIS C 112 PHE 0.031 0.002 PHE C 21 TYR 0.023 0.002 TYR C 125 ARG 0.007 0.001 ARG C 439 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 630) hydrogen bonds : angle 4.50426 ( 1878) covalent geometry : bond 0.00405 (10067) covalent geometry : angle 0.73809 (13507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4482.31 seconds wall clock time: 79 minutes 29.16 seconds (4769.16 seconds total)