Starting phenix.real_space_refine on Sat Jul 20 04:43:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_36961.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_36961.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_36961.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_36961.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k8t_36961/07_2024/8k8t_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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.09, 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 - 3.50 Amino acid : False - 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: 3.85 Conformation dependent library (CDL) restraints added in 1.7 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: 1.01 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: 2.78 Time building geometry restraints manager: 4.26 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: 97.85 - 109.05: 517 109.05 - 120.25: 9150 120.25 - 131.45: 3831 131.45 - 142.65: 8 142.65 - 153.85: 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 2.440 nonbonded pdb=" NH1 ARG D 90 " pdb=" OE1 GLN D 150 " model vdw 2.201 2.520 nonbonded pdb=" OE2 GLU D 206 " pdb=" OG1 THR D 256 " model vdw 2.203 2.440 nonbonded pdb=" N GLU L 150 " pdb=" OE1 GLU L 150 " model vdw 2.226 2.520 nonbonded pdb=" N GLU D 137 " pdb=" OE1 GLU D 137 " model vdw 2.243 2.520 ... (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 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: 9.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 30.460 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- 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= 1.075 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 *********************** 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 fitting. rotamer outliers: 31 poor density : 355 time to evaluate : 1.141 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: 0.2529 time to fit residues: 123.0237 Evaluate side-chains 349 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 337 time to evaluate : 1.106 ------------------------------------------------------------------------------- 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: 2.9990 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 0.2980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 0.0970 chunk 108 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1569 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= 0.248 Angle : 0.670 20.673 13507 Z= 0.356 Chirality : 0.042 0.319 1515 Planarity : 0.003 0.027 1726 Dihedral : 5.727 72.193 1346 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.29 % Allowed : 26.17 % Favored : 67.54 % 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: 0.82 (0.26), residues: 1173 helix: 1.08 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 146 HIS 0.004 0.001 HIS D 112 PHE 0.025 0.002 PHE C 224 TYR 0.018 0.002 TYR D 29 ARG 0.006 0.001 ARG D 153 *********************** 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 416 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 346 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 MET cc_start: 0.8044 (tpp) cc_final: 0.7707 (tpp) REVERT: C 72 LYS cc_start: 0.8480 (tptm) cc_final: 0.8245 (tptm) REVERT: C 83 GLU cc_start: 0.7785 (tp30) cc_final: 0.7199 (tp30) REVERT: C 163 GLN cc_start: 0.7182 (mp-120) cc_final: 0.6923 (mp10) REVERT: C 191 MET cc_start: 0.8037 (mtt) cc_final: 0.7799 (mtt) REVERT: C 213 SER cc_start: 0.8288 (t) cc_final: 0.7966 (p) REVERT: C 218 GLN cc_start: 0.7589 (pp30) cc_final: 0.7261 (pp30) REVERT: C 258 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7137 (mm-30) REVERT: C 262 LYS cc_start: 0.7438 (mmtm) cc_final: 0.6855 (mmtm) REVERT: C 300 TYR cc_start: 0.7956 (t80) cc_final: 0.7742 (t80) REVERT: C 315 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: C 326 LYS cc_start: 0.8006 (tptp) cc_final: 0.7558 (tptp) REVERT: D 58 TYR cc_start: 0.7578 (t80) cc_final: 0.7349 (t80) REVERT: D 64 MET cc_start: 0.7189 (mtp) cc_final: 0.6979 (mtp) REVERT: D 78 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7814 (ttm-80) REVERT: D 83 GLU cc_start: 0.7621 (tp30) cc_final: 0.7337 (tp30) REVERT: D 124 MET cc_start: 0.6461 (tmm) cc_final: 0.6245 (tmm) REVERT: D 128 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7649 (mmm-85) REVERT: D 163 GLN cc_start: 0.7922 (mm-40) cc_final: 0.7491 (mm-40) REVERT: D 167 ASP cc_start: 0.7472 (m-30) cc_final: 0.7222 (m-30) REVERT: D 180 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8206 (ttm170) REVERT: D 203 GLU cc_start: 0.7198 (mt-10) cc_final: 0.6634 (mp0) REVERT: D 267 GLU cc_start: 0.7732 (tp30) cc_final: 0.7143 (tp30) REVERT: D 315 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7144 (mm-30) REVERT: D 367 LYS cc_start: 0.8271 (tptt) cc_final: 0.7834 (tptt) REVERT: D 416 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6427 (mmm) REVERT: D 424 GLU cc_start: 0.7556 (mp0) cc_final: 0.7130 (tp30) REVERT: D 438 ARG cc_start: 0.8021 (mmt90) cc_final: 0.7478 (mmt90) REVERT: D 442 THR cc_start: 0.7023 (OUTLIER) cc_final: 0.6496 (t) REVERT: K 27 TYR cc_start: 0.8442 (m-10) cc_final: 0.8088 (m-10) REVERT: L 38 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7487 (mtm-85) REVERT: L 122 GLU cc_start: 0.6966 (pm20) cc_final: 0.6661 (pm20) REVERT: L 169 GLU cc_start: 0.7361 (pp20) cc_final: 0.7141 (pp20) outliers start: 70 outliers final: 35 residues processed: 377 average time/residue: 0.2373 time to fit residues: 119.9713 Evaluate side-chains 384 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 346 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 151 VAL 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 118 MET 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 411 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 440 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 155 VAL Chi-restraints excluded: chain K residue 171 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 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.4980 chunk 117 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 106 ASN D 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2076 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= 0.270 Angle : 0.646 18.994 13507 Z= 0.347 Chirality : 0.042 0.308 1515 Planarity : 0.003 0.027 1726 Dihedral : 4.799 48.010 1330 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 5.94 % Allowed : 29.23 % Favored : 64.84 % 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: 0.83 (0.26), residues: 1173 helix: 1.09 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 146 HIS 0.005 0.001 HIS D 112 PHE 0.019 0.002 PHE C 428 TYR 0.022 0.002 TYR C 130 ARG 0.005 0.000 ARG D 153 *********************** 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 403 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 337 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.7755 (tp30) cc_final: 0.7159 (tp30) REVERT: C 125 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.7829 (t80) REVERT: C 159 ASP cc_start: 0.7414 (t0) cc_final: 0.7040 (t0) REVERT: C 163 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: C 173 ARG cc_start: 0.8147 (mtt180) cc_final: 0.7842 (mtt180) REVERT: C 243 GLU cc_start: 0.7672 (tp30) cc_final: 0.7340 (tp30) REVERT: C 258 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7181 (mm-30) REVERT: C 262 LYS cc_start: 0.7437 (mmtm) cc_final: 0.7220 (mmtm) REVERT: C 279 MET cc_start: 0.6200 (mtm) cc_final: 0.5947 (mpp) REVERT: C 315 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 326 LYS cc_start: 0.7968 (tptp) cc_final: 0.7569 (tptp) REVERT: C 383 ARG cc_start: 0.5921 (mmm160) cc_final: 0.5631 (mmt180) REVERT: D 58 TYR cc_start: 0.7513 (t80) cc_final: 0.7309 (t80) REVERT: D 64 MET cc_start: 0.7303 (mtp) cc_final: 0.7015 (mtp) REVERT: D 78 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: D 83 GLU cc_start: 0.7665 (tp30) cc_final: 0.7331 (tp30) REVERT: D 88 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7292 (tppt) REVERT: D 94 LEU cc_start: 0.8094 (mm) cc_final: 0.7783 (mt) REVERT: D 107 GLN cc_start: 0.8436 (tp40) cc_final: 0.8213 (tp40) REVERT: D 124 MET cc_start: 0.6391 (tmm) cc_final: 0.6179 (tmm) REVERT: D 125 TYR cc_start: 0.8017 (t80) cc_final: 0.7609 (t80) REVERT: D 128 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7569 (mmm-85) REVERT: D 163 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7534 (mm-40) REVERT: D 167 ASP cc_start: 0.7507 (m-30) cc_final: 0.7213 (m-30) REVERT: D 191 MET cc_start: 0.7969 (mtt) cc_final: 0.7763 (mtt) REVERT: D 203 GLU cc_start: 0.7266 (mt-10) cc_final: 0.6665 (mp0) REVERT: D 218 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.7121 (pp30) REVERT: D 223 LYS cc_start: 0.8099 (tmtt) cc_final: 0.7708 (tmtt) REVERT: D 236 LYS cc_start: 0.7923 (tmmt) cc_final: 0.7634 (tmmt) REVERT: D 267 GLU cc_start: 0.7765 (tp30) cc_final: 0.7161 (tp30) REVERT: D 315 GLU cc_start: 0.7340 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 323 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6740 (tm-30) REVERT: D 367 LYS cc_start: 0.8269 (tptt) cc_final: 0.7750 (tptt) REVERT: D 416 MET cc_start: 0.6755 (OUTLIER) cc_final: 0.6373 (mmm) REVERT: D 434 GLN cc_start: 0.7488 (tm-30) cc_final: 0.7193 (tm-30) REVERT: D 442 THR cc_start: 0.7000 (OUTLIER) cc_final: 0.6467 (t) REVERT: D 457 LYS cc_start: 0.8396 (mmmt) cc_final: 0.7988 (mmmt) REVERT: K 27 TYR cc_start: 0.8473 (m-10) cc_final: 0.8163 (m-10) REVERT: K 105 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7829 (mm) REVERT: K 130 LEU cc_start: 0.7791 (mp) cc_final: 0.7474 (mp) REVERT: L 38 ARG cc_start: 0.7774 (mtm-85) cc_final: 0.7367 (mtm-85) REVERT: L 169 GLU cc_start: 0.7427 (pp20) cc_final: 0.7198 (pp20) outliers start: 66 outliers final: 38 residues processed: 362 average time/residue: 0.2352 time to fit residues: 114.1670 Evaluate side-chains 382 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 336 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 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 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 66 LEU Chi-restraints excluded: chain D residue 88 LYS Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 218 GLN 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 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 411 ILE 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 37 LEU 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 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 37 LEU Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 87 GLU 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 107 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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** C 435 HIS D 106 ASN D 381 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2340 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= 0.246 Angle : 0.625 18.687 13507 Z= 0.335 Chirality : 0.041 0.292 1515 Planarity : 0.003 0.027 1726 Dihedral : 4.493 50.390 1323 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.65 % Allowed : 30.40 % Favored : 62.95 % 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: 1.19 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 297 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 0.031 0.002 PHE C 377 TYR 0.017 0.002 TYR D 29 ARG 0.003 0.000 ARG D 153 *********************** 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 420 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 346 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 83 GLU cc_start: 0.7749 (tp30) cc_final: 0.7118 (tp30) REVERT: C 159 ASP cc_start: 0.7439 (t0) cc_final: 0.6572 (t0) REVERT: C 163 GLN cc_start: 0.7309 (OUTLIER) cc_final: 0.6478 (mp10) REVERT: C 173 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7652 (mtt180) REVERT: C 213 SER cc_start: 0.8425 (p) cc_final: 0.8124 (p) REVERT: C 315 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: C 326 LYS cc_start: 0.7943 (tptp) cc_final: 0.7534 (tptp) REVERT: C 383 ARG cc_start: 0.5854 (mmm160) cc_final: 0.5457 (mmt180) REVERT: C 395 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7021 (ttpt) REVERT: D 46 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7615 (mtm110) REVERT: D 52 LEU cc_start: 0.8613 (mt) cc_final: 0.8227 (mt) REVERT: D 58 TYR cc_start: 0.7547 (t80) cc_final: 0.7310 (t80) REVERT: D 64 MET cc_start: 0.7332 (mtp) cc_final: 0.7044 (mtp) REVERT: D 78 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: D 83 GLU cc_start: 0.7690 (tp30) cc_final: 0.7303 (tp30) REVERT: D 88 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7228 (tppt) REVERT: D 124 MET cc_start: 0.6450 (tmm) cc_final: 0.6152 (tmm) REVERT: D 125 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7593 (t80) REVERT: D 163 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7450 (mm-40) REVERT: D 167 ASP cc_start: 0.7504 (m-30) cc_final: 0.7169 (m-30) REVERT: D 218 GLN cc_start: 0.7449 (pp30) cc_final: 0.7147 (pp30) REVERT: D 223 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7668 (tmtt) REVERT: D 236 LYS cc_start: 0.8002 (tmmt) cc_final: 0.7745 (pttt) REVERT: D 267 GLU cc_start: 0.7779 (tp30) cc_final: 0.7186 (tp30) REVERT: D 315 GLU cc_start: 0.7323 (mm-30) cc_final: 0.7046 (mm-30) REVERT: D 323 GLU cc_start: 0.7001 (tm-30) cc_final: 0.6678 (tm-30) REVERT: D 367 LYS cc_start: 0.8272 (tptt) cc_final: 0.7795 (tptt) REVERT: D 416 MET cc_start: 0.6738 (OUTLIER) cc_final: 0.6373 (mmm) REVERT: D 434 GLN cc_start: 0.7475 (tm-30) cc_final: 0.7174 (tm-30) REVERT: D 442 THR cc_start: 0.6973 (OUTLIER) cc_final: 0.6424 (t) REVERT: D 457 LYS cc_start: 0.8376 (mmmt) cc_final: 0.7993 (mmmt) REVERT: K 27 TYR cc_start: 0.8477 (m-10) cc_final: 0.8161 (m-10) REVERT: K 104 ILE cc_start: 0.8551 (tt) cc_final: 0.8349 (tt) REVERT: K 122 GLU cc_start: 0.7065 (pm20) cc_final: 0.6684 (pm20) REVERT: L 38 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7479 (mtm-85) REVERT: L 84 LYS cc_start: 0.7837 (ttpp) cc_final: 0.7180 (ttpp) REVERT: L 122 GLU cc_start: 0.6976 (pm20) cc_final: 0.6659 (pm20) REVERT: L 129 GLN cc_start: 0.8026 (mm110) cc_final: 0.7725 (tp40) REVERT: L 169 GLU cc_start: 0.7434 (pp20) cc_final: 0.7197 (pp20) outliers start: 74 outliers final: 51 residues processed: 375 average time/residue: 0.2548 time to fit residues: 126.4110 Evaluate side-chains 399 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 341 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 222 GLN 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 355 PHE Chi-restraints excluded: chain C residue 395 LYS 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 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 164 THR 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 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 411 ILE 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 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 155 VAL 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 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 98 optimal weight: 0.2980 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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** C 434 GLN D 381 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.2556 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= 0.230 Angle : 0.626 18.188 13507 Z= 0.333 Chirality : 0.041 0.290 1515 Planarity : 0.003 0.027 1726 Dihedral : 4.464 52.636 1323 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 6.65 % Allowed : 30.94 % 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: 1.02 (0.26), residues: 1173 helix: 1.26 (0.18), residues: 876 sheet: None (None), residues: 0 loop : -0.99 (0.39), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP L 146 HIS 0.003 0.001 HIS C 112 PHE 0.044 0.002 PHE D 377 TYR 0.016 0.002 TYR D 29 ARG 0.006 0.000 ARG D 153 *********************** 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 419 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 345 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 43 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7606 (mm-30) REVERT: C 83 GLU cc_start: 0.7746 (tp30) cc_final: 0.7133 (tp30) REVERT: C 90 ARG cc_start: 0.8107 (ttt180) cc_final: 0.7839 (ttt180) REVERT: C 159 ASP cc_start: 0.7410 (t0) cc_final: 0.6518 (t0) REVERT: C 163 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6385 (mp10) REVERT: C 169 ILE cc_start: 0.8291 (tp) cc_final: 0.8053 (tp) REVERT: C 219 MET cc_start: 0.7008 (mmm) cc_final: 0.6366 (mmm) REVERT: C 262 LYS cc_start: 0.7610 (mmtm) cc_final: 0.7336 (mmtm) REVERT: C 315 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: C 326 LYS cc_start: 0.7929 (tptp) cc_final: 0.7503 (tptp) REVERT: C 382 SER cc_start: 0.7794 (t) cc_final: 0.7427 (p) REVERT: C 383 ARG cc_start: 0.5737 (mmm160) cc_final: 0.5410 (mmt180) REVERT: C 395 LYS cc_start: 0.7408 (OUTLIER) cc_final: 0.7070 (ttpt) REVERT: C 438 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7579 (mmm-85) REVERT: C 444 LYS cc_start: 0.7149 (mptt) cc_final: 0.6829 (mptt) REVERT: C 457 LYS cc_start: 0.8278 (mmmt) cc_final: 0.8030 (mmmt) REVERT: D 46 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7610 (mtm110) REVERT: D 52 LEU cc_start: 0.8677 (mt) cc_final: 0.8299 (mt) REVERT: D 58 TYR cc_start: 0.7595 (t80) cc_final: 0.7344 (t80) REVERT: D 64 MET cc_start: 0.7352 (mtp) cc_final: 0.7074 (mtp) REVERT: D 78 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7808 (ttm-80) REVERT: D 83 GLU cc_start: 0.7691 (tp30) cc_final: 0.7276 (tp30) REVERT: D 88 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7245 (tppt) REVERT: D 101 PHE cc_start: 0.8315 (t80) cc_final: 0.8111 (t80) REVERT: D 124 MET cc_start: 0.6454 (tmm) cc_final: 0.6092 (tmm) REVERT: D 125 TYR cc_start: 0.8018 (OUTLIER) cc_final: 0.7490 (t80) REVERT: D 149 ASP cc_start: 0.7229 (t0) cc_final: 0.6995 (t0) REVERT: D 163 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7484 (mm-40) REVERT: D 167 ASP cc_start: 0.7524 (m-30) cc_final: 0.7220 (m-30) REVERT: D 219 MET cc_start: 0.6754 (tmm) cc_final: 0.6401 (tmm) REVERT: D 223 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7704 (tmtt) REVERT: D 236 LYS cc_start: 0.8087 (tmmt) cc_final: 0.7648 (pttp) REVERT: D 267 GLU cc_start: 0.7774 (tp30) cc_final: 0.7175 (tp30) REVERT: D 279 MET cc_start: 0.6080 (mtm) cc_final: 0.5570 (ptt) REVERT: D 315 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6965 (mm-30) REVERT: D 323 GLU cc_start: 0.7031 (tm-30) cc_final: 0.6626 (tm-30) REVERT: D 367 LYS cc_start: 0.8275 (tptt) cc_final: 0.7721 (tptt) REVERT: D 416 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6366 (mmm) REVERT: D 434 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7191 (tm-30) REVERT: D 442 THR cc_start: 0.6924 (OUTLIER) cc_final: 0.6375 (t) REVERT: D 457 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7941 (mmmt) REVERT: K 27 TYR cc_start: 0.8480 (m-10) cc_final: 0.8221 (m-10) REVERT: K 90 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: K 146 TRP cc_start: 0.5547 (m-90) cc_final: 0.5228 (m-90) REVERT: L 38 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.7432 (mtm-85) REVERT: L 84 LYS cc_start: 0.7777 (ttpp) cc_final: 0.7175 (ttpp) REVERT: L 85 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7166 (tm-30) REVERT: L 122 GLU cc_start: 0.6947 (pm20) cc_final: 0.6616 (pm20) REVERT: L 129 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7589 (tp40) REVERT: L 169 GLU cc_start: 0.7424 (pp20) cc_final: 0.7160 (pp20) outliers start: 74 outliers final: 54 residues processed: 372 average time/residue: 0.2607 time to fit residues: 127.9372 Evaluate side-chains 404 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 341 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 275 THR 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 355 PHE Chi-restraints excluded: chain C residue 395 LYS Chi-restraints excluded: chain C residue 424 GLU Chi-restraints excluded: chain C residue 436 LEU 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 164 THR Chi-restraints excluded: chain D residue 222 GLN 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 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 411 ILE 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 90 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10067 Z= 0.288 Angle : 0.658 18.183 13507 Z= 0.351 Chirality : 0.042 0.290 1515 Planarity : 0.003 0.028 1726 Dihedral : 4.607 55.026 1323 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 7.37 % Allowed : 30.76 % Favored : 61.87 % 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: 0.86 (0.26), residues: 1173 helix: 1.17 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -1.13 (0.40), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP L 146 HIS 0.005 0.001 HIS D 112 PHE 0.024 0.002 PHE C 377 TYR 0.016 0.002 TYR D 29 ARG 0.005 0.000 ARG D 153 *********************** 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 426 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 344 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7591 (m-10) cc_final: 0.7294 (m-10) REVERT: C 83 GLU cc_start: 0.7761 (tp30) cc_final: 0.7119 (tp30) REVERT: C 90 ARG cc_start: 0.8135 (ttt180) cc_final: 0.7802 (ttt180) REVERT: C 125 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7821 (t80) REVERT: C 159 ASP cc_start: 0.7395 (t0) cc_final: 0.6584 (t0) REVERT: C 163 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: C 169 ILE cc_start: 0.8342 (tp) cc_final: 0.8128 (tt) REVERT: C 173 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7733 (mtt180) REVERT: C 179 ASP cc_start: 0.8133 (p0) cc_final: 0.7774 (p0) REVERT: C 218 GLN cc_start: 0.7711 (pp30) cc_final: 0.7355 (pp30) REVERT: C 219 MET cc_start: 0.6989 (mmm) cc_final: 0.6365 (mmm) REVERT: C 262 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7372 (mmtm) REVERT: C 269 ILE cc_start: 0.7223 (OUTLIER) cc_final: 0.6894 (pt) REVERT: C 315 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: C 326 LYS cc_start: 0.7924 (tptp) cc_final: 0.7517 (tptp) REVERT: C 382 SER cc_start: 0.7840 (t) cc_final: 0.7403 (p) REVERT: C 438 ARG cc_start: 0.7918 (mmt90) cc_final: 0.7638 (mmm-85) REVERT: C 457 LYS cc_start: 0.8333 (mmmt) cc_final: 0.8100 (mmmt) REVERT: D 46 ARG cc_start: 0.7878 (mtp180) cc_final: 0.7671 (mtm110) REVERT: D 58 TYR cc_start: 0.7658 (t80) cc_final: 0.7408 (t80) REVERT: D 64 MET cc_start: 0.7394 (mtp) cc_final: 0.7154 (mtp) REVERT: D 78 ARG cc_start: 0.8045 (ttm-80) cc_final: 0.7811 (ttm-80) REVERT: D 83 GLU cc_start: 0.7686 (tp30) cc_final: 0.7271 (tp30) REVERT: D 88 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7356 (tppt) REVERT: D 94 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7703 (mt) REVERT: D 124 MET cc_start: 0.6524 (tmm) cc_final: 0.6152 (tmm) REVERT: D 125 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7480 (t80) REVERT: D 149 ASP cc_start: 0.7267 (t0) cc_final: 0.6928 (t0) REVERT: D 163 GLN cc_start: 0.7876 (mm-40) cc_final: 0.7346 (mm-40) REVERT: D 167 ASP cc_start: 0.7522 (m-30) cc_final: 0.7225 (m-30) REVERT: D 219 MET cc_start: 0.6763 (tmm) cc_final: 0.6406 (tmm) REVERT: D 223 LYS cc_start: 0.8117 (tmtt) cc_final: 0.7703 (tmtt) REVERT: D 236 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7877 (ttpp) REVERT: D 267 GLU cc_start: 0.7832 (tp30) cc_final: 0.7193 (tp30) REVERT: D 315 GLU cc_start: 0.7337 (mm-30) cc_final: 0.7053 (mm-30) REVERT: D 323 GLU cc_start: 0.7069 (tm-30) cc_final: 0.6641 (tm-30) REVERT: D 367 LYS cc_start: 0.8309 (tptt) cc_final: 0.7724 (tptt) REVERT: D 416 MET cc_start: 0.6826 (OUTLIER) cc_final: 0.6454 (mmm) REVERT: D 434 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 442 THR cc_start: 0.6971 (OUTLIER) cc_final: 0.6432 (t) REVERT: D 457 LYS cc_start: 0.8316 (mmmt) cc_final: 0.7978 (mmmt) REVERT: K 27 TYR cc_start: 0.8474 (m-10) cc_final: 0.8237 (m-10) REVERT: K 90 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.7072 (mp0) REVERT: K 154 ASP cc_start: 0.7165 (OUTLIER) cc_final: 0.6887 (p0) REVERT: L 38 ARG cc_start: 0.7806 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: L 78 MET cc_start: 0.7837 (ttt) cc_final: 0.7461 (ttp) REVERT: L 85 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7208 (tm-30) REVERT: L 129 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7530 (tp40) REVERT: L 169 GLU cc_start: 0.7432 (pp20) cc_final: 0.7165 (pp20) outliers start: 82 outliers final: 58 residues processed: 376 average time/residue: 0.2486 time to fit residues: 124.4279 Evaluate side-chains 410 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 340 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 85 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 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN 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 269 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 275 THR 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 455 ILE 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 94 LEU 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 164 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 222 GLN 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 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 363 ASP Chi-restraints excluded: chain D residue 379 ASN Chi-restraints excluded: chain D residue 411 ILE 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 89 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 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 61 ILE Chi-restraints excluded: chain L residue 87 GLU Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 129 GLN 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 111 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 115 optimal weight: 0.2980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.0270 chunk 53 optimal weight: 0.9980 overall best weight: 0.3438 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10067 Z= 0.210 Angle : 0.643 17.696 13507 Z= 0.337 Chirality : 0.040 0.286 1515 Planarity : 0.003 0.028 1726 Dihedral : 4.387 55.140 1321 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 6.92 % Allowed : 31.83 % Favored : 61.24 % 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: 1.06 (0.26), residues: 1173 helix: 1.31 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -1.08 (0.40), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 146 HIS 0.003 0.001 HIS D 112 PHE 0.026 0.001 PHE D 377 TYR 0.016 0.001 TYR D 29 ARG 0.005 0.000 ARG D 153 *********************** 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 420 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 343 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7632 (m-10) cc_final: 0.7182 (m-10) REVERT: C 83 GLU cc_start: 0.7747 (tp30) cc_final: 0.7094 (tp30) REVERT: C 91 GLU cc_start: 0.7373 (pm20) cc_final: 0.7171 (pm20) REVERT: C 125 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7654 (t80) REVERT: C 159 ASP cc_start: 0.7385 (t0) cc_final: 0.6534 (t0) REVERT: C 163 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6511 (mp10) REVERT: C 173 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7581 (mtt90) REVERT: C 187 CYS cc_start: 0.6911 (OUTLIER) cc_final: 0.6262 (t) REVERT: C 218 GLN cc_start: 0.7685 (pp30) cc_final: 0.7307 (pp30) REVERT: C 219 MET cc_start: 0.6949 (mmm) cc_final: 0.6315 (mmm) REVERT: C 262 LYS cc_start: 0.7631 (mmtm) cc_final: 0.7327 (mmtm) REVERT: C 315 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: C 326 LYS cc_start: 0.7892 (tptp) cc_final: 0.7453 (tptp) REVERT: C 381 ASN cc_start: 0.7097 (t0) cc_final: 0.6874 (t0) REVERT: C 382 SER cc_start: 0.7878 (t) cc_final: 0.7318 (p) REVERT: C 430 ARG cc_start: 0.6372 (ttm170) cc_final: 0.5640 (ttm170) REVERT: C 438 ARG cc_start: 0.7887 (mmt90) cc_final: 0.7604 (mmm-85) REVERT: C 457 LYS cc_start: 0.8327 (mmmt) cc_final: 0.8105 (mmmt) REVERT: D 46 ARG cc_start: 0.7812 (mtp180) cc_final: 0.7578 (mtm110) REVERT: D 64 MET cc_start: 0.7370 (mtp) cc_final: 0.7163 (mtp) REVERT: D 78 ARG cc_start: 0.8026 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: D 83 GLU cc_start: 0.7654 (tp30) cc_final: 0.7239 (tp30) REVERT: D 88 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7245 (tppt) REVERT: D 94 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7618 (mt) REVERT: D 125 TYR cc_start: 0.8004 (OUTLIER) cc_final: 0.7682 (t80) REVERT: D 149 ASP cc_start: 0.7249 (t0) cc_final: 0.6848 (t0) REVERT: D 153 ARG cc_start: 0.8392 (mtt90) cc_final: 0.8073 (mtp85) REVERT: D 163 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7291 (mm-40) REVERT: D 167 ASP cc_start: 0.7505 (m-30) cc_final: 0.7187 (m-30) REVERT: D 219 MET cc_start: 0.6810 (tmm) cc_final: 0.6391 (tmm) REVERT: D 223 LYS cc_start: 0.8058 (tmtt) cc_final: 0.7679 (tmtt) REVERT: D 236 LYS cc_start: 0.8206 (tmmt) cc_final: 0.7740 (pttp) REVERT: D 262 LYS cc_start: 0.7264 (mmtm) cc_final: 0.6989 (mmtm) REVERT: D 267 GLU cc_start: 0.7775 (tp30) cc_final: 0.7179 (tp30) REVERT: D 279 MET cc_start: 0.6039 (mtm) cc_final: 0.5545 (ptt) REVERT: D 315 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6936 (mm-30) REVERT: D 323 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6554 (tm-30) REVERT: D 367 LYS cc_start: 0.8279 (tptt) cc_final: 0.7731 (tptt) REVERT: D 416 MET cc_start: 0.6774 (OUTLIER) cc_final: 0.6420 (mmm) REVERT: D 424 GLU cc_start: 0.7335 (tp30) cc_final: 0.6847 (tp30) REVERT: D 434 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7181 (tm-30) REVERT: D 442 THR cc_start: 0.6915 (OUTLIER) cc_final: 0.6367 (t) REVERT: D 457 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7933 (mmmt) REVERT: K 27 TYR cc_start: 0.8436 (m-10) cc_final: 0.8203 (m-10) REVERT: K 101 MET cc_start: 0.8256 (tpp) cc_final: 0.8043 (tpt) REVERT: K 154 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6726 (p0) REVERT: K 169 GLU cc_start: 0.7507 (pp20) cc_final: 0.7194 (pp20) REVERT: L 38 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: L 78 MET cc_start: 0.7808 (ttt) cc_final: 0.7574 (ttp) REVERT: L 85 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7048 (mm-30) REVERT: L 129 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7566 (tp40) outliers start: 77 outliers final: 52 residues processed: 372 average time/residue: 0.2596 time to fit residues: 129.1558 Evaluate side-chains 398 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 335 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET 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 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN 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 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 94 LEU 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 164 THR Chi-restraints excluded: chain D residue 222 GLN 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 301 LYS 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 411 ILE 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 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 37 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 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 71 optimal weight: 0.2980 chunk 46 optimal weight: 0.1980 chunk 69 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 78 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10067 Z= 0.200 Angle : 0.645 17.728 13507 Z= 0.337 Chirality : 0.040 0.284 1515 Planarity : 0.003 0.027 1726 Dihedral : 4.333 55.593 1321 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.94 % Allowed : 33.27 % Favored : 60.79 % 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: 1.19 (0.26), residues: 1173 helix: 1.42 (0.18), residues: 874 sheet: None (None), residues: 0 loop : -1.03 (0.40), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 146 HIS 0.005 0.001 HIS L 32 PHE 0.042 0.001 PHE D 377 TYR 0.016 0.001 TYR D 29 ARG 0.005 0.000 ARG D 153 *********************** 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 401 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 335 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7586 (m-10) cc_final: 0.7176 (m-10) REVERT: C 83 GLU cc_start: 0.7709 (tp30) cc_final: 0.7063 (tp30) REVERT: C 91 GLU cc_start: 0.7266 (pm20) cc_final: 0.7053 (pm20) REVERT: C 125 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7588 (t80) REVERT: C 173 ARG cc_start: 0.7930 (mtt180) cc_final: 0.7632 (mtt180) REVERT: C 187 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6271 (t) REVERT: C 218 GLN cc_start: 0.7663 (pp30) cc_final: 0.7312 (pp30) REVERT: C 219 MET cc_start: 0.6911 (mmm) cc_final: 0.6318 (mmm) REVERT: C 224 PHE cc_start: 0.7271 (m-10) cc_final: 0.7063 (m-80) REVERT: C 262 LYS cc_start: 0.7620 (mmtm) cc_final: 0.7333 (mmtm) REVERT: C 315 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6814 (mp0) REVERT: C 326 LYS cc_start: 0.7878 (tptp) cc_final: 0.7441 (tptp) REVERT: C 382 SER cc_start: 0.7935 (t) cc_final: 0.7525 (m) REVERT: C 430 ARG cc_start: 0.6215 (ttm170) cc_final: 0.5705 (ttm170) REVERT: C 438 ARG cc_start: 0.7856 (mmt90) cc_final: 0.7548 (mmm-85) REVERT: C 457 LYS cc_start: 0.8316 (mmmt) cc_final: 0.8087 (mmmt) REVERT: D 46 ARG cc_start: 0.7788 (mtp180) cc_final: 0.7571 (mtm110) REVERT: D 64 MET cc_start: 0.7388 (mtp) cc_final: 0.7163 (mtp) REVERT: D 78 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7806 (ttm-80) REVERT: D 83 GLU cc_start: 0.7657 (tp30) cc_final: 0.7224 (tp30) REVERT: D 88 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7261 (tppt) REVERT: D 94 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7508 (mt) REVERT: D 125 TYR cc_start: 0.7966 (OUTLIER) cc_final: 0.7620 (t80) REVERT: D 149 ASP cc_start: 0.7243 (t0) cc_final: 0.6854 (t0) REVERT: D 153 ARG cc_start: 0.8345 (mtt90) cc_final: 0.8070 (mtp85) REVERT: D 163 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7177 (mm-40) REVERT: D 167 ASP cc_start: 0.7512 (m-30) cc_final: 0.7192 (m-30) REVERT: D 219 MET cc_start: 0.6803 (tmm) cc_final: 0.6368 (tmm) REVERT: D 223 LYS cc_start: 0.8026 (tmtt) cc_final: 0.7680 (tmtt) REVERT: D 236 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7750 (pttp) REVERT: D 240 ARG cc_start: 0.7943 (tpp-160) cc_final: 0.7595 (tpp-160) REVERT: D 262 LYS cc_start: 0.7232 (mmtm) cc_final: 0.6984 (mmtm) REVERT: D 267 GLU cc_start: 0.7763 (tp30) cc_final: 0.7181 (tp30) REVERT: D 279 MET cc_start: 0.6002 (mtm) cc_final: 0.5464 (ptt) REVERT: D 315 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6930 (mm-30) REVERT: D 323 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6495 (tm-30) REVERT: D 330 SER cc_start: 0.8339 (p) cc_final: 0.8137 (p) REVERT: D 367 LYS cc_start: 0.8269 (tptt) cc_final: 0.7670 (tptt) REVERT: D 416 MET cc_start: 0.6763 (OUTLIER) cc_final: 0.6416 (mmm) REVERT: D 424 GLU cc_start: 0.7310 (tp30) cc_final: 0.6820 (tp30) REVERT: D 434 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7164 (tm-30) REVERT: D 457 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7914 (mmmt) REVERT: K 27 TYR cc_start: 0.8430 (m-10) cc_final: 0.8163 (m-10) REVERT: K 101 MET cc_start: 0.8284 (tpp) cc_final: 0.7976 (tpt) REVERT: K 154 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6711 (p0) REVERT: L 38 ARG cc_start: 0.7700 (mtm-85) cc_final: 0.7346 (mtm-85) REVERT: L 78 MET cc_start: 0.7824 (ttt) cc_final: 0.7561 (ttp) REVERT: L 101 MET cc_start: 0.8367 (tpp) cc_final: 0.8151 (tpt) REVERT: L 129 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7443 (tp40) outliers start: 66 outliers final: 51 residues processed: 358 average time/residue: 0.2527 time to fit residues: 120.2636 Evaluate side-chains 396 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 336 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 125 TYR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 269 ILE Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 287 MET 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 94 LEU 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 164 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 222 GLN 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 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 411 ILE 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 37 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 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 110 optimal weight: 0.4980 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.4980 chunk 113 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 381 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10067 Z= 0.238 Angle : 0.679 17.715 13507 Z= 0.353 Chirality : 0.041 0.284 1515 Planarity : 0.003 0.028 1726 Dihedral : 4.394 56.530 1321 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 5.76 % Allowed : 32.91 % Favored : 61.33 % 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: 1.16 (0.26), residues: 1173 helix: 1.38 (0.18), residues: 875 sheet: None (None), residues: 0 loop : -0.98 (0.40), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 146 HIS 0.004 0.001 HIS L 32 PHE 0.030 0.001 PHE D 377 TYR 0.020 0.002 TYR C 130 ARG 0.004 0.000 ARG D 153 *********************** 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 400 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 336 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7566 (m-10) cc_final: 0.7113 (m-10) REVERT: C 83 GLU cc_start: 0.7731 (tp30) cc_final: 0.7105 (tp30) REVERT: C 91 GLU cc_start: 0.7385 (pm20) cc_final: 0.7138 (pm20) REVERT: C 187 CYS cc_start: 0.6858 (OUTLIER) cc_final: 0.6201 (t) REVERT: C 219 MET cc_start: 0.6919 (mmm) cc_final: 0.6445 (mmm) REVERT: C 262 LYS cc_start: 0.7657 (mmtm) cc_final: 0.7354 (mmtm) REVERT: C 269 ILE cc_start: 0.7288 (pp) cc_final: 0.6985 (pt) REVERT: C 315 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: C 326 LYS cc_start: 0.7900 (tptp) cc_final: 0.7454 (tptp) REVERT: C 367 LYS cc_start: 0.8436 (tptt) cc_final: 0.7708 (tptt) REVERT: C 382 SER cc_start: 0.8014 (t) cc_final: 0.7617 (m) REVERT: C 430 ARG cc_start: 0.6304 (ttm170) cc_final: 0.5357 (ttp-170) REVERT: C 438 ARG cc_start: 0.7862 (mmt90) cc_final: 0.7420 (mmt90) REVERT: C 457 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8094 (mmmt) REVERT: D 46 ARG cc_start: 0.7841 (mtp180) cc_final: 0.7601 (mtm110) REVERT: D 64 MET cc_start: 0.7371 (mtp) cc_final: 0.7114 (mtp) REVERT: D 78 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7812 (ttm-80) REVERT: D 83 GLU cc_start: 0.7663 (tp30) cc_final: 0.7208 (tp30) REVERT: D 88 LYS cc_start: 0.7943 (OUTLIER) cc_final: 0.7288 (tppt) REVERT: D 94 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7518 (mt) REVERT: D 125 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7613 (t80) REVERT: D 149 ASP cc_start: 0.7255 (t0) cc_final: 0.6822 (t0) REVERT: D 153 ARG cc_start: 0.8377 (mtt90) cc_final: 0.8167 (mtp85) REVERT: D 163 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7166 (mm-40) REVERT: D 167 ASP cc_start: 0.7513 (m-30) cc_final: 0.7199 (m-30) REVERT: D 219 MET cc_start: 0.6810 (tmm) cc_final: 0.6381 (tmm) REVERT: D 223 LYS cc_start: 0.8017 (tmtt) cc_final: 0.7672 (tmtt) REVERT: D 236 LYS cc_start: 0.8235 (tmmt) cc_final: 0.7948 (ttpp) REVERT: D 240 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7568 (tpp-160) REVERT: D 262 LYS cc_start: 0.7241 (mmtm) cc_final: 0.6977 (mmtm) REVERT: D 267 GLU cc_start: 0.7758 (tp30) cc_final: 0.7212 (tp30) REVERT: D 279 MET cc_start: 0.6005 (mtm) cc_final: 0.5494 (ptt) REVERT: D 315 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6935 (mm-30) REVERT: D 323 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6494 (tm-30) REVERT: D 367 LYS cc_start: 0.8285 (tptt) cc_final: 0.7703 (tptt) REVERT: D 416 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6199 (mmm) REVERT: D 434 GLN cc_start: 0.7448 (tm-30) cc_final: 0.7157 (tm-30) REVERT: D 442 THR cc_start: 0.6845 (OUTLIER) cc_final: 0.6304 (t) REVERT: D 457 LYS cc_start: 0.8309 (mmmt) cc_final: 0.7936 (mmmt) REVERT: K 27 TYR cc_start: 0.8443 (m-10) cc_final: 0.8168 (m-10) REVERT: K 101 MET cc_start: 0.8252 (tpp) cc_final: 0.8035 (tpt) REVERT: K 129 GLN cc_start: 0.7524 (tp40) cc_final: 0.7120 (tt0) REVERT: K 154 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6685 (p0) REVERT: L 38 ARG cc_start: 0.7736 (mtm-85) cc_final: 0.7467 (mtm-85) REVERT: L 78 MET cc_start: 0.7793 (ttt) cc_final: 0.7558 (ttp) REVERT: L 129 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7288 (tp40) REVERT: L 169 GLU cc_start: 0.7462 (pp20) cc_final: 0.7182 (pp20) outliers start: 64 outliers final: 53 residues processed: 364 average time/residue: 0.2617 time to fit residues: 125.2793 Evaluate side-chains 398 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 336 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 187 CYS 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 287 MET 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 94 LEU 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 164 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 222 GLN 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 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 411 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.1980 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.0980 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 0.0470 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10067 Z= 0.214 Angle : 0.682 17.546 13507 Z= 0.353 Chirality : 0.041 0.284 1515 Planarity : 0.003 0.030 1726 Dihedral : 4.353 56.528 1321 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.94 % Allowed : 32.82 % Favored : 61.24 % 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: 1.20 (0.26), residues: 1173 helix: 1.43 (0.18), residues: 875 sheet: None (None), residues: 0 loop : -1.04 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 146 HIS 0.003 0.001 HIS L 32 PHE 0.041 0.001 PHE C 377 TYR 0.021 0.002 TYR C 130 ARG 0.005 0.000 ARG C 266 ********************** 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 398 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 332 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 21 PHE cc_start: 0.7518 (m-10) cc_final: 0.7118 (m-10) REVERT: C 78 ARG cc_start: 0.7954 (ttm-80) cc_final: 0.7711 (ttm-80) REVERT: C 83 GLU cc_start: 0.7733 (tp30) cc_final: 0.7100 (tp30) REVERT: C 91 GLU cc_start: 0.7349 (pm20) cc_final: 0.7100 (pm20) REVERT: C 173 ARG cc_start: 0.8097 (mtt180) cc_final: 0.7883 (mtt180) REVERT: C 187 CYS cc_start: 0.6883 (OUTLIER) cc_final: 0.6198 (t) REVERT: C 219 MET cc_start: 0.6917 (mmm) cc_final: 0.6406 (mmm) REVERT: C 262 LYS cc_start: 0.7648 (mmtm) cc_final: 0.7341 (mmtm) REVERT: C 269 ILE cc_start: 0.7321 (pp) cc_final: 0.7002 (pt) REVERT: C 315 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: C 326 LYS cc_start: 0.7876 (tptp) cc_final: 0.7449 (tptp) REVERT: C 367 LYS cc_start: 0.8432 (tptt) cc_final: 0.7680 (tptt) REVERT: C 430 ARG cc_start: 0.6304 (ttm170) cc_final: 0.5811 (ttm170) REVERT: C 438 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7442 (mmt90) REVERT: C 457 LYS cc_start: 0.8314 (mmmt) cc_final: 0.8065 (mmmt) REVERT: D 64 MET cc_start: 0.7311 (mtp) cc_final: 0.7083 (mtp) REVERT: D 78 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7801 (ttm-80) REVERT: D 83 GLU cc_start: 0.7655 (tp30) cc_final: 0.7249 (tp30) REVERT: D 88 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7226 (tppt) REVERT: D 94 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7503 (mt) REVERT: D 125 TYR cc_start: 0.7874 (OUTLIER) cc_final: 0.7564 (t80) REVERT: D 149 ASP cc_start: 0.7253 (t0) cc_final: 0.6798 (t0) REVERT: D 153 ARG cc_start: 0.8322 (mtt90) cc_final: 0.8074 (mtp85) REVERT: D 163 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7131 (mm-40) REVERT: D 167 ASP cc_start: 0.7516 (m-30) cc_final: 0.7199 (m-30) REVERT: D 219 MET cc_start: 0.6786 (tmm) cc_final: 0.6359 (tmm) REVERT: D 223 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7655 (tmtt) REVERT: D 236 LYS cc_start: 0.8227 (tmmt) cc_final: 0.7932 (ttpp) REVERT: D 240 ARG cc_start: 0.7933 (tpp-160) cc_final: 0.7569 (tpp-160) REVERT: D 262 LYS cc_start: 0.7256 (mmtm) cc_final: 0.6964 (mmtm) REVERT: D 267 GLU cc_start: 0.7769 (tp30) cc_final: 0.7199 (tp30) REVERT: D 315 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6911 (mm-30) REVERT: D 323 GLU cc_start: 0.6976 (tm-30) cc_final: 0.6494 (tm-30) REVERT: D 367 LYS cc_start: 0.8283 (tptt) cc_final: 0.7699 (tptt) REVERT: D 381 ASN cc_start: 0.7475 (t0) cc_final: 0.7186 (t0) REVERT: D 416 MET cc_start: 0.6729 (OUTLIER) cc_final: 0.6401 (mmm) REVERT: D 425 LYS cc_start: 0.6928 (mtpt) cc_final: 0.6670 (pttp) REVERT: D 434 GLN cc_start: 0.7445 (tm-30) cc_final: 0.6553 (tm-30) REVERT: D 438 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7395 (mmt90) REVERT: D 457 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7933 (mmmt) REVERT: K 27 TYR cc_start: 0.8422 (m-10) cc_final: 0.8145 (m-10) REVERT: K 101 MET cc_start: 0.8269 (tpp) cc_final: 0.7980 (tpt) REVERT: K 129 GLN cc_start: 0.7496 (tp40) cc_final: 0.7084 (tt0) REVERT: K 154 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6697 (p0) REVERT: L 122 GLU cc_start: 0.7098 (pm20) cc_final: 0.6780 (pm20) REVERT: L 129 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7340 (tp40) REVERT: L 169 GLU cc_start: 0.7455 (pp20) cc_final: 0.7165 (pp20) outliers start: 66 outliers final: 50 residues processed: 361 average time/residue: 0.2556 time to fit residues: 121.9490 Evaluate side-chains 389 residues out of total 1112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 331 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 MET Chi-restraints excluded: chain C residue 29 TYR Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 187 CYS Chi-restraints excluded: chain C residue 204 ASP Chi-restraints excluded: chain C residue 222 GLN Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain C residue 305 ARG 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 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 94 LEU 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 164 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 222 GLN 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 345 LEU Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain D residue 411 ILE 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 D residue 477 MET Chi-restraints excluded: chain K residue 54 LEU 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 37 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 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 87 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 0.1980 chunk 17 optimal weight: 0.4980 chunk 83 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 68 optimal weight: 0.0980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 150 GLN ** C 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.141703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127670 restraints weight = 18677.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131296 restraints weight = 8939.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.133623 restraints weight = 5086.130| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10067 Z= 0.220 Angle : 0.692 17.492 13507 Z= 0.358 Chirality : 0.040 0.282 1515 Planarity : 0.003 0.027 1726 Dihedral : 4.337 56.083 1321 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 5.40 % Allowed : 33.45 % 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: 1.22 (0.26), residues: 1173 helix: 1.45 (0.18), residues: 874 sheet: None (None), residues: 0 loop : -1.02 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 34 HIS 0.003 0.001 HIS L 32 PHE 0.035 0.001 PHE C 377 TYR 0.022 0.002 TYR C 130 ARG 0.009 0.000 ARG D 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3121.43 seconds wall clock time: 55 minutes 54.10 seconds (3354.10 seconds total)