Starting phenix.real_space_refine on Sun Jul 5 15:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.map" model { file = "/net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otq_13065/07_2026/7otq_13065.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 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: 6 Type Number sf(0) Gaussians P 297 5.49 5 S 27 5.16 5 C 9024 2.51 5 N 2900 2.21 5 O 3527 1.98 5 H 13365 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29140 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 7359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 459, 7359 Classifications: {'peptide': 459} Link IDs: {'PTRANS': 13, 'TRANS': 445} Chain: "A" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1642 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1642 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1519 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1639 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1279 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1674 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 1474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1474 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 4709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 4709 Classifications: {'DNA': 149} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 148} Chain: "J" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 4744 Classifications: {'DNA': 149} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 148} Time building chain proxies: 4.85, per 1000 atoms: 0.17 Number of scatterers: 29140 At special positions: 0 Unit cell: (151.603, 98.9184, 124.723, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 27 16.00 P 297 15.00 O 3527 8.00 N 2900 7.00 C 9024 6.00 H 13365 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.74 Conformation dependent library (CDL) restraints added in 768.3 milliseconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2274 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 67.6% alpha, 5.8% beta 132 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 5.75 Creating SS restraints... Processing helix chain 'K' and resid 48 through 63 removed outlier: 4.615A pdb=" N GLU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 106 through 118 removed outlier: 3.692A pdb=" N PHE K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 140 Processing helix chain 'K' and resid 152 through 159 Processing helix chain 'K' and resid 159 through 166 removed outlier: 3.857A pdb=" N LEU K 163 " --> pdb=" O ASP K 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 176 through 181 Processing helix chain 'K' and resid 184 through 191 Processing helix chain 'K' and resid 209 through 221 removed outlier: 3.635A pdb=" N LEU K 213 " --> pdb=" O SER K 209 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL K 220 " --> pdb=" O LEU K 216 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 230 removed outlier: 6.592A pdb=" N LYS K 227 " --> pdb=" O ASP K 223 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N GLU K 228 " --> pdb=" O LEU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 231 through 237 removed outlier: 3.535A pdb=" N GLN K 235 " --> pdb=" O GLY K 231 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 241 Processing helix chain 'K' and resid 242 through 255 removed outlier: 5.444A pdb=" N SER K 248 " --> pdb=" O SER K 244 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU K 249 " --> pdb=" O GLU K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 262 through 267 Processing helix chain 'K' and resid 283 through 295 Processing helix chain 'K' and resid 299 through 304 Processing helix chain 'K' and resid 313 through 324 Processing helix chain 'K' and resid 325 through 328 Processing helix chain 'K' and resid 339 through 346 removed outlier: 3.666A pdb=" N THR K 343 " --> pdb=" O GLY K 339 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER K 346 " --> pdb=" O LEU K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 346 through 362 removed outlier: 4.166A pdb=" N LYS K 354 " --> pdb=" O HIS K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 387 Processing helix chain 'K' and resid 398 through 410 Processing helix chain 'K' and resid 421 through 425 Processing helix chain 'K' and resid 444 through 453 removed outlier: 3.580A pdb=" N ASP K 448 " --> pdb=" O ASN K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 495 removed outlier: 3.570A pdb=" N ILE K 478 " --> pdb=" O THR K 474 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET K 492 " --> pdb=" O GLN K 488 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ILE K 493 " --> pdb=" O LEU K 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.787A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.688A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 48 through 76 removed outlier: 4.179A pdb=" N GLU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.647A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.757A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 88 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.658A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.934A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.632A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.549A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.726A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.560A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.374A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 97 Processing helix chain 'H' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'K' and resid 123 through 125 removed outlier: 6.471A pdb=" N VAL K 124 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N PHE K 98 " --> pdb=" O LEU K 149 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N THR K 151 " --> pdb=" O PHE K 98 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE K 100 " --> pdb=" O THR K 151 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU K 171 " --> pdb=" O LEU K 199 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU K 201 " --> pdb=" O LEU K 171 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL K 173 " --> pdb=" O LEU K 201 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS K 67 " --> pdb=" O SER K 198 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ILE K 68 " --> pdb=" O LEU K 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 273 through 280 removed outlier: 5.917A pdb=" N THR K 274 " --> pdb=" O VAL K 466 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ARG K 468 " --> pdb=" O THR K 274 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL K 276 " --> pdb=" O ARG K 468 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE K 470 " --> pdb=" O VAL K 276 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE K 278 " --> pdb=" O ILE K 470 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU K 367 " --> pdb=" O ILE K 437 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLU K 391 " --> pdb=" O LEU K 418 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N SER K 420 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL K 393 " --> pdb=" O SER K 420 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.921A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.477A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.674A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.937A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.862A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 77 through 78 569 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 328 hydrogen bonds 656 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 7.50 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 13357 1.03 - 1.22: 76 1.22 - 1.42: 7349 1.42 - 1.61: 9207 1.61 - 1.81: 46 Bond restraints: 30035 Sorted by residual: bond pdb=" C1' DT J -73 " pdb=" N1 DT J -73 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.67e+01 bond pdb=" C1' DT I -6 " pdb=" N1 DT I -6 " ideal model delta sigma weight residual 1.468 1.521 -0.053 1.40e-02 5.10e+03 1.45e+01 bond pdb=" C3' DA J -72 " pdb=" C2' DA J -72 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.43e+01 bond pdb=" C3' DT J -57 " pdb=" C2' DT J -57 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.41e+01 bond pdb=" C1' DT J -32 " pdb=" N1 DT J -32 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.39e+01 ... (remaining 30030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 51456 1.64 - 3.27: 2609 3.27 - 4.91: 298 4.91 - 6.55: 49 6.55 - 8.18: 3 Bond angle restraints: 54415 Sorted by residual: angle pdb=" O4' DC I 66 " pdb=" C1' DC I 66 " pdb=" N1 DC I 66 " ideal model delta sigma weight residual 108.00 113.30 -5.30 7.00e-01 2.04e+00 5.73e+01 angle pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " pdb=" N9 DA I 73 " ideal model delta sigma weight residual 108.00 113.00 -5.00 7.00e-01 2.04e+00 5.09e+01 angle pdb=" O4' DA I 63 " pdb=" C4' DA I 63 " pdb=" C3' DA I 63 " ideal model delta sigma weight residual 106.00 102.25 3.75 6.00e-01 2.78e+00 3.92e+01 angle pdb=" O4' DA J -30 " pdb=" C4' DA J -30 " pdb=" C3' DA J -30 " ideal model delta sigma weight residual 106.00 102.46 3.54 6.00e-01 2.78e+00 3.48e+01 angle pdb=" C4' DC I -18 " pdb=" O4' DC I -18 " pdb=" C1' DC I -18 " ideal model delta sigma weight residual 110.10 104.43 5.67 1.00e+00 1.00e+00 3.22e+01 ... (remaining 54410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.77: 11252 35.77 - 71.55: 1526 71.55 - 107.32: 57 107.32 - 143.10: 0 143.10 - 178.87: 1 Dihedral angle restraints: 12836 sinusoidal: 8806 harmonic: 4030 Sorted by residual: dihedral pdb=" CA VAL K 170 " pdb=" C VAL K 170 " pdb=" N LEU K 171 " pdb=" CA LEU K 171 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ALA K 306 " pdb=" C ALA K 306 " pdb=" N LYS K 307 " pdb=" CA LYS K 307 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA THR K 152 " pdb=" C THR K 152 " pdb=" N TYR K 153 " pdb=" CA TYR K 153 " ideal model delta harmonic sigma weight residual -180.00 -151.91 -28.09 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 12833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2023 0.056 - 0.111: 396 0.111 - 0.167: 170 0.167 - 0.223: 98 0.223 - 0.278: 13 Chirality restraints: 2700 Sorted by residual: chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.45 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' DC I 7 " pdb=" C4' DC I 7 " pdb=" O3' DC I 7 " pdb=" C2' DC I 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' DC I 35 " pdb=" C4' DC I 35 " pdb=" O3' DC I 35 " pdb=" C2' DC I 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.48 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2697 not shown) Planarity restraints: 3390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 454 " -0.139 9.50e-02 1.11e+02 7.34e-02 7.50e+01 pdb=" NE ARG K 454 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG K 454 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG K 454 " 0.102 2.00e-02 2.50e+03 pdb=" NH2 ARG K 454 " -0.057 2.00e-02 2.50e+03 pdb="HH11 ARG K 454 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG K 454 " -0.106 2.00e-02 2.50e+03 pdb="HH21 ARG K 454 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG K 454 " 0.056 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 17 " -0.312 9.50e-02 1.11e+02 1.16e-01 7.10e+01 pdb=" NE ARG B 17 " -0.047 2.00e-02 2.50e+03 pdb=" CZ ARG B 17 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG B 17 " 0.042 2.00e-02 2.50e+03 pdb=" NH2 ARG B 17 " 0.092 2.00e-02 2.50e+03 pdb="HH11 ARG B 17 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG B 17 " -0.029 2.00e-02 2.50e+03 pdb="HH21 ARG B 17 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG B 17 " -0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 40 " -0.374 9.50e-02 1.11e+02 1.32e-01 5.99e+01 pdb=" NE ARG B 40 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 40 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG B 40 " 0.096 2.00e-02 2.50e+03 pdb=" NH2 ARG B 40 " 0.012 2.00e-02 2.50e+03 pdb="HH11 ARG B 40 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B 40 " -0.084 2.00e-02 2.50e+03 pdb="HH21 ARG B 40 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B 40 " -0.012 2.00e-02 2.50e+03 ... (remaining 3387 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 1087 2.14 - 2.75: 50382 2.75 - 3.37: 84562 3.37 - 3.98: 110204 3.98 - 4.60: 167694 Nonbonded interactions: 413929 Sorted by model distance: nonbonded pdb=" HZ1 LYS D 28 " pdb=" OP1 DG J 51 " model vdw 1.524 2.450 nonbonded pdb=" HH TYR K 289 " pdb=" OE1 GLU K 304 " model vdw 1.545 2.450 nonbonded pdb=" OE1 GLN K 450 " pdb="HH21 ARG K 454 " model vdw 1.581 2.450 nonbonded pdb="HH22 ARG E 116 " pdb=" OD2 ASP E 123 " model vdw 1.599 2.450 nonbonded pdb=" O GLY K 70 " pdb="HH11 ARG K 260 " model vdw 1.606 2.450 ... (remaining 413924 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.390 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 32.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.006 0.057 16670 Z= 0.511 Angle : 0.875 8.183 23791 Z= 0.725 Chirality : 0.065 0.278 2700 Planarity : 0.012 0.144 1988 Dihedral : 24.903 178.871 6990 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.10 % Favored : 95.48 % Rotamer: Outliers : 1.26 % Allowed : 4.95 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.22), residues: 1196 helix: -0.85 (0.16), residues: 761 sheet: -0.35 (0.81), residues: 49 loop : -0.89 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.003 ARG E 116 TYR 0.043 0.006 TYR K 237 PHE 0.016 0.003 PHE K 369 TRP 0.021 0.006 TRP K 168 HIS 0.011 0.003 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.51 (16670) covalent geometry : angle 0.87488 / 0.73 (23791) hydrogen bonds : bond 0.20980 / 13.98 ( 897) hydrogen bonds : angle 8.60311 / 5.99 ( 2330) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 501 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 72 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.5094 (tp30) REVERT: K 100 ILE cc_start: 0.9610 (mt) cc_final: 0.9406 (tp) REVERT: K 110 TRP cc_start: 0.9739 (t-100) cc_final: 0.9500 (t-100) REVERT: K 194 SER cc_start: 0.9397 (t) cc_final: 0.9156 (p) REVERT: K 372 MET cc_start: 0.8868 (mtm) cc_final: 0.8547 (pmm) REVERT: A 60 LEU cc_start: 0.8761 (mt) cc_final: 0.8042 (mt) REVERT: A 63 ARG cc_start: 0.9287 (mmt180) cc_final: 0.9054 (mmm-85) REVERT: A 67 PHE cc_start: 0.9629 (t80) cc_final: 0.9164 (t80) REVERT: A 84 PHE cc_start: 0.9386 (m-80) cc_final: 0.8908 (m-80) REVERT: A 103 LEU cc_start: 0.9835 (tp) cc_final: 0.9624 (mt) REVERT: A 105 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9327 (mm-30) REVERT: A 108 ASN cc_start: 0.9613 (t0) cc_final: 0.9249 (t0) REVERT: A 119 ILE cc_start: 0.9709 (pt) cc_final: 0.9171 (tp) REVERT: A 120 MET cc_start: 0.7712 (mtm) cc_final: 0.7130 (mpp) REVERT: A 123 ASP cc_start: 0.9633 (m-30) cc_final: 0.9377 (m-30) REVERT: A 125 GLN cc_start: 0.9733 (mt0) cc_final: 0.9477 (mm110) REVERT: A 129 ARG cc_start: 0.9493 (tpt90) cc_final: 0.9258 (tpt90) REVERT: B 64 ASN cc_start: 0.9516 (m-40) cc_final: 0.9218 (t0) REVERT: B 72 TYR cc_start: 0.9261 (m-80) cc_final: 0.8886 (m-80) REVERT: B 74 GLU cc_start: 0.9751 (tt0) cc_final: 0.9432 (tp30) REVERT: C 90 ASP cc_start: 0.9107 (t0) cc_final: 0.8888 (t0) REVERT: C 92 GLU cc_start: 0.9657 (pm20) cc_final: 0.9395 (tt0) REVERT: D 45 VAL cc_start: 0.9276 (m) cc_final: 0.8934 (p) REVERT: D 59 MET cc_start: 0.9782 (mmm) cc_final: 0.9455 (mmp) REVERT: D 65 ASP cc_start: 0.9503 (t70) cc_final: 0.9026 (t0) REVERT: D 79 HIS cc_start: 0.9702 (t70) cc_final: 0.9478 (t-90) REVERT: E 64 LYS cc_start: 0.9648 (mtmm) cc_final: 0.9373 (mtmm) REVERT: E 81 ASP cc_start: 0.9554 (m-30) cc_final: 0.9211 (p0) REVERT: F 62 LEU cc_start: 0.9691 (mt) cc_final: 0.9469 (mt) REVERT: F 68 ASP cc_start: 0.9477 (m-30) cc_final: 0.9011 (t0) REVERT: F 72 TYR cc_start: 0.9469 (m-80) cc_final: 0.9176 (m-80) REVERT: F 77 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9305 (mmmm) REVERT: G 25 PHE cc_start: 0.9260 (m-80) cc_final: 0.8880 (m-10) REVERT: G 64 GLU cc_start: 0.9561 (tt0) cc_final: 0.9266 (pt0) REVERT: G 81 ARG cc_start: 0.9433 (tpt170) cc_final: 0.9159 (tpt170) REVERT: G 84 GLN cc_start: 0.9740 (tp40) cc_final: 0.9539 (tp-100) REVERT: G 110 ASN cc_start: 0.9645 (t0) cc_final: 0.9389 (t0) REVERT: G 112 GLN cc_start: 0.8356 (mp10) cc_final: 0.7873 (mp10) REVERT: H 65 ASP cc_start: 0.9593 (t0) cc_final: 0.9217 (t70) REVERT: H 69 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8768 (mmm-85) REVERT: H 79 HIS cc_start: 0.9748 (t-90) cc_final: 0.9544 (t-90) REVERT: H 86 ILE cc_start: 0.9337 (mm) cc_final: 0.8951 (tp) REVERT: H 96 ARG cc_start: 0.9661 (mmm-85) cc_final: 0.9322 (tpp80) REVERT: H 110 GLU cc_start: 0.9543 (tp30) cc_final: 0.9169 (mm-30) outliers start: 13 outliers final: 7 residues processed: 511 average time/residue: 0.3588 time to fit residues: 249.3581 Evaluate side-chains 437 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 429 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.044109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.034447 restraints weight = 308767.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.036486 restraints weight = 113688.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.037732 restraints weight = 57230.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.038505 restraints weight = 34868.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.039059 restraints weight = 24901.975| |-----------------------------------------------------------------------------| r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 16670 Z= 0.242 Angle : 0.828 9.602 23791 Z= 0.512 Chirality : 0.050 0.240 2700 Planarity : 0.009 0.176 1988 Dihedral : 28.282 174.382 4597 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.09 % Favored : 96.66 % Rotamer: Outliers : 0.10 % Allowed : 1.94 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.23), residues: 1196 helix: 0.39 (0.17), residues: 776 sheet: -0.80 (0.64), residues: 68 loop : -0.93 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.040 0.001 ARG A 42 TYR 0.015 0.002 TYR K 360 PHE 0.028 0.002 PHE K 417 TRP 0.006 0.001 TRP K 168 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.24 (16670) covalent geometry : angle 0.82795 / 0.51 (23791) hydrogen bonds : bond 0.09837 / 6.50 ( 897) hydrogen bonds : angle 4.92021 / 3.50 ( 2330) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 194 SER cc_start: 0.9393 (t) cc_final: 0.9157 (p) REVERT: K 210 LEU cc_start: 0.9525 (pt) cc_final: 0.9210 (pt) REVERT: K 372 MET cc_start: 0.8793 (mtm) cc_final: 0.8455 (pmm) REVERT: K 419 LEU cc_start: 0.9344 (mt) cc_final: 0.9070 (mt) REVERT: K 426 VAL cc_start: 0.8365 (m) cc_final: 0.8113 (m) REVERT: K 428 MET cc_start: 0.8985 (mtm) cc_final: 0.8452 (mtm) REVERT: K 454 ARG cc_start: 0.7901 (mmp-170) cc_final: 0.7155 (mmp-170) REVERT: K 491 ASN cc_start: 0.9591 (t0) cc_final: 0.9200 (p0) REVERT: A 61 LEU cc_start: 0.9194 (mt) cc_final: 0.8910 (mt) REVERT: A 62 ILE cc_start: 0.9267 (mm) cc_final: 0.8986 (mm) REVERT: A 67 PHE cc_start: 0.9576 (t80) cc_final: 0.9352 (t80) REVERT: A 73 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9205 (mt-10) REVERT: A 84 PHE cc_start: 0.9235 (m-80) cc_final: 0.8829 (m-80) REVERT: A 103 LEU cc_start: 0.9864 (tp) cc_final: 0.9508 (mt) REVERT: A 105 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9170 (mm-30) REVERT: A 108 ASN cc_start: 0.9615 (t0) cc_final: 0.9357 (t0) REVERT: A 119 ILE cc_start: 0.9680 (pt) cc_final: 0.9000 (tp) REVERT: A 120 MET cc_start: 0.7827 (mtm) cc_final: 0.6892 (mpp) REVERT: B 43 VAL cc_start: 0.8874 (t) cc_final: 0.8519 (t) REVERT: B 44 LYS cc_start: 0.9494 (ttmm) cc_final: 0.9242 (ttmt) REVERT: B 50 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8373 (tp) REVERT: B 68 ASP cc_start: 0.9692 (m-30) cc_final: 0.9398 (m-30) REVERT: B 72 TYR cc_start: 0.9249 (m-80) cc_final: 0.8924 (m-80) REVERT: B 74 GLU cc_start: 0.9739 (tt0) cc_final: 0.9413 (tp30) REVERT: C 90 ASP cc_start: 0.9310 (t0) cc_final: 0.9080 (t0) REVERT: C 108 LEU cc_start: 0.9608 (tp) cc_final: 0.9382 (tt) REVERT: D 59 MET cc_start: 0.9829 (mmm) cc_final: 0.9514 (mmp) REVERT: D 65 ASP cc_start: 0.9582 (t70) cc_final: 0.9240 (t0) REVERT: E 62 ILE cc_start: 0.9510 (mp) cc_final: 0.8664 (mp) REVERT: E 81 ASP cc_start: 0.9569 (m-30) cc_final: 0.9230 (p0) REVERT: E 90 MET cc_start: 0.9699 (mtm) cc_final: 0.9270 (mmm) REVERT: E 97 GLU cc_start: 0.9467 (tt0) cc_final: 0.9121 (tt0) REVERT: E 109 LEU cc_start: 0.9813 (mm) cc_final: 0.9443 (mm) REVERT: F 62 LEU cc_start: 0.9689 (mt) cc_final: 0.9479 (mt) REVERT: F 68 ASP cc_start: 0.9516 (m-30) cc_final: 0.8901 (t70) REVERT: F 77 LYS cc_start: 0.9648 (mmtt) cc_final: 0.9322 (mmmm) REVERT: F 100 PHE cc_start: 0.7540 (m-80) cc_final: 0.7202 (m-80) REVERT: G 25 PHE cc_start: 0.9215 (m-80) cc_final: 0.8971 (m-80) REVERT: G 75 LYS cc_start: 0.9038 (mttt) cc_final: 0.8838 (mmmt) REVERT: G 85 LEU cc_start: 0.9436 (mt) cc_final: 0.9047 (tt) REVERT: G 110 ASN cc_start: 0.9537 (t0) cc_final: 0.9242 (t0) REVERT: G 112 GLN cc_start: 0.8946 (mp10) cc_final: 0.8483 (mp10) REVERT: H 34 TYR cc_start: 0.8924 (m-80) cc_final: 0.8262 (m-10) REVERT: H 39 TYR cc_start: 0.9392 (t80) cc_final: 0.9103 (t80) REVERT: H 59 MET cc_start: 0.9836 (mmm) cc_final: 0.9471 (mmm) REVERT: H 63 VAL cc_start: 0.9707 (t) cc_final: 0.9504 (t) REVERT: H 64 ASN cc_start: 0.9645 (m110) cc_final: 0.9372 (m110) REVERT: H 96 ARG cc_start: 0.9584 (mmm-85) cc_final: 0.9260 (tpp80) REVERT: H 97 LEU cc_start: 0.9601 (mt) cc_final: 0.9309 (tp) REVERT: H 110 GLU cc_start: 0.9491 (tp30) cc_final: 0.9248 (mm-30) outliers start: 1 outliers final: 0 residues processed: 473 average time/residue: 0.3582 time to fit residues: 231.3900 Evaluate side-chains 426 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 425 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 34 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 138 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 GLN A 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.042216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.032697 restraints weight = 315938.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.034621 restraints weight = 117675.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.035830 restraints weight = 60015.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.036591 restraints weight = 36929.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.037129 restraints weight = 26391.512| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 16670 Z= 0.312 Angle : 0.793 8.184 23791 Z= 0.497 Chirality : 0.045 0.218 2700 Planarity : 0.007 0.084 1988 Dihedral : 28.585 177.588 4597 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.43 % Favored : 95.32 % Rotamer: Outliers : 0.10 % Allowed : 1.07 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1196 helix: 0.00 (0.17), residues: 771 sheet: -1.40 (0.60), residues: 68 loop : -1.13 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 95 TYR 0.027 0.002 TYR C 39 PHE 0.016 0.002 PHE K 233 TRP 0.023 0.004 TRP K 110 HIS 0.011 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.31 (16670) covalent geometry : angle 0.79265 / 0.50 (23791) hydrogen bonds : bond 0.09971 / 6.57 ( 897) hydrogen bonds : angle 4.98387 / 3.53 ( 2330) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 449 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.8289 (pmm) cc_final: 0.7950 (pmm) REVERT: K 100 ILE cc_start: 0.9590 (mt) cc_final: 0.9309 (tp) REVERT: K 194 SER cc_start: 0.9398 (t) cc_final: 0.9165 (p) REVERT: K 372 MET cc_start: 0.8899 (mtm) cc_final: 0.8552 (pmm) REVERT: K 426 VAL cc_start: 0.8560 (m) cc_final: 0.8325 (m) REVERT: K 428 MET cc_start: 0.9120 (mtm) cc_final: 0.8656 (mpp) REVERT: A 67 PHE cc_start: 0.9514 (t80) cc_final: 0.9303 (t80) REVERT: A 74 ILE cc_start: 0.9734 (tp) cc_final: 0.9468 (tp) REVERT: A 82 LEU cc_start: 0.9619 (tp) cc_final: 0.9384 (tp) REVERT: A 84 PHE cc_start: 0.9193 (m-80) cc_final: 0.8844 (m-80) REVERT: A 103 LEU cc_start: 0.9866 (tp) cc_final: 0.9641 (mt) REVERT: A 105 GLU cc_start: 0.9635 (mt-10) cc_final: 0.9214 (mm-30) REVERT: A 108 ASN cc_start: 0.9658 (t0) cc_final: 0.9383 (t0) REVERT: B 43 VAL cc_start: 0.9000 (t) cc_final: 0.8547 (t) REVERT: B 62 LEU cc_start: 0.9810 (mt) cc_final: 0.9518 (tt) REVERT: B 68 ASP cc_start: 0.9705 (m-30) cc_final: 0.9482 (m-30) REVERT: B 72 TYR cc_start: 0.9305 (m-80) cc_final: 0.9077 (m-80) REVERT: B 74 GLU cc_start: 0.9744 (tt0) cc_final: 0.9470 (tp30) REVERT: B 84 MET cc_start: 0.9420 (mmm) cc_final: 0.9179 (mmm) REVERT: C 108 LEU cc_start: 0.9572 (tp) cc_final: 0.9262 (tt) REVERT: D 44 GLN cc_start: 0.9530 (tm-30) cc_final: 0.9323 (tm-30) REVERT: D 73 GLU cc_start: 0.9689 (mm-30) cc_final: 0.9444 (mm-30) REVERT: D 79 HIS cc_start: 0.9771 (t-90) cc_final: 0.9559 (t-90) REVERT: E 48 LEU cc_start: 0.9658 (mp) cc_final: 0.9292 (mp) REVERT: E 51 ILE cc_start: 0.9665 (mt) cc_final: 0.8687 (mt) REVERT: E 60 LEU cc_start: 0.8648 (mm) cc_final: 0.8412 (mm) REVERT: E 62 ILE cc_start: 0.9457 (mp) cc_final: 0.8670 (mp) REVERT: E 81 ASP cc_start: 0.9606 (m-30) cc_final: 0.9243 (p0) REVERT: E 97 GLU cc_start: 0.9515 (tt0) cc_final: 0.9239 (tt0) REVERT: E 118 THR cc_start: 0.8606 (m) cc_final: 0.8276 (m) REVERT: E 120 MET cc_start: 0.8857 (mtp) cc_final: 0.8466 (mtp) REVERT: F 39 ARG cc_start: 0.9252 (mmt-90) cc_final: 0.8772 (mmt-90) REVERT: F 44 LYS cc_start: 0.9355 (tttt) cc_final: 0.9022 (tppt) REVERT: F 62 LEU cc_start: 0.9685 (mt) cc_final: 0.9484 (mt) REVERT: F 77 LYS cc_start: 0.9674 (mmtt) cc_final: 0.9366 (mmmm) REVERT: G 75 LYS cc_start: 0.9143 (mttt) cc_final: 0.8938 (mmmt) REVERT: G 85 LEU cc_start: 0.9421 (mt) cc_final: 0.9125 (tt) REVERT: G 110 ASN cc_start: 0.9504 (t0) cc_final: 0.9200 (t0) REVERT: H 59 MET cc_start: 0.9801 (mmm) cc_final: 0.9460 (mmm) REVERT: H 96 ARG cc_start: 0.9606 (mmm-85) cc_final: 0.9276 (tpp80) outliers start: 1 outliers final: 0 residues processed: 450 average time/residue: 0.3460 time to fit residues: 212.8421 Evaluate side-chains 410 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.043093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.033429 restraints weight = 307035.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.035414 restraints weight = 113301.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.036631 restraints weight = 57588.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.037453 restraints weight = 35442.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.037994 restraints weight = 25103.465| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16670 Z= 0.223 Angle : 0.719 8.458 23791 Z= 0.458 Chirality : 0.044 0.239 2700 Planarity : 0.006 0.078 1988 Dihedral : 28.670 177.982 4597 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.34 % Favored : 96.40 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.23), residues: 1196 helix: 0.34 (0.18), residues: 774 sheet: -1.45 (0.71), residues: 49 loop : -1.14 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG E 131 TYR 0.015 0.002 TYR H 39 PHE 0.021 0.002 PHE A 104 TRP 0.002 0.001 TRP K 110 HIS 0.019 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.22 (16670) covalent geometry : angle 0.71875 / 0.46 (23791) hydrogen bonds : bond 0.08092 / 5.35 ( 897) hydrogen bonds : angle 4.64115 / 3.28 ( 2330) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.8229 (pmm) cc_final: 0.7885 (pmm) REVERT: K 194 SER cc_start: 0.9406 (t) cc_final: 0.9178 (p) REVERT: K 210 LEU cc_start: 0.9392 (pt) cc_final: 0.9116 (pt) REVERT: K 426 VAL cc_start: 0.8532 (m) cc_final: 0.8325 (m) REVERT: K 428 MET cc_start: 0.9131 (mtm) cc_final: 0.8777 (mpp) REVERT: A 77 ASP cc_start: 0.9201 (m-30) cc_final: 0.8861 (m-30) REVERT: A 82 LEU cc_start: 0.9599 (tp) cc_final: 0.9281 (tp) REVERT: A 84 PHE cc_start: 0.9172 (m-80) cc_final: 0.8766 (m-80) REVERT: A 97 GLU cc_start: 0.9725 (mt-10) cc_final: 0.9394 (mt-10) REVERT: A 105 GLU cc_start: 0.9632 (mt-10) cc_final: 0.9367 (mm-30) REVERT: B 68 ASP cc_start: 0.9666 (m-30) cc_final: 0.9440 (m-30) REVERT: B 72 TYR cc_start: 0.9245 (m-80) cc_final: 0.9000 (m-80) REVERT: B 74 GLU cc_start: 0.9742 (tt0) cc_final: 0.9461 (tp30) REVERT: B 80 THR cc_start: 0.9240 (t) cc_final: 0.8986 (t) REVERT: B 84 MET cc_start: 0.9395 (mmm) cc_final: 0.9103 (mmm) REVERT: C 108 LEU cc_start: 0.9583 (tp) cc_final: 0.9302 (tt) REVERT: D 73 GLU cc_start: 0.9721 (mm-30) cc_final: 0.9447 (mm-30) REVERT: D 79 HIS cc_start: 0.9776 (t-90) cc_final: 0.9528 (t-90) REVERT: E 48 LEU cc_start: 0.9643 (mp) cc_final: 0.9311 (mp) REVERT: E 51 ILE cc_start: 0.9652 (mt) cc_final: 0.8569 (mt) REVERT: E 62 ILE cc_start: 0.9465 (mp) cc_final: 0.8787 (mp) REVERT: E 81 ASP cc_start: 0.9610 (m-30) cc_final: 0.9234 (p0) REVERT: E 97 GLU cc_start: 0.9532 (tt0) cc_final: 0.9314 (tt0) REVERT: F 39 ARG cc_start: 0.9261 (mmt-90) cc_final: 0.8801 (mmt-90) REVERT: F 44 LYS cc_start: 0.9347 (tttt) cc_final: 0.8961 (tppt) REVERT: F 62 LEU cc_start: 0.9631 (mt) cc_final: 0.9404 (mt) REVERT: F 77 LYS cc_start: 0.9675 (mmtt) cc_final: 0.9369 (mmmm) REVERT: G 25 PHE cc_start: 0.9427 (m-80) cc_final: 0.8686 (m-10) REVERT: G 61 GLU cc_start: 0.9588 (tp30) cc_final: 0.9346 (mm-30) REVERT: G 75 LYS cc_start: 0.9137 (mttt) cc_final: 0.8927 (mmmt) REVERT: G 85 LEU cc_start: 0.9493 (mt) cc_final: 0.9033 (tt) REVERT: H 59 MET cc_start: 0.9796 (mmm) cc_final: 0.9447 (mmm) REVERT: H 65 ASP cc_start: 0.9718 (t70) cc_final: 0.9432 (t70) REVERT: H 96 ARG cc_start: 0.9564 (mmm-85) cc_final: 0.9305 (tpp80) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3130 time to fit residues: 188.1055 Evaluate side-chains 410 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 36 optimal weight: 7.9990 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 137 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 116 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 74 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.043344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2505 r_free = 0.2505 target = 0.033674 restraints weight = 312063.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.035632 restraints weight = 118008.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.036853 restraints weight = 60837.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.037681 restraints weight = 37753.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.038156 restraints weight = 26752.028| |-----------------------------------------------------------------------------| r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 16670 Z= 0.217 Angle : 0.709 8.122 23791 Z= 0.449 Chirality : 0.043 0.265 2700 Planarity : 0.005 0.060 1988 Dihedral : 28.728 177.431 4597 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.93 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1196 helix: 0.58 (0.18), residues: 774 sheet: -1.58 (0.70), residues: 49 loop : -1.29 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 42 TYR 0.029 0.002 TYR C 39 PHE 0.016 0.001 PHE K 417 TRP 0.003 0.001 TRP K 110 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.22 (16670) covalent geometry : angle 0.70946 / 0.45 (23791) hydrogen bonds : bond 0.07204 / 4.74 ( 897) hydrogen bonds : angle 4.44137 / 3.14 ( 2330) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.8155 (pmm) cc_final: 0.7744 (pmm) REVERT: K 131 GLU cc_start: 0.9791 (mp0) cc_final: 0.9558 (pm20) REVERT: K 194 SER cc_start: 0.9425 (t) cc_final: 0.9196 (p) REVERT: K 426 VAL cc_start: 0.8490 (m) cc_final: 0.8261 (m) REVERT: K 428 MET cc_start: 0.9112 (mtm) cc_final: 0.8807 (mpp) REVERT: A 60 LEU cc_start: 0.8021 (mt) cc_final: 0.7660 (mt) REVERT: A 77 ASP cc_start: 0.9175 (m-30) cc_final: 0.8855 (m-30) REVERT: A 97 GLU cc_start: 0.9727 (mt-10) cc_final: 0.9254 (mt-10) REVERT: A 105 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9292 (mm-30) REVERT: B 68 ASP cc_start: 0.9619 (m-30) cc_final: 0.9360 (m-30) REVERT: B 74 GLU cc_start: 0.9756 (tt0) cc_final: 0.9406 (tp30) REVERT: B 84 MET cc_start: 0.9356 (mmm) cc_final: 0.9044 (mmm) REVERT: B 92 ARG cc_start: 0.9167 (ttp80) cc_final: 0.8604 (ttp80) REVERT: C 108 LEU cc_start: 0.9589 (tp) cc_final: 0.9321 (tt) REVERT: D 65 ASP cc_start: 0.9348 (t70) cc_final: 0.9103 (t0) REVERT: D 68 GLU cc_start: 0.9211 (pp20) cc_final: 0.8995 (pp20) REVERT: D 79 HIS cc_start: 0.9782 (t-90) cc_final: 0.9518 (t-90) REVERT: E 62 ILE cc_start: 0.9467 (mp) cc_final: 0.8755 (mp) REVERT: E 81 ASP cc_start: 0.9622 (m-30) cc_final: 0.9253 (p0) REVERT: E 105 GLU cc_start: 0.8930 (pp20) cc_final: 0.8668 (pp20) REVERT: E 106 ASP cc_start: 0.9230 (m-30) cc_final: 0.8813 (m-30) REVERT: F 68 ASP cc_start: 0.9604 (m-30) cc_final: 0.8941 (t0) REVERT: F 72 TYR cc_start: 0.9530 (m-80) cc_final: 0.8482 (m-80) REVERT: F 77 LYS cc_start: 0.9683 (mmtt) cc_final: 0.9371 (mmmm) REVERT: G 25 PHE cc_start: 0.9402 (m-80) cc_final: 0.8652 (m-10) REVERT: G 54 VAL cc_start: 0.9791 (t) cc_final: 0.9489 (t) REVERT: G 61 GLU cc_start: 0.9583 (tp30) cc_final: 0.9337 (mm-30) REVERT: G 71 ARG cc_start: 0.9410 (tmm-80) cc_final: 0.9077 (tmm-80) REVERT: G 72 ASP cc_start: 0.9195 (m-30) cc_final: 0.8886 (m-30) REVERT: G 75 LYS cc_start: 0.9160 (mttt) cc_final: 0.8940 (mmmt) REVERT: G 85 LEU cc_start: 0.9391 (mt) cc_final: 0.9043 (tt) REVERT: H 59 MET cc_start: 0.9795 (mmm) cc_final: 0.9441 (mmm) REVERT: H 96 ARG cc_start: 0.9577 (mmm-85) cc_final: 0.9184 (tpp80) REVERT: H 105 LYS cc_start: 0.9792 (mmtp) cc_final: 0.9468 (mmmt) REVERT: H 110 GLU cc_start: 0.9554 (tp30) cc_final: 0.8890 (tm-30) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.3265 time to fit residues: 196.3279 Evaluate side-chains 415 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 120 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.043402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.033964 restraints weight = 310900.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.035912 restraints weight = 116225.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.037150 restraints weight = 59607.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.037956 restraints weight = 36786.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.038431 restraints weight = 26043.084| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16670 Z= 0.191 Angle : 0.678 7.748 23791 Z= 0.433 Chirality : 0.042 0.270 2700 Planarity : 0.005 0.059 1988 Dihedral : 28.721 177.238 4597 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.23), residues: 1196 helix: 0.85 (0.18), residues: 779 sheet: -1.66 (0.68), residues: 49 loop : -1.25 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.015 0.002 TYR B 72 PHE 0.012 0.001 PHE K 417 TRP 0.003 0.001 TRP K 110 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.19 (16670) covalent geometry : angle 0.67770 / 0.43 (23791) hydrogen bonds : bond 0.06450 / 4.26 ( 897) hydrogen bonds : angle 4.30138 / 3.03 ( 2330) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.8002 (pmm) cc_final: 0.7501 (pmm) REVERT: K 131 GLU cc_start: 0.9783 (mp0) cc_final: 0.9537 (pm20) REVERT: K 194 SER cc_start: 0.9450 (t) cc_final: 0.9224 (p) REVERT: A 67 PHE cc_start: 0.9449 (t80) cc_final: 0.9195 (t80) REVERT: A 77 ASP cc_start: 0.9175 (m-30) cc_final: 0.8835 (m-30) REVERT: A 105 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9042 (mm-30) REVERT: A 123 ASP cc_start: 0.9621 (m-30) cc_final: 0.8990 (t70) REVERT: B 72 TYR cc_start: 0.9278 (m-80) cc_final: 0.8973 (m-80) REVERT: B 74 GLU cc_start: 0.9733 (tt0) cc_final: 0.9403 (tp30) REVERT: B 84 MET cc_start: 0.9320 (mmm) cc_final: 0.8976 (mmm) REVERT: B 92 ARG cc_start: 0.9162 (ttp80) cc_final: 0.8725 (ttp80) REVERT: C 73 ASN cc_start: 0.9537 (t0) cc_final: 0.9311 (t0) REVERT: C 89 ASN cc_start: 0.9489 (m-40) cc_final: 0.9159 (m110) REVERT: C 108 LEU cc_start: 0.9600 (tp) cc_final: 0.9338 (tt) REVERT: D 32 GLU cc_start: 0.8641 (pp20) cc_final: 0.8255 (pp20) REVERT: D 65 ASP cc_start: 0.9299 (t70) cc_final: 0.9054 (t0) REVERT: D 73 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9423 (mm-30) REVERT: D 79 HIS cc_start: 0.9790 (t-90) cc_final: 0.9511 (t-90) REVERT: E 48 LEU cc_start: 0.9627 (mp) cc_final: 0.9386 (mp) REVERT: E 81 ASP cc_start: 0.9613 (m-30) cc_final: 0.9240 (p0) REVERT: E 84 PHE cc_start: 0.9545 (m-80) cc_final: 0.9187 (m-80) REVERT: E 105 GLU cc_start: 0.8931 (pp20) cc_final: 0.8602 (pp20) REVERT: E 106 ASP cc_start: 0.9243 (m-30) cc_final: 0.8820 (m-30) REVERT: E 109 LEU cc_start: 0.9783 (mm) cc_final: 0.9568 (mt) REVERT: E 120 MET cc_start: 0.9228 (mtp) cc_final: 0.8909 (mtt) REVERT: F 44 LYS cc_start: 0.9334 (tttt) cc_final: 0.9034 (tppt) REVERT: F 68 ASP cc_start: 0.9589 (m-30) cc_final: 0.8930 (t0) REVERT: G 25 PHE cc_start: 0.9390 (m-80) cc_final: 0.8599 (m-10) REVERT: G 54 VAL cc_start: 0.9790 (t) cc_final: 0.9461 (t) REVERT: G 71 ARG cc_start: 0.9409 (tmm-80) cc_final: 0.9072 (tmm-80) REVERT: G 72 ASP cc_start: 0.9166 (m-30) cc_final: 0.8870 (m-30) REVERT: G 75 LYS cc_start: 0.9167 (mttt) cc_final: 0.8939 (mmmt) REVERT: G 85 LEU cc_start: 0.9382 (mt) cc_final: 0.9043 (tt) REVERT: G 112 GLN cc_start: 0.9083 (mp10) cc_final: 0.8545 (mp10) REVERT: H 59 MET cc_start: 0.9786 (mmm) cc_final: 0.9419 (mmm) REVERT: H 96 ARG cc_start: 0.9573 (mmm-85) cc_final: 0.9142 (tpp80) REVERT: H 105 LYS cc_start: 0.9785 (mmtp) cc_final: 0.9442 (mmmt) REVERT: H 110 GLU cc_start: 0.9551 (tp30) cc_final: 0.8932 (tm-30) outliers start: 0 outliers final: 0 residues processed: 449 average time/residue: 0.3123 time to fit residues: 192.2070 Evaluate side-chains 410 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 8 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.042796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2495 r_free = 0.2495 target = 0.033428 restraints weight = 318278.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.035326 restraints weight = 117725.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.036508 restraints weight = 60341.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.037300 restraints weight = 37453.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.037779 restraints weight = 26668.723| |-----------------------------------------------------------------------------| r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 16670 Z= 0.261 Angle : 0.712 7.338 23791 Z= 0.450 Chirality : 0.042 0.270 2700 Planarity : 0.005 0.044 1988 Dihedral : 28.760 177.902 4597 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.18 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.23), residues: 1196 helix: 0.54 (0.18), residues: 774 sheet: -1.97 (0.65), residues: 49 loop : -1.45 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.015 0.002 TYR C 39 PHE 0.012 0.001 PHE K 417 TRP 0.002 0.001 TRP K 168 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.26 (16670) covalent geometry : angle 0.71186 / 0.45 (23791) hydrogen bonds : bond 0.07521 / 4.95 ( 897) hydrogen bonds : angle 4.51431 / 3.19 ( 2330) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7995 (pmm) cc_final: 0.7523 (pmm) REVERT: K 131 GLU cc_start: 0.9786 (mp0) cc_final: 0.9546 (pm20) REVERT: K 194 SER cc_start: 0.9472 (t) cc_final: 0.9266 (p) REVERT: K 422 ARG cc_start: 0.9492 (ttm-80) cc_final: 0.9118 (mtp85) REVERT: A 60 LEU cc_start: 0.7669 (mt) cc_final: 0.7269 (mt) REVERT: A 62 ILE cc_start: 0.8988 (mm) cc_final: 0.8786 (mm) REVERT: A 77 ASP cc_start: 0.9188 (m-30) cc_final: 0.8932 (m-30) REVERT: A 97 GLU cc_start: 0.9721 (mt-10) cc_final: 0.9312 (mt-10) REVERT: A 105 GLU cc_start: 0.9615 (mt-10) cc_final: 0.9063 (mm-30) REVERT: B 74 GLU cc_start: 0.9745 (tt0) cc_final: 0.9412 (tp30) REVERT: B 84 MET cc_start: 0.9345 (mmm) cc_final: 0.9002 (mmm) REVERT: C 108 LEU cc_start: 0.9609 (tp) cc_final: 0.9362 (tt) REVERT: D 32 GLU cc_start: 0.8682 (pp20) cc_final: 0.8152 (pp20) REVERT: D 65 ASP cc_start: 0.9368 (t70) cc_final: 0.9092 (t0) REVERT: D 68 GLU cc_start: 0.9267 (pp20) cc_final: 0.9025 (pp20) REVERT: D 73 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9371 (mm-30) REVERT: D 79 HIS cc_start: 0.9800 (t-90) cc_final: 0.9519 (t-90) REVERT: E 81 ASP cc_start: 0.9651 (m-30) cc_final: 0.9281 (p0) REVERT: E 84 PHE cc_start: 0.9518 (m-80) cc_final: 0.9171 (m-80) REVERT: E 105 GLU cc_start: 0.8908 (pp20) cc_final: 0.8578 (pp20) REVERT: E 106 ASP cc_start: 0.9245 (m-30) cc_final: 0.8811 (m-30) REVERT: E 109 LEU cc_start: 0.9778 (mm) cc_final: 0.9561 (mt) REVERT: F 68 ASP cc_start: 0.9633 (m-30) cc_final: 0.9051 (t0) REVERT: F 72 TYR cc_start: 0.9516 (m-80) cc_final: 0.8491 (m-80) REVERT: G 25 PHE cc_start: 0.9386 (m-80) cc_final: 0.8584 (m-10) REVERT: G 61 GLU cc_start: 0.9579 (tp30) cc_final: 0.9348 (mm-30) REVERT: G 71 ARG cc_start: 0.9424 (tmm-80) cc_final: 0.9076 (tmm-80) REVERT: G 72 ASP cc_start: 0.9126 (m-30) cc_final: 0.8832 (m-30) REVERT: G 75 LYS cc_start: 0.9187 (mttt) cc_final: 0.8956 (mmmt) REVERT: G 85 LEU cc_start: 0.9384 (mt) cc_final: 0.9049 (tt) REVERT: G 104 GLN cc_start: 0.9520 (mp10) cc_final: 0.9260 (mp10) REVERT: G 112 GLN cc_start: 0.9117 (mp10) cc_final: 0.8536 (mp10) REVERT: H 59 MET cc_start: 0.9799 (mmm) cc_final: 0.9448 (mmm) REVERT: H 65 ASP cc_start: 0.9721 (t70) cc_final: 0.9457 (t70) REVERT: H 96 ARG cc_start: 0.9582 (mmm-85) cc_final: 0.9171 (tpp80) REVERT: H 105 LYS cc_start: 0.9799 (mmtp) cc_final: 0.9466 (mmmt) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.3354 time to fit residues: 197.8289 Evaluate side-chains 403 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 105 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 133 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.043635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.034131 restraints weight = 311170.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.036087 restraints weight = 115861.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.037307 restraints weight = 59192.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.038127 restraints weight = 36559.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.038667 restraints weight = 25828.592| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16670 Z= 0.185 Angle : 0.668 7.521 23791 Z= 0.426 Chirality : 0.042 0.274 2700 Planarity : 0.005 0.066 1988 Dihedral : 28.782 177.169 4597 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1196 helix: 0.87 (0.18), residues: 777 sheet: -1.96 (0.66), residues: 49 loop : -1.32 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 96 TYR 0.019 0.002 TYR B 72 PHE 0.012 0.001 PHE K 162 TRP 0.002 0.001 TRP K 110 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.19 (16670) covalent geometry : angle 0.66788 / 0.43 (23791) hydrogen bonds : bond 0.06108 / 4.07 ( 897) hydrogen bonds : angle 4.25019 / 3.00 ( 2330) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7777 (pmm) cc_final: 0.7154 (pmm) REVERT: K 131 GLU cc_start: 0.9778 (mp0) cc_final: 0.9530 (pm20) REVERT: K 194 SER cc_start: 0.9483 (t) cc_final: 0.9274 (p) REVERT: A 60 LEU cc_start: 0.7354 (mt) cc_final: 0.7144 (mt) REVERT: A 67 PHE cc_start: 0.9420 (t80) cc_final: 0.9154 (t80) REVERT: A 77 ASP cc_start: 0.9181 (m-30) cc_final: 0.8915 (m-30) REVERT: A 97 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9298 (mt-10) REVERT: B 43 VAL cc_start: 0.9056 (p) cc_final: 0.8378 (p) REVERT: B 74 GLU cc_start: 0.9725 (tt0) cc_final: 0.9400 (tp30) REVERT: B 84 MET cc_start: 0.9296 (mmm) cc_final: 0.8941 (mmm) REVERT: C 36 LYS cc_start: 0.9745 (mmmm) cc_final: 0.9540 (mmmm) REVERT: C 89 ASN cc_start: 0.9505 (m-40) cc_final: 0.9191 (m-40) REVERT: D 32 GLU cc_start: 0.8550 (pp20) cc_final: 0.8111 (pp20) REVERT: D 65 ASP cc_start: 0.9333 (t70) cc_final: 0.9044 (t0) REVERT: D 68 GLU cc_start: 0.9229 (pp20) cc_final: 0.9010 (pp20) REVERT: D 73 GLU cc_start: 0.9658 (mm-30) cc_final: 0.9391 (mm-30) REVERT: D 79 HIS cc_start: 0.9806 (t-90) cc_final: 0.9516 (t-90) REVERT: E 81 ASP cc_start: 0.9597 (m-30) cc_final: 0.9216 (p0) REVERT: E 84 PHE cc_start: 0.9544 (m-80) cc_final: 0.9242 (m-80) REVERT: E 105 GLU cc_start: 0.8919 (pp20) cc_final: 0.8612 (pp20) REVERT: E 106 ASP cc_start: 0.9251 (m-30) cc_final: 0.8858 (m-30) REVERT: E 109 LEU cc_start: 0.9779 (mm) cc_final: 0.9542 (mt) REVERT: E 131 ARG cc_start: 0.9065 (mtt180) cc_final: 0.8847 (mtt180) REVERT: F 68 ASP cc_start: 0.9623 (m-30) cc_final: 0.8977 (t0) REVERT: G 25 PHE cc_start: 0.9389 (m-80) cc_final: 0.8565 (m-10) REVERT: G 64 GLU cc_start: 0.9485 (tt0) cc_final: 0.8864 (tp30) REVERT: G 65 LEU cc_start: 0.9612 (mp) cc_final: 0.9370 (mp) REVERT: G 71 ARG cc_start: 0.9414 (tmm-80) cc_final: 0.9072 (tmm-80) REVERT: G 72 ASP cc_start: 0.9113 (m-30) cc_final: 0.8826 (m-30) REVERT: G 75 LYS cc_start: 0.9171 (mttt) cc_final: 0.8960 (mmmt) REVERT: G 85 LEU cc_start: 0.9340 (mt) cc_final: 0.8995 (tt) REVERT: G 100 VAL cc_start: 0.9396 (t) cc_final: 0.9190 (t) REVERT: G 112 GLN cc_start: 0.9116 (mp10) cc_final: 0.8503 (mp10) REVERT: H 59 MET cc_start: 0.9780 (mmm) cc_final: 0.9409 (mmm) REVERT: H 96 ARG cc_start: 0.9589 (mmm-85) cc_final: 0.9133 (tpp80) REVERT: H 105 LYS cc_start: 0.9784 (mmtp) cc_final: 0.9427 (mmmt) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.3562 time to fit residues: 213.8467 Evaluate side-chains 401 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 76 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.043568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2524 r_free = 0.2524 target = 0.034067 restraints weight = 302456.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.036031 restraints weight = 112072.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.037243 restraints weight = 57137.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.038061 restraints weight = 35276.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.038552 restraints weight = 25052.910| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16670 Z= 0.181 Angle : 0.664 7.561 23791 Z= 0.421 Chirality : 0.042 0.272 2700 Planarity : 0.005 0.070 1988 Dihedral : 28.723 176.878 4597 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.60 % Favored : 96.24 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1196 helix: 0.98 (0.18), residues: 779 sheet: -2.13 (0.54), residues: 68 loop : -1.29 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 19 TYR 0.035 0.002 TYR C 39 PHE 0.020 0.001 PHE A 104 TRP 0.003 0.001 TRP K 110 HIS 0.015 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.18 (16670) covalent geometry : angle 0.66435 / 0.42 (23791) hydrogen bonds : bond 0.05809 / 3.89 ( 897) hydrogen bonds : angle 4.16536 / 2.94 ( 2330) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7678 (pmm) cc_final: 0.7057 (pmm) REVERT: K 131 GLU cc_start: 0.9778 (mp0) cc_final: 0.9536 (pm20) REVERT: K 194 SER cc_start: 0.9505 (t) cc_final: 0.9299 (p) REVERT: K 422 ARG cc_start: 0.9487 (ttm-80) cc_final: 0.9112 (mtp85) REVERT: A 60 LEU cc_start: 0.7818 (mt) cc_final: 0.7355 (mt) REVERT: A 67 PHE cc_start: 0.9401 (t80) cc_final: 0.9134 (t80) REVERT: A 97 GLU cc_start: 0.9701 (mt-10) cc_final: 0.9317 (mt-10) REVERT: B 43 VAL cc_start: 0.9148 (p) cc_final: 0.8608 (p) REVERT: B 68 ASP cc_start: 0.9496 (m-30) cc_final: 0.8931 (t70) REVERT: B 72 TYR cc_start: 0.9253 (m-80) cc_final: 0.7888 (m-80) REVERT: B 74 GLU cc_start: 0.9709 (tt0) cc_final: 0.9372 (tp30) REVERT: B 84 MET cc_start: 0.9298 (mmm) cc_final: 0.9092 (mmm) REVERT: C 36 LYS cc_start: 0.9747 (mmmm) cc_final: 0.9539 (mmmm) REVERT: D 32 GLU cc_start: 0.8714 (pp20) cc_final: 0.8186 (pp20) REVERT: D 34 TYR cc_start: 0.9566 (m-80) cc_final: 0.9287 (m-80) REVERT: D 65 ASP cc_start: 0.9294 (t70) cc_final: 0.9064 (t0) REVERT: D 68 GLU cc_start: 0.9217 (pp20) cc_final: 0.9007 (pp20) REVERT: D 73 GLU cc_start: 0.9615 (mm-30) cc_final: 0.9308 (mm-30) REVERT: D 79 HIS cc_start: 0.9806 (t-90) cc_final: 0.9492 (t-90) REVERT: E 51 ILE cc_start: 0.9642 (mt) cc_final: 0.9300 (mt) REVERT: E 64 LYS cc_start: 0.9605 (mtmm) cc_final: 0.9352 (mtmm) REVERT: E 81 ASP cc_start: 0.9593 (m-30) cc_final: 0.9195 (p0) REVERT: E 84 PHE cc_start: 0.9538 (m-80) cc_final: 0.9238 (m-80) REVERT: E 105 GLU cc_start: 0.8906 (pp20) cc_final: 0.8695 (pp20) REVERT: E 106 ASP cc_start: 0.9240 (m-30) cc_final: 0.8876 (m-30) REVERT: E 120 MET cc_start: 0.9053 (mtp) cc_final: 0.8667 (mtt) REVERT: E 131 ARG cc_start: 0.8975 (mtt180) cc_final: 0.8753 (mtt180) REVERT: F 62 LEU cc_start: 0.9702 (mt) cc_final: 0.9475 (mt) REVERT: G 25 PHE cc_start: 0.9393 (m-80) cc_final: 0.9023 (m-10) REVERT: G 64 GLU cc_start: 0.9478 (tt0) cc_final: 0.8850 (tp30) REVERT: G 65 LEU cc_start: 0.9608 (mp) cc_final: 0.9362 (mp) REVERT: G 71 ARG cc_start: 0.9416 (tmm-80) cc_final: 0.9064 (tmm-80) REVERT: G 72 ASP cc_start: 0.9105 (m-30) cc_final: 0.8824 (m-30) REVERT: G 75 LYS cc_start: 0.9194 (mttt) cc_final: 0.8987 (mmmt) REVERT: G 85 LEU cc_start: 0.9332 (mt) cc_final: 0.9002 (tt) REVERT: G 104 GLN cc_start: 0.9569 (mp10) cc_final: 0.9310 (mp10) REVERT: G 112 GLN cc_start: 0.9058 (mp10) cc_final: 0.8432 (mp10) REVERT: H 59 MET cc_start: 0.9768 (mmm) cc_final: 0.9409 (mmm) REVERT: H 65 ASP cc_start: 0.9697 (t70) cc_final: 0.9394 (t70) REVERT: H 96 ARG cc_start: 0.9596 (mmm-85) cc_final: 0.9140 (tpp80) REVERT: H 105 LYS cc_start: 0.9788 (mmtp) cc_final: 0.9430 (mmmt) outliers start: 0 outliers final: 0 residues processed: 434 average time/residue: 0.3177 time to fit residues: 189.5605 Evaluate side-chains 403 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 126 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 41 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN D 60 ASN D 92 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.044401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.034816 restraints weight = 296869.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.036796 restraints weight = 108241.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.038057 restraints weight = 54711.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.038901 restraints weight = 33528.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.039426 restraints weight = 23756.378| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16670 Z= 0.169 Angle : 0.655 7.668 23791 Z= 0.416 Chirality : 0.042 0.269 2700 Planarity : 0.005 0.050 1988 Dihedral : 28.675 176.756 4597 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1196 helix: 1.08 (0.18), residues: 774 sheet: -1.84 (0.63), residues: 51 loop : -1.35 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 35 TYR 0.027 0.002 TYR C 39 PHE 0.010 0.001 PHE K 162 TRP 0.004 0.001 TRP K 110 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.17 (16670) covalent geometry : angle 0.65522 / 0.42 (23791) hydrogen bonds : bond 0.05431 / 3.65 ( 897) hydrogen bonds : angle 4.08569 / 2.88 ( 2330) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 434 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7619 (pmm) cc_final: 0.6968 (pmm) REVERT: K 131 GLU cc_start: 0.9771 (mp0) cc_final: 0.9526 (pm20) REVERT: K 194 SER cc_start: 0.9530 (t) cc_final: 0.9330 (p) REVERT: K 375 MET cc_start: 0.8953 (mmm) cc_final: 0.8737 (mmm) REVERT: A 60 LEU cc_start: 0.7798 (mt) cc_final: 0.7347 (mt) REVERT: A 62 ILE cc_start: 0.8926 (mm) cc_final: 0.8698 (mm) REVERT: A 97 GLU cc_start: 0.9732 (mt-10) cc_final: 0.9304 (mt-10) REVERT: A 105 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9148 (tm-30) REVERT: A 120 MET cc_start: 0.8044 (mpp) cc_final: 0.7776 (mpp) REVERT: B 72 TYR cc_start: 0.9279 (m-80) cc_final: 0.8896 (m-80) REVERT: B 74 GLU cc_start: 0.9685 (tt0) cc_final: 0.9361 (tp30) REVERT: B 84 MET cc_start: 0.9312 (mmm) cc_final: 0.8948 (mmm) REVERT: C 36 LYS cc_start: 0.9744 (mmmm) cc_final: 0.9533 (mmmm) REVERT: C 83 LEU cc_start: 0.9624 (mm) cc_final: 0.9395 (mm) REVERT: D 32 GLU cc_start: 0.8698 (pp20) cc_final: 0.8153 (pp20) REVERT: D 34 TYR cc_start: 0.9618 (m-80) cc_final: 0.9339 (m-80) REVERT: D 65 ASP cc_start: 0.9296 (t70) cc_final: 0.9086 (t0) REVERT: D 73 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9363 (mm-30) REVERT: E 64 LYS cc_start: 0.9617 (mtmm) cc_final: 0.9164 (pttm) REVERT: E 81 ASP cc_start: 0.9651 (m-30) cc_final: 0.9183 (p0) REVERT: E 84 PHE cc_start: 0.9545 (m-80) cc_final: 0.9289 (m-80) REVERT: F 59 LYS cc_start: 0.9638 (tmmt) cc_final: 0.9416 (tppt) REVERT: F 62 LEU cc_start: 0.9707 (mt) cc_final: 0.9474 (mt) REVERT: F 68 ASP cc_start: 0.9508 (m-30) cc_final: 0.9078 (t70) REVERT: G 25 PHE cc_start: 0.9392 (m-80) cc_final: 0.9015 (m-10) REVERT: G 64 GLU cc_start: 0.9472 (tt0) cc_final: 0.8843 (tp30) REVERT: G 65 LEU cc_start: 0.9602 (mp) cc_final: 0.9361 (mp) REVERT: G 71 ARG cc_start: 0.9407 (tmm-80) cc_final: 0.9050 (tmm-80) REVERT: G 72 ASP cc_start: 0.9120 (m-30) cc_final: 0.8817 (m-30) REVERT: G 73 ASN cc_start: 0.9196 (t0) cc_final: 0.8793 (t0) REVERT: G 85 LEU cc_start: 0.9346 (mt) cc_final: 0.9000 (tt) REVERT: G 92 GLU cc_start: 0.9699 (mp0) cc_final: 0.9460 (mp0) REVERT: G 112 GLN cc_start: 0.9013 (mp10) cc_final: 0.8695 (mp10) REVERT: H 59 MET cc_start: 0.9770 (mmm) cc_final: 0.9402 (mmm) REVERT: H 96 ARG cc_start: 0.9564 (mmm-85) cc_final: 0.9112 (tpp80) REVERT: H 105 LYS cc_start: 0.9785 (mmtp) cc_final: 0.9414 (mmmt) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.3306 time to fit residues: 196.5691 Evaluate side-chains 402 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN ** H 64 ASN ** 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 = 0.2846 r_free = 0.2846 target = 0.044920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.035521 restraints weight = 305437.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.037422 restraints weight = 115675.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.038630 restraints weight = 59541.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.039424 restraints weight = 37001.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2697 r_free = 0.2697 target = 0.039947 restraints weight = 26411.494| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16670 Z= 0.186 Angle : 0.660 7.648 23791 Z= 0.417 Chirality : 0.041 0.266 2700 Planarity : 0.005 0.053 1988 Dihedral : 28.650 176.888 4597 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1196 helix: 1.08 (0.19), residues: 779 sheet: -1.99 (0.62), residues: 52 loop : -1.37 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 35 TYR 0.037 0.002 TYR D 80 PHE 0.012 0.001 PHE H 67 TRP 0.014 0.002 TRP K 110 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.19 (16670) covalent geometry : angle 0.65962 / 0.42 (23791) hydrogen bonds : bond 0.05661 / 3.81 ( 897) hydrogen bonds : angle 4.08958 / 2.88 ( 2330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5478.67 seconds wall clock time: 94 minutes 1.95 seconds (5641.95 seconds total)