Starting phenix.real_space_refine on Mon Sep 14 06:33:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otq_13065/09_2026/7otq_13065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otq_13065/09_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_13065/09_2026/7otq_13065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otq_13065/09_2026/7otq_13065.map" model { file = "/net/cci-nas-00/data/ceres_data/7otq_13065/09_2026/7otq_13065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otq_13065/09_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-2.2.1-6174/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: 5.39, per 1000 atoms: 0.18 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: 2.86 Conformation dependent library (CDL) restraints added in 596.7 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: 5.95 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: 8.16 Time building geometry restraints manager: 3.93 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: 51420 1.64 - 3.27: 2642 3.27 - 4.91: 300 4.91 - 6.55: 50 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.660 Find NCS groups from input model: 0.230 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.680 ------------------------------------------------------------------------------- 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 : 0.881 8.183 23791 Z= 0.731 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 0.88090 / 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 : 0.759 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: K 72 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.5095 (tp30) REVERT: K 100 ILE cc_start: 0.9610 (mt) cc_final: 0.9404 (tp) REVERT: K 110 TRP cc_start: 0.9739 (t-100) cc_final: 0.9499 (t-100) REVERT: K 194 SER cc_start: 0.9397 (t) cc_final: 0.9157 (p) REVERT: K 372 MET cc_start: 0.8868 (mtm) cc_final: 0.8549 (pmm) REVERT: K 422 ARG cc_start: 0.9296 (ttm-80) cc_final: 0.9035 (mtp85) REVERT: A 60 LEU cc_start: 0.8761 (mt) cc_final: 0.8017 (mt) REVERT: A 67 PHE cc_start: 0.9629 (t80) cc_final: 0.9157 (t80) REVERT: A 84 PHE cc_start: 0.9386 (m-80) cc_final: 0.8889 (m-80) REVERT: A 103 LEU cc_start: 0.9835 (tp) cc_final: 0.9622 (mt) REVERT: A 105 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9326 (mm-30) REVERT: A 108 ASN cc_start: 0.9613 (t0) cc_final: 0.9247 (t0) REVERT: A 119 ILE cc_start: 0.9709 (pt) cc_final: 0.9175 (tp) REVERT: A 120 MET cc_start: 0.7712 (mtm) cc_final: 0.7134 (mpp) REVERT: A 123 ASP cc_start: 0.9633 (m-30) cc_final: 0.9376 (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: 0.9257 (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: 0.8884 (m-80) REVERT: B 74 GLU cc_start: 0.9751 (tt0) cc_final: 0.9431 (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: 0.9394 (tt0) REVERT: D 45 VAL cc_start: 0.9276 (m) cc_final: 0.8933 (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: 0.9479 (t-90) REVERT: E 81 ASP cc_start: 0.9554 (m-30) cc_final: 0.9209 (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: 0.9010 (t0) REVERT: F 72 TYR cc_start: 0.9469 (m-80) cc_final: 0.9178 (m-80) REVERT: F 77 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9304 (mmmm) REVERT: G 25 PHE cc_start: 0.9260 (m-80) cc_final: 0.8881 (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: 0.9386 (t0) REVERT: G 112 GLN cc_start: 0.8356 (mp10) cc_final: 0.7869 (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: 0.8771 (mmm-85) REVERT: H 79 HIS cc_start: 0.9748 (t-90) cc_final: 0.9543 (t-90) REVERT: H 86 ILE cc_start: 0.9337 (mm) cc_final: 0.8947 (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: 0.3738 time to fit residues: 260.9942 Evaluate side-chains 440 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 432 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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: 9.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- 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 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 = 0.044055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.034409 restraints weight = 310371.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.036414 restraints weight = 115063.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.037673 restraints weight = 58312.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038505 restraints weight = 35609.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.038974 restraints weight = 24870.516| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.152 16670 Z= 0.255 Angle : 0.845 9.591 23791 Z= 0.517 Chirality : 0.051 0.249 2700 Planarity : 0.009 0.176 1988 Dihedral : 28.279 173.389 4597 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.93 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: -0.26 (0.23), residues: 1196 helix: 0.34 (0.17), residues: 775 sheet: -0.86 (0.76), residues: 49 loop : -0.97 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG A 42 TYR 0.015 0.002 TYR K 214 PHE 0.038 0.002 PHE K 417 TRP 0.007 0.001 TRP K 168 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.25 (16670) covalent geometry : angle 0.84484 / 0.52 (23791) hydrogen bonds : bond 0.09923 / 6.56 ( 897) hydrogen bonds : angle 4.96321 / 3.53 ( 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 478 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 477 time to evaluate : 0.664 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: K 174 ASP cc_start: 0.9149 (t0) cc_final: 0.8911 (t0) REVERT: K 194 SER cc_start: 0.9388 (t) cc_final: 0.9152 (p) REVERT: K 210 LEU cc_start: 0.9523 (pt) cc_final: 0.9207 (pt) REVERT: K 372 MET cc_start: 0.8793 (mtm) cc_final: 0.8451 (pmm) REVERT: K 419 LEU cc_start: 0.9340 (mt) cc_final: 0.9090 (mt) REVERT: K 422 ARG cc_start: 0.9350 (ttm-80) cc_final: 0.9046 (mtp85) REVERT: K 426 VAL cc_start: 0.8378 (m) cc_final: 0.8084 (m) REVERT: K 428 MET cc_start: 0.9017 (mtm) cc_final: 0.8618 (mpp) REVERT: K 491 ASN cc_start: 0.9594 (t0) cc_final: 0.9053 (p0) REVERT: A 67 PHE cc_start: 0.9571 (t80) cc_final: 0.9344 (t80) REVERT: A 73 GLU cc_start: 0.9642 (mt-10) cc_final: 0.9208 (mt-10) REVERT: A 84 PHE cc_start: 0.9273 (m-80) cc_final: 0.8932 (m-80) REVERT: A 103 LEU cc_start: 0.9866 (tp) cc_final: 0.9504 (mt) REVERT: A 105 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9321 (mm-30) REVERT: A 108 ASN cc_start: 0.9622 (t0) cc_final: 0.9337 (t0) REVERT: A 119 ILE cc_start: 0.9680 (pt) cc_final: 0.9002 (tp) REVERT: A 120 MET cc_start: 0.7844 (mtm) cc_final: 0.6909 (mpp) REVERT: A 129 ARG cc_start: 0.9539 (tpt90) cc_final: 0.9305 (tpt90) REVERT: B 43 VAL cc_start: 0.8895 (t) cc_final: 0.8516 (t) REVERT: B 44 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9254 (ttmt) REVERT: B 50 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8367 (tp) REVERT: B 68 ASP cc_start: 0.9693 (m-30) cc_final: 0.9403 (m-30) REVERT: B 72 TYR cc_start: 0.9247 (m-80) cc_final: 0.8928 (m-80) REVERT: B 74 GLU cc_start: 0.9739 (tt0) cc_final: 0.9443 (tp30) REVERT: C 90 ASP cc_start: 0.9346 (t0) cc_final: 0.9097 (t0) REVERT: C 108 LEU cc_start: 0.9599 (tp) cc_final: 0.9366 (tt) REVERT: D 59 MET cc_start: 0.9829 (mmm) cc_final: 0.9516 (mmp) REVERT: D 65 ASP cc_start: 0.9578 (t70) cc_final: 0.9166 (t0) REVERT: D 68 GLU cc_start: 0.9567 (tm-30) cc_final: 0.9362 (tm-30) REVERT: E 62 ILE cc_start: 0.9509 (mp) cc_final: 0.8678 (mp) REVERT: E 81 ASP cc_start: 0.9570 (m-30) cc_final: 0.9231 (p0) REVERT: E 90 MET cc_start: 0.9699 (mtm) cc_final: 0.9274 (mmm) REVERT: E 97 GLU cc_start: 0.9467 (tt0) cc_final: 0.9133 (tt0) REVERT: E 109 LEU cc_start: 0.9813 (mm) cc_final: 0.9604 (mm) REVERT: E 118 THR cc_start: 0.8553 (m) cc_final: 0.8247 (m) REVERT: E 120 MET cc_start: 0.8817 (mtp) cc_final: 0.8461 (mtp) REVERT: F 62 LEU cc_start: 0.9687 (mt) cc_final: 0.9463 (mt) REVERT: F 68 ASP cc_start: 0.9518 (m-30) cc_final: 0.8908 (t70) REVERT: F 77 LYS cc_start: 0.9650 (mmtt) cc_final: 0.9325 (mmmm) REVERT: F 100 PHE cc_start: 0.7549 (m-80) cc_final: 0.7198 (m-80) REVERT: G 25 PHE cc_start: 0.9219 (m-80) cc_final: 0.9008 (m-80) REVERT: G 85 LEU cc_start: 0.9439 (mt) cc_final: 0.9053 (tt) REVERT: G 110 ASN cc_start: 0.9537 (t0) cc_final: 0.9240 (t0) REVERT: G 112 GLN cc_start: 0.8919 (mp10) cc_final: 0.8376 (mp10) REVERT: H 34 TYR cc_start: 0.8929 (m-80) cc_final: 0.8271 (m-10) REVERT: H 59 MET cc_start: 0.9836 (mmm) cc_final: 0.9471 (mmm) REVERT: H 64 ASN cc_start: 0.9646 (m110) cc_final: 0.9364 (m110) REVERT: H 96 ARG cc_start: 0.9588 (mmm-85) cc_final: 0.9267 (tpp80) REVERT: H 97 LEU cc_start: 0.9605 (mt) cc_final: 0.9313 (tp) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.3688 time to fit residues: 241.2458 Evaluate side-chains 432 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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: 10.0000 chunk 120 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.041360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.032008 restraints weight = 324293.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.033884 restraints weight = 121660.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.035044 restraints weight = 62223.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.035817 restraints weight = 38451.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.036297 restraints weight = 27239.679| |-----------------------------------------------------------------------------| r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.145 16670 Z= 0.391 Angle : 0.872 12.063 23791 Z= 0.534 Chirality : 0.047 0.238 2700 Planarity : 0.007 0.081 1988 Dihedral : 28.631 178.095 4597 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 24.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.77 % Favored : 94.98 % Rotamer: Outliers : 0.10 % Allowed : 1.55 % Favored : 98.35 % 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: -0.58 (0.17), residues: 761 sheet: -1.51 (0.60), residues: 68 loop : -1.32 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 145 TYR 0.030 0.003 TYR C 39 PHE 0.017 0.002 PHE K 417 TRP 0.011 0.003 TRP K 110 HIS 0.012 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00677 / 0.39 (16670) covalent geometry : angle 0.87239 / 0.53 (23791) hydrogen bonds : bond 0.11589 / 7.61 ( 897) hydrogen bonds : angle 5.37476 / 3.80 ( 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 445 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 444 time to evaluate : 0.699 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: 0.8390 (pmm) cc_final: 0.8069 (pmm) REVERT: K 113 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8970 (mt-10) REVERT: K 194 SER cc_start: 0.9370 (t) cc_final: 0.9131 (p) REVERT: K 372 MET cc_start: 0.8920 (mtm) cc_final: 0.8576 (pmm) REVERT: K 419 LEU cc_start: 0.9386 (mt) cc_final: 0.9132 (mt) REVERT: K 428 MET cc_start: 0.9090 (mtm) cc_final: 0.8738 (mpp) REVERT: A 53 ARG cc_start: 0.9416 (ttp-170) cc_final: 0.8995 (ttp-170) REVERT: A 82 LEU cc_start: 0.9636 (tp) cc_final: 0.9301 (tp) REVERT: A 84 PHE cc_start: 0.9290 (m-80) cc_final: 0.8833 (m-80) REVERT: A 97 GLU cc_start: 0.9743 (mt-10) cc_final: 0.9432 (mt-10) REVERT: A 103 LEU cc_start: 0.9866 (tp) cc_final: 0.9643 (mt) REVERT: A 105 GLU cc_start: 0.9663 (mt-10) cc_final: 0.9254 (mm-30) REVERT: A 108 ASN cc_start: 0.9674 (t0) cc_final: 0.9365 (t0) REVERT: A 119 ILE cc_start: 0.9508 (pt) cc_final: 0.9148 (tp) REVERT: A 120 MET cc_start: 0.7268 (mpp) cc_final: 0.6796 (mpp) REVERT: B 74 GLU cc_start: 0.9758 (tt0) cc_final: 0.9474 (tp30) REVERT: C 108 LEU cc_start: 0.9571 (tp) cc_final: 0.9293 (tt) REVERT: D 73 GLU cc_start: 0.9727 (mm-30) cc_final: 0.9500 (mm-30) REVERT: E 60 LEU cc_start: 0.8698 (mm) cc_final: 0.8410 (mm) REVERT: E 62 ILE cc_start: 0.9411 (mp) cc_final: 0.8589 (mp) REVERT: E 81 ASP cc_start: 0.9646 (m-30) cc_final: 0.9285 (p0) REVERT: E 97 GLU cc_start: 0.9529 (tt0) cc_final: 0.9303 (tt0) REVERT: E 122 LYS cc_start: 0.9408 (ptmt) cc_final: 0.9152 (pttp) REVERT: F 62 LEU cc_start: 0.9698 (mt) cc_final: 0.9475 (mt) REVERT: F 77 LYS cc_start: 0.9665 (mmtt) cc_final: 0.9365 (mmmm) REVERT: G 36 LYS cc_start: 0.9843 (mmmt) cc_final: 0.9532 (mmmm) REVERT: G 61 GLU cc_start: 0.9592 (tp30) cc_final: 0.9386 (mm-30) REVERT: G 85 LEU cc_start: 0.9429 (mt) cc_final: 0.9141 (tt) REVERT: G 110 ASN cc_start: 0.9540 (t0) cc_final: 0.9244 (t0) REVERT: H 59 MET cc_start: 0.9809 (mmm) cc_final: 0.9493 (mmm) REVERT: H 96 ARG cc_start: 0.9603 (mmm-85) cc_final: 0.9129 (tpp80) REVERT: H 105 LYS cc_start: 0.9800 (mmtp) cc_final: 0.9551 (mmmt) outliers start: 1 outliers final: 0 residues processed: 445 average time/residue: 0.3671 time to fit residues: 224.4425 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 : 0.846 ------------------------------------------------------------------------------- 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: 0.6980 chunk 132 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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** D 81 ASN ** 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 = 0.2810 r_free = 0.2810 target = 0.043514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.033812 restraints weight = 306341.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.035792 restraints weight = 113401.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.037025 restraints weight = 57696.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.037839 restraints weight = 35560.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2651 r_free = 0.2651 target = 0.038327 restraints weight = 25246.842| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16670 Z= 0.183 Angle : 0.728 9.146 23791 Z= 0.458 Chirality : 0.046 0.273 2700 Planarity : 0.006 0.092 1988 Dihedral : 28.680 177.914 4597 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % 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: -0.32 (0.23), residues: 1196 helix: 0.39 (0.18), residues: 774 sheet: -1.79 (0.70), residues: 49 loop : -1.08 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 131 TYR 0.031 0.002 TYR B 88 PHE 0.031 0.002 PHE G 25 TRP 0.004 0.001 TRP K 110 HIS 0.027 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.18 (16670) covalent geometry : angle 0.72771 / 0.46 (23791) hydrogen bonds : bond 0.07696 / 5.10 ( 897) hydrogen bonds : angle 4.52985 / 3.21 ( 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 451 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.703 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: K 73 MET cc_start: 0.8268 (pmm) cc_final: 0.7939 (pmm) REVERT: K 194 SER cc_start: 0.9406 (t) cc_final: 0.9177 (p) REVERT: K 426 VAL cc_start: 0.8474 (m) cc_final: 0.8251 (m) REVERT: K 428 MET cc_start: 0.9059 (mtm) cc_final: 0.8657 (mpp) REVERT: A 60 LEU cc_start: 0.7968 (mt) cc_final: 0.7341 (mt) REVERT: A 62 ILE cc_start: 0.9313 (mm) cc_final: 0.8881 (mm) REVERT: A 64 LYS cc_start: 0.9698 (mtpp) cc_final: 0.9391 (mmmm) REVERT: A 67 PHE cc_start: 0.9539 (t80) cc_final: 0.9281 (t80) REVERT: A 77 ASP cc_start: 0.9157 (m-30) cc_final: 0.8796 (m-30) REVERT: A 97 GLU cc_start: 0.9731 (mt-10) cc_final: 0.9241 (mt-10) REVERT: A 105 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9298 (mm-30) REVERT: A 108 ASN cc_start: 0.9585 (t0) cc_final: 0.9270 (t0) REVERT: A 119 ILE cc_start: 0.9529 (pt) cc_final: 0.9209 (tp) REVERT: A 120 MET cc_start: 0.7414 (mpp) cc_final: 0.7190 (mpp) REVERT: A 123 ASP cc_start: 0.9668 (m-30) cc_final: 0.9166 (m-30) REVERT: B 43 VAL cc_start: 0.8951 (t) cc_final: 0.8610 (t) REVERT: B 74 GLU cc_start: 0.9737 (tt0) cc_final: 0.9451 (tp30) REVERT: C 83 LEU cc_start: 0.9542 (mm) cc_final: 0.9325 (mm) REVERT: C 108 LEU cc_start: 0.9592 (tp) cc_final: 0.9320 (tt) REVERT: D 59 MET cc_start: 0.9840 (mmm) cc_final: 0.9591 (mmp) REVERT: D 73 GLU cc_start: 0.9700 (mm-30) cc_final: 0.9480 (mm-30) REVERT: D 86 ILE cc_start: 0.9584 (mt) cc_final: 0.9366 (mt) REVERT: E 50 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8792 (mt-10) REVERT: E 62 ILE cc_start: 0.9463 (mp) cc_final: 0.8716 (mp) REVERT: E 81 ASP cc_start: 0.9611 (m-30) cc_final: 0.9244 (p0) REVERT: E 97 GLU cc_start: 0.9516 (tt0) cc_final: 0.9242 (tt0) REVERT: E 122 LYS cc_start: 0.9399 (ptmt) cc_final: 0.9164 (pttp) REVERT: G 61 GLU cc_start: 0.9569 (tp30) cc_final: 0.9280 (mm-30) REVERT: G 85 LEU cc_start: 0.9485 (mt) cc_final: 0.9023 (tt) REVERT: G 107 VAL cc_start: 0.9243 (p) cc_final: 0.9033 (p) REVERT: H 59 MET cc_start: 0.9779 (mmm) cc_final: 0.9371 (mmm) REVERT: H 96 ARG cc_start: 0.9573 (mmm-85) cc_final: 0.9209 (tpp80) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.3566 time to fit residues: 222.6472 Evaluate side-chains 412 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 9.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 137 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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** A 39 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 = 0.2786 r_free = 0.2786 target = 0.042607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.033166 restraints weight = 310995.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.035122 restraints weight = 114338.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.036340 restraints weight = 58398.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2617 r_free = 0.2617 target = 0.037118 restraints weight = 36047.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.037677 restraints weight = 25715.624| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 16670 Z= 0.233 Angle : 0.735 8.772 23791 Z= 0.458 Chirality : 0.044 0.277 2700 Planarity : 0.005 0.064 1988 Dihedral : 28.678 177.371 4597 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.65 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: -0.33 (0.23), residues: 1196 helix: 0.47 (0.18), residues: 776 sheet: -2.10 (0.55), residues: 68 loop : -1.20 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 42 TYR 0.023 0.002 TYR C 39 PHE 0.014 0.002 PHE K 417 TRP 0.002 0.001 TRP K 110 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.23 (16670) covalent geometry : angle 0.73470 / 0.46 (23791) hydrogen bonds : bond 0.07792 / 5.12 ( 897) hydrogen bonds : angle 4.53128 / 3.21 ( 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 438 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 0.690 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: K 73 MET cc_start: 0.8186 (pmm) cc_final: 0.7773 (pmm) REVERT: K 113 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8952 (mt-10) REVERT: K 131 GLU cc_start: 0.9782 (mp0) cc_final: 0.9532 (pm20) REVERT: K 194 SER cc_start: 0.9418 (t) cc_final: 0.9188 (p) REVERT: K 207 GLN cc_start: 0.8162 (mp10) cc_final: 0.7950 (mm-40) REVERT: K 426 VAL cc_start: 0.8525 (m) cc_final: 0.8296 (m) REVERT: K 428 MET cc_start: 0.9173 (mtm) cc_final: 0.8800 (mpp) REVERT: A 60 LEU cc_start: 0.8039 (mt) cc_final: 0.7646 (mt) REVERT: A 62 ILE cc_start: 0.9309 (mm) cc_final: 0.9076 (mm) REVERT: A 77 ASP cc_start: 0.9188 (m-30) cc_final: 0.8952 (m-30) REVERT: A 84 PHE cc_start: 0.9296 (m-80) cc_final: 0.8923 (m-80) REVERT: A 94 GLU cc_start: 0.9893 (mm-30) cc_final: 0.9667 (mm-30) REVERT: A 97 GLU cc_start: 0.9737 (mt-10) cc_final: 0.9242 (mt-10) REVERT: A 105 GLU cc_start: 0.9619 (mt-10) cc_final: 0.9252 (mm-30) REVERT: A 108 ASN cc_start: 0.9586 (t0) cc_final: 0.9292 (t0) REVERT: A 119 ILE cc_start: 0.9543 (pt) cc_final: 0.9214 (tp) REVERT: A 120 MET cc_start: 0.7578 (mpp) cc_final: 0.7373 (mpp) REVERT: A 123 ASP cc_start: 0.9676 (m-30) cc_final: 0.9292 (m-30) REVERT: B 43 VAL cc_start: 0.8904 (t) cc_final: 0.8588 (t) REVERT: B 74 GLU cc_start: 0.9751 (tt0) cc_final: 0.9430 (tp30) REVERT: C 108 LEU cc_start: 0.9587 (tp) cc_final: 0.9321 (tt) REVERT: D 32 GLU cc_start: 0.8703 (pp20) cc_final: 0.8053 (pp20) REVERT: D 73 GLU cc_start: 0.9696 (mm-30) cc_final: 0.9465 (mm-30) REVERT: E 48 LEU cc_start: 0.9638 (mp) cc_final: 0.9421 (mp) REVERT: E 62 ILE cc_start: 0.9477 (mp) cc_final: 0.8788 (mp) REVERT: E 81 ASP cc_start: 0.9619 (m-30) cc_final: 0.9244 (p0) REVERT: E 105 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8994 (tm-30) REVERT: E 106 ASP cc_start: 0.9358 (m-30) cc_final: 0.8870 (m-30) REVERT: E 122 LYS cc_start: 0.9382 (ptmt) cc_final: 0.9123 (pttp) REVERT: F 44 LYS cc_start: 0.9314 (tttt) cc_final: 0.9027 (tppt) REVERT: F 68 ASP cc_start: 0.9619 (m-30) cc_final: 0.8965 (t0) REVERT: F 72 TYR cc_start: 0.9553 (m-80) cc_final: 0.8531 (m-80) REVERT: G 61 GLU cc_start: 0.9549 (tp30) cc_final: 0.9326 (mm-30) REVERT: G 71 ARG cc_start: 0.9404 (tmm-80) cc_final: 0.9071 (tmm-80) REVERT: G 72 ASP cc_start: 0.9179 (m-30) cc_final: 0.8860 (m-30) REVERT: G 85 LEU cc_start: 0.9395 (mt) cc_final: 0.9046 (tt) REVERT: G 104 GLN cc_start: 0.9513 (mp10) cc_final: 0.9242 (mp10) REVERT: H 59 MET cc_start: 0.9769 (mmm) cc_final: 0.9416 (mmm) REVERT: H 96 ARG cc_start: 0.9566 (mmm-85) cc_final: 0.9159 (tpp80) REVERT: H 105 LYS cc_start: 0.9790 (mmtp) cc_final: 0.9475 (mmmt) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.3614 time to fit residues: 218.3078 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 : 0.671 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 0.0870 chunk 65 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.2835 r_free = 0.2835 target = 0.044560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.034795 restraints weight = 303350.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.036845 restraints weight = 111521.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.038115 restraints weight = 56470.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.038911 restraints weight = 34648.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.039486 restraints weight = 24775.910| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16670 Z= 0.163 Angle : 0.685 8.535 23791 Z= 0.433 Chirality : 0.043 0.289 2700 Planarity : 0.005 0.053 1988 Dihedral : 28.652 176.698 4597 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.42 (0.24), residues: 1196 helix: 1.08 (0.18), residues: 779 sheet: -1.90 (0.67), residues: 49 loop : -1.05 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG D 76 TYR 0.021 0.002 TYR D 80 PHE 0.014 0.001 PHE A 104 TRP 0.005 0.001 TRP K 110 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.16 (16670) covalent geometry : angle 0.68541 / 0.43 (23791) hydrogen bonds : bond 0.05826 / 3.89 ( 897) hydrogen bonds : angle 4.15652 / 2.94 ( 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 448 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 0.681 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 73 MET cc_start: 0.7873 (pmm) cc_final: 0.7286 (pmm) REVERT: K 131 GLU cc_start: 0.9782 (mp0) cc_final: 0.9530 (pm20) REVERT: K 194 SER cc_start: 0.9463 (t) cc_final: 0.9242 (p) REVERT: A 60 LEU cc_start: 0.8048 (mt) cc_final: 0.7468 (mt) REVERT: A 62 ILE cc_start: 0.9345 (mm) cc_final: 0.9123 (mm) REVERT: A 67 PHE cc_start: 0.9553 (t80) cc_final: 0.9335 (t80) REVERT: A 77 ASP cc_start: 0.9184 (m-30) cc_final: 0.8859 (m-30) REVERT: A 94 GLU cc_start: 0.9900 (mm-30) cc_final: 0.9685 (mm-30) REVERT: A 97 GLU cc_start: 0.9713 (mt-10) cc_final: 0.9265 (mt-10) REVERT: A 105 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9267 (mm-30) REVERT: A 108 ASN cc_start: 0.9550 (t0) cc_final: 0.9275 (t0) REVERT: A 119 ILE cc_start: 0.9589 (pt) cc_final: 0.9233 (tp) REVERT: A 120 MET cc_start: 0.7503 (mpp) cc_final: 0.7254 (mpp) REVERT: A 123 ASP cc_start: 0.9630 (m-30) cc_final: 0.9156 (m-30) REVERT: B 74 GLU cc_start: 0.9737 (tt0) cc_final: 0.9403 (tp30) REVERT: C 36 LYS cc_start: 0.9740 (mmmm) cc_final: 0.9534 (mmmm) REVERT: C 73 ASN cc_start: 0.9523 (t0) cc_final: 0.9314 (t0) REVERT: C 108 LEU cc_start: 0.9613 (tp) cc_final: 0.9372 (tt) REVERT: D 32 GLU cc_start: 0.8437 (pp20) cc_final: 0.7813 (pp20) REVERT: D 34 TYR cc_start: 0.9303 (m-10) cc_final: 0.8902 (m-10) REVERT: D 44 GLN cc_start: 0.9524 (tm-30) cc_final: 0.9310 (tm-30) REVERT: D 79 HIS cc_start: 0.9746 (t-90) cc_final: 0.9484 (t-90) REVERT: E 50 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8842 (mt-10) REVERT: E 81 ASP cc_start: 0.9584 (m-30) cc_final: 0.9184 (p0) REVERT: E 84 PHE cc_start: 0.9559 (m-80) cc_final: 0.9233 (m-80) REVERT: E 105 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8923 (tm-30) REVERT: E 118 THR cc_start: 0.8836 (m) cc_final: 0.8135 (m) REVERT: E 120 MET cc_start: 0.9198 (mtp) cc_final: 0.8837 (mtt) REVERT: F 51 TYR cc_start: 0.9020 (m-80) cc_final: 0.8768 (m-80) REVERT: F 59 LYS cc_start: 0.9629 (tmmt) cc_final: 0.9414 (tppt) REVERT: G 64 GLU cc_start: 0.9506 (tt0) cc_final: 0.8932 (tp30) REVERT: G 65 LEU cc_start: 0.9572 (mp) cc_final: 0.9362 (mp) REVERT: G 71 ARG cc_start: 0.9384 (tmm-80) cc_final: 0.9028 (tmm-80) REVERT: G 72 ASP cc_start: 0.9173 (m-30) cc_final: 0.8900 (m-30) REVERT: G 85 LEU cc_start: 0.9350 (mt) cc_final: 0.8985 (tt) REVERT: G 104 GLN cc_start: 0.9524 (mp10) cc_final: 0.9235 (mp10) REVERT: G 112 GLN cc_start: 0.9109 (mp10) cc_final: 0.8490 (mp10) REVERT: H 59 MET cc_start: 0.9728 (mmm) cc_final: 0.9341 (mmm) REVERT: H 79 HIS cc_start: 0.9803 (t-90) cc_final: 0.9599 (t-90) REVERT: H 96 ARG cc_start: 0.9589 (mmm-85) cc_final: 0.9296 (tpp80) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.3619 time to fit residues: 225.1744 Evaluate side-chains 412 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 7.9990 chunk 127 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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** ** 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 = 0.2832 r_free = 0.2832 target = 0.044450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.034883 restraints weight = 299974.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.036859 restraints weight = 109289.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.038112 restraints weight = 55278.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.038945 restraints weight = 33904.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.039481 restraints weight = 23946.125| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16670 Z= 0.175 Angle : 0.671 8.268 23791 Z= 0.425 Chirality : 0.042 0.285 2700 Planarity : 0.005 0.047 1988 Dihedral : 28.585 176.954 4597 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.34 % Favored : 96.49 % 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: 0.43 (0.24), residues: 1196 helix: 1.20 (0.18), residues: 774 sheet: -2.17 (0.54), residues: 68 loop : -1.16 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 76 TYR 0.033 0.002 TYR C 39 PHE 0.022 0.001 PHE A 104 TRP 0.002 0.001 TRP K 110 HIS 0.009 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.18 (16670) covalent geometry : angle 0.67081 / 0.42 (23791) hydrogen bonds : bond 0.05888 / 3.89 ( 897) hydrogen bonds : angle 4.14038 / 2.92 ( 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 437 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.838 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: 0.7825 (pmm) cc_final: 0.7194 (pmm) REVERT: K 131 GLU cc_start: 0.9778 (mp0) cc_final: 0.9531 (pm20) REVERT: A 60 LEU cc_start: 0.7929 (mt) cc_final: 0.7500 (mt) REVERT: A 67 PHE cc_start: 0.9556 (t80) cc_final: 0.9336 (t80) REVERT: A 70 LEU cc_start: 0.9658 (tt) cc_final: 0.9328 (mt) REVERT: A 77 ASP cc_start: 0.9165 (m-30) cc_final: 0.8828 (m-30) REVERT: A 94 GLU cc_start: 0.9898 (mm-30) cc_final: 0.9675 (mm-30) REVERT: A 97 GLU cc_start: 0.9705 (mt-10) cc_final: 0.9257 (mt-10) REVERT: A 105 GLU cc_start: 0.9608 (mt-10) cc_final: 0.9253 (mm-30) REVERT: A 108 ASN cc_start: 0.9552 (t0) cc_final: 0.9249 (t0) REVERT: A 119 ILE cc_start: 0.9574 (pt) cc_final: 0.9210 (tp) REVERT: A 120 MET cc_start: 0.7569 (mpp) cc_final: 0.7304 (mpp) REVERT: A 123 ASP cc_start: 0.9618 (m-30) cc_final: 0.9218 (m-30) REVERT: B 74 GLU cc_start: 0.9724 (tt0) cc_final: 0.9407 (tp30) REVERT: C 36 LYS cc_start: 0.9741 (mmmm) cc_final: 0.9539 (mmmm) REVERT: D 34 TYR cc_start: 0.9329 (m-10) cc_final: 0.8980 (m-10) REVERT: D 44 GLN cc_start: 0.9516 (tm-30) cc_final: 0.9315 (tm-30) REVERT: D 65 ASP cc_start: 0.9281 (t70) cc_final: 0.8931 (t0) REVERT: D 68 GLU cc_start: 0.9190 (pp20) cc_final: 0.8952 (pp20) REVERT: D 69 ARG cc_start: 0.9562 (ttm110) cc_final: 0.9329 (ttm110) REVERT: D 79 HIS cc_start: 0.9743 (t-90) cc_final: 0.9496 (t-90) REVERT: D 82 LYS cc_start: 0.9811 (mmmm) cc_final: 0.9607 (mmmm) REVERT: E 51 ILE cc_start: 0.9647 (mt) cc_final: 0.9340 (mt) REVERT: E 81 ASP cc_start: 0.9675 (m-30) cc_final: 0.9205 (p0) REVERT: E 84 PHE cc_start: 0.9526 (m-80) cc_final: 0.9188 (m-80) REVERT: E 105 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9029 (tm-30) REVERT: E 106 ASP cc_start: 0.9409 (m-30) cc_final: 0.8930 (m-30) REVERT: E 118 THR cc_start: 0.8861 (m) cc_final: 0.8242 (m) REVERT: E 120 MET cc_start: 0.9234 (mtp) cc_final: 0.8860 (mtt) REVERT: F 59 LYS cc_start: 0.9628 (tmmt) cc_final: 0.9418 (tppt) REVERT: F 62 LEU cc_start: 0.9702 (mt) cc_final: 0.9489 (mt) REVERT: F 68 ASP cc_start: 0.9533 (m-30) cc_final: 0.8880 (t70) REVERT: G 64 GLU cc_start: 0.9513 (tt0) cc_final: 0.8937 (tp30) REVERT: G 65 LEU cc_start: 0.9582 (mp) cc_final: 0.9356 (mp) REVERT: G 71 ARG cc_start: 0.9395 (tmm-80) cc_final: 0.9042 (tmm-80) REVERT: G 72 ASP cc_start: 0.9142 (m-30) cc_final: 0.8841 (m-30) REVERT: G 85 LEU cc_start: 0.9362 (mt) cc_final: 0.9015 (tt) REVERT: G 104 GLN cc_start: 0.9524 (mp10) cc_final: 0.9234 (mp10) REVERT: G 112 GLN cc_start: 0.9112 (mp10) cc_final: 0.8528 (mp10) REVERT: H 59 MET cc_start: 0.9746 (mmm) cc_final: 0.9403 (mmm) REVERT: H 69 ARG cc_start: 0.9510 (mtp85) cc_final: 0.9265 (mtp85) REVERT: H 96 ARG cc_start: 0.9593 (mmm-85) cc_final: 0.9326 (tpp80) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3606 time to fit residues: 218.9288 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 : 0.749 ------------------------------------------------------------------------------- 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: 4.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 133 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 187 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.035053 restraints weight = 298570.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.037033 restraints weight = 109280.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.038287 restraints weight = 55457.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.039084 restraints weight = 34191.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.039636 restraints weight = 24513.985| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.5317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16670 Z= 0.172 Angle : 0.658 8.333 23791 Z= 0.419 Chirality : 0.042 0.286 2700 Planarity : 0.005 0.050 1988 Dihedral : 28.574 177.229 4597 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.43 % Favored : 96.40 % 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: 0.48 (0.24), residues: 1196 helix: 1.24 (0.18), residues: 774 sheet: -1.96 (0.64), residues: 49 loop : -1.26 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 42 TYR 0.034 0.002 TYR C 39 PHE 0.020 0.001 PHE A 104 TRP 0.003 0.001 TRP K 110 HIS 0.008 0.001 HIS K 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.17 (16670) covalent geometry : angle 0.65816 / 0.42 (23791) hydrogen bonds : bond 0.05624 / 3.73 ( 897) hydrogen bonds : angle 4.07429 / 2.88 ( 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 437 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.594 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: K 73 MET cc_start: 0.7771 (pmm) cc_final: 0.7100 (pmm) REVERT: K 131 GLU cc_start: 0.9775 (mp0) cc_final: 0.9529 (pm20) REVERT: K 174 ASP cc_start: 0.9138 (t0) cc_final: 0.8915 (t0) REVERT: A 60 LEU cc_start: 0.7942 (mt) cc_final: 0.7543 (mt) REVERT: A 67 PHE cc_start: 0.9547 (t80) cc_final: 0.9324 (t80) REVERT: A 77 ASP cc_start: 0.9164 (m-30) cc_final: 0.8820 (m-30) REVERT: A 94 GLU cc_start: 0.9901 (mm-30) cc_final: 0.9684 (mm-30) REVERT: A 97 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9258 (mt-10) REVERT: A 105 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9269 (mm-30) REVERT: A 108 ASN cc_start: 0.9554 (t0) cc_final: 0.9247 (t0) REVERT: A 119 ILE cc_start: 0.9554 (pt) cc_final: 0.9241 (tp) REVERT: A 120 MET cc_start: 0.7606 (mpp) cc_final: 0.7376 (mpp) REVERT: A 123 ASP cc_start: 0.9619 (m-30) cc_final: 0.8790 (t70) REVERT: B 43 VAL cc_start: 0.9030 (t) cc_final: 0.8701 (p) REVERT: B 74 GLU cc_start: 0.9726 (tt0) cc_final: 0.9403 (tp30) REVERT: C 36 LYS cc_start: 0.9743 (mmmm) cc_final: 0.9539 (mmmm) REVERT: C 39 TYR cc_start: 0.9560 (m-10) cc_final: 0.9350 (m-10) REVERT: D 59 MET cc_start: 0.9812 (mmm) cc_final: 0.9558 (mmp) REVERT: D 65 ASP cc_start: 0.9303 (t70) cc_final: 0.9038 (t0) REVERT: D 68 GLU cc_start: 0.9210 (pp20) cc_final: 0.8972 (pp20) REVERT: D 73 GLU cc_start: 0.9703 (mm-30) cc_final: 0.9400 (mm-30) REVERT: D 79 HIS cc_start: 0.9742 (t-90) cc_final: 0.9502 (t-90) REVERT: E 74 ILE cc_start: 0.9744 (tp) cc_final: 0.9544 (tp) REVERT: E 81 ASP cc_start: 0.9650 (m-30) cc_final: 0.9196 (p0) REVERT: E 84 PHE cc_start: 0.9517 (m-80) cc_final: 0.9203 (m-80) REVERT: E 106 ASP cc_start: 0.9417 (m-30) cc_final: 0.8977 (m-30) REVERT: E 112 ILE cc_start: 0.9019 (mt) cc_final: 0.8782 (mt) REVERT: E 118 THR cc_start: 0.8770 (m) cc_final: 0.8136 (m) REVERT: E 120 MET cc_start: 0.9244 (mtp) cc_final: 0.8864 (mtt) REVERT: F 43 VAL cc_start: 0.9525 (p) cc_final: 0.9308 (p) REVERT: F 59 LYS cc_start: 0.9630 (tmmt) cc_final: 0.9422 (tppt) REVERT: F 62 LEU cc_start: 0.9705 (mt) cc_final: 0.9484 (mt) REVERT: F 68 ASP cc_start: 0.9504 (m-30) cc_final: 0.8783 (t70) REVERT: G 64 GLU cc_start: 0.9514 (tt0) cc_final: 0.8928 (tp30) REVERT: G 65 LEU cc_start: 0.9569 (mp) cc_final: 0.9354 (mp) REVERT: G 71 ARG cc_start: 0.9401 (tmm-80) cc_final: 0.9045 (tmm-80) REVERT: G 72 ASP cc_start: 0.9113 (m-30) cc_final: 0.8808 (m-30) REVERT: G 85 LEU cc_start: 0.9357 (mt) cc_final: 0.9004 (tt) REVERT: G 104 GLN cc_start: 0.9523 (mp10) cc_final: 0.9253 (mp10) REVERT: G 112 GLN cc_start: 0.9122 (mp10) cc_final: 0.8481 (mp10) REVERT: H 59 MET cc_start: 0.9725 (mmm) cc_final: 0.9364 (mmm) REVERT: H 69 ARG cc_start: 0.9586 (mtp85) cc_final: 0.9265 (mtp85) REVERT: H 79 HIS cc_start: 0.9803 (t-90) cc_final: 0.9602 (t-90) REVERT: H 96 ARG cc_start: 0.9595 (mmm-85) cc_final: 0.9152 (tpp80) REVERT: H 105 LYS cc_start: 0.9778 (mmtp) cc_final: 0.9427 (mmmt) outliers start: 0 outliers final: 0 residues processed: 437 average time/residue: 0.3480 time to fit residues: 210.3592 Evaluate side-chains 409 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 409 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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: 3.9990 chunk 132 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.2825 r_free = 0.2825 target = 0.044418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.034842 restraints weight = 302571.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.036824 restraints weight = 111000.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.038055 restraints weight = 56386.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.038897 restraints weight = 34787.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.039405 restraints weight = 24647.934| |-----------------------------------------------------------------------------| r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16670 Z= 0.192 Angle : 0.665 8.176 23791 Z= 0.420 Chirality : 0.041 0.285 2700 Planarity : 0.005 0.047 1988 Dihedral : 28.556 177.420 4597 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % 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: 0.34 (0.24), residues: 1196 helix: 1.15 (0.18), residues: 772 sheet: -2.13 (0.64), residues: 49 loop : -1.34 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.023 0.002 TYR C 39 PHE 0.013 0.001 PHE H 67 TRP 0.004 0.001 TRP K 110 HIS 0.030 0.002 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.19 (16670) covalent geometry : angle 0.66473 / 0.42 (23791) hydrogen bonds : bond 0.05942 / 3.95 ( 897) hydrogen bonds : angle 4.11583 / 2.90 ( 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 435 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.668 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: 0.7729 (pmm) cc_final: 0.7072 (pmm) REVERT: K 131 GLU cc_start: 0.9780 (mp0) cc_final: 0.9537 (pm20) REVERT: K 174 ASP cc_start: 0.9094 (t0) cc_final: 0.8880 (t0) REVERT: K 201 LEU cc_start: 0.9456 (mt) cc_final: 0.9251 (mt) REVERT: A 60 LEU cc_start: 0.7965 (mt) cc_final: 0.7475 (mt) REVERT: A 62 ILE cc_start: 0.9369 (mm) cc_final: 0.9130 (mm) REVERT: A 67 PHE cc_start: 0.9554 (t80) cc_final: 0.9346 (t80) REVERT: A 77 ASP cc_start: 0.9167 (m-30) cc_final: 0.8817 (m-30) REVERT: A 94 GLU cc_start: 0.9901 (mm-30) cc_final: 0.9686 (mm-30) REVERT: A 97 GLU cc_start: 0.9704 (mt-10) cc_final: 0.9236 (mt-10) REVERT: A 105 GLU cc_start: 0.9625 (mt-10) cc_final: 0.9189 (mm-30) REVERT: A 108 ASN cc_start: 0.9567 (t0) cc_final: 0.9292 (t0) REVERT: A 119 ILE cc_start: 0.9565 (pt) cc_final: 0.9242 (tp) REVERT: A 120 MET cc_start: 0.7661 (mpp) cc_final: 0.7460 (mpp) REVERT: A 123 ASP cc_start: 0.9602 (m-30) cc_final: 0.8884 (t70) REVERT: B 43 VAL cc_start: 0.9088 (t) cc_final: 0.8870 (p) REVERT: B 74 GLU cc_start: 0.9721 (tt0) cc_final: 0.9420 (tp30) REVERT: B 88 TYR cc_start: 0.8646 (m-10) cc_final: 0.8189 (m-80) REVERT: C 36 LYS cc_start: 0.9742 (mmmm) cc_final: 0.9528 (mmmm) REVERT: C 89 ASN cc_start: 0.9527 (m-40) cc_final: 0.9212 (m-40) REVERT: D 69 ARG cc_start: 0.9594 (ttm110) cc_final: 0.9392 (ttm110) REVERT: D 79 HIS cc_start: 0.9718 (t-90) cc_final: 0.9475 (t-90) REVERT: E 81 ASP cc_start: 0.9645 (m-30) cc_final: 0.9200 (p0) REVERT: E 84 PHE cc_start: 0.9518 (m-80) cc_final: 0.9238 (m-80) REVERT: E 106 ASP cc_start: 0.9435 (m-30) cc_final: 0.9012 (m-30) REVERT: E 120 MET cc_start: 0.9205 (mtp) cc_final: 0.8813 (mtt) REVERT: E 122 LYS cc_start: 0.9246 (ptmm) cc_final: 0.9015 (ptmm) REVERT: F 59 LYS cc_start: 0.9627 (tmmt) cc_final: 0.9414 (tppt) REVERT: F 68 ASP cc_start: 0.9504 (m-30) cc_final: 0.8803 (t70) REVERT: G 64 GLU cc_start: 0.9527 (tt0) cc_final: 0.8950 (tp30) REVERT: G 71 ARG cc_start: 0.9408 (tmm-80) cc_final: 0.9052 (tmm-80) REVERT: G 72 ASP cc_start: 0.9103 (m-30) cc_final: 0.8809 (m-30) REVERT: G 75 LYS cc_start: 0.9183 (mttt) cc_final: 0.8937 (mmmt) REVERT: G 85 LEU cc_start: 0.9346 (mt) cc_final: 0.8994 (tt) REVERT: G 104 GLN cc_start: 0.9523 (mp10) cc_final: 0.9291 (mp10) REVERT: G 112 GLN cc_start: 0.9079 (mp10) cc_final: 0.8441 (mp10) REVERT: H 59 MET cc_start: 0.9743 (mmm) cc_final: 0.9368 (mmm) REVERT: H 69 ARG cc_start: 0.9586 (mtp85) cc_final: 0.9285 (mtp85) REVERT: H 79 HIS cc_start: 0.9809 (t-90) cc_final: 0.9609 (t-90) REVERT: H 96 ARG cc_start: 0.9593 (mmm-85) cc_final: 0.9155 (tpp80) REVERT: H 105 LYS cc_start: 0.9781 (mmtp) cc_final: 0.9433 (mmmt) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.3479 time to fit residues: 210.1438 Evaluate side-chains 407 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 0.8980 chunk 116 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 122 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** 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 = 0.2836 r_free = 0.2836 target = 0.044726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.035063 restraints weight = 297082.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.037068 restraints weight = 108744.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.038324 restraints weight = 55056.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.039123 restraints weight = 33856.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.039660 restraints weight = 24440.805| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.5612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16670 Z= 0.165 Angle : 0.653 8.342 23791 Z= 0.413 Chirality : 0.041 0.286 2700 Planarity : 0.004 0.050 1988 Dihedral : 28.556 177.073 4597 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % 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: 0.55 (0.24), residues: 1196 helix: 1.33 (0.19), residues: 774 sheet: -2.11 (0.64), residues: 49 loop : -1.30 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 99 TYR 0.017 0.002 TYR D 80 PHE 0.009 0.001 PHE K 409 TRP 0.004 0.001 TRP K 110 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.17 (16670) covalent geometry : angle 0.65302 / 0.41 (23791) hydrogen bonds : bond 0.05325 / 3.57 ( 897) hydrogen bonds : angle 4.00610 / 2.82 ( 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 432 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 0.642 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: 0.7568 (pmm) cc_final: 0.6781 (pmm) REVERT: K 131 GLU cc_start: 0.9772 (mp0) cc_final: 0.9532 (pm20) REVERT: K 174 ASP cc_start: 0.9079 (t0) cc_final: 0.8815 (t0) REVERT: K 375 MET cc_start: 0.8936 (mmm) cc_final: 0.8700 (mmm) REVERT: A 60 LEU cc_start: 0.7979 (mt) cc_final: 0.7480 (mt) REVERT: A 62 ILE cc_start: 0.9350 (mm) cc_final: 0.9113 (mm) REVERT: A 67 PHE cc_start: 0.9553 (t80) cc_final: 0.9348 (t80) REVERT: A 84 PHE cc_start: 0.9333 (m-80) cc_final: 0.8815 (m-80) REVERT: A 94 GLU cc_start: 0.9896 (mm-30) cc_final: 0.9687 (mm-30) REVERT: A 97 GLU cc_start: 0.9710 (mt-10) cc_final: 0.9224 (mt-10) REVERT: A 105 GLU cc_start: 0.9611 (mt-10) cc_final: 0.9165 (mm-30) REVERT: A 108 ASN cc_start: 0.9560 (t0) cc_final: 0.9284 (t0) REVERT: A 119 ILE cc_start: 0.9566 (pt) cc_final: 0.9228 (tp) REVERT: A 120 MET cc_start: 0.7593 (mpp) cc_final: 0.7191 (mpp) REVERT: B 43 VAL cc_start: 0.9115 (t) cc_final: 0.8882 (p) REVERT: B 74 GLU cc_start: 0.9719 (tt0) cc_final: 0.9456 (tp30) REVERT: B 88 TYR cc_start: 0.8648 (m-10) cc_final: 0.8195 (m-80) REVERT: C 36 LYS cc_start: 0.9735 (mmmm) cc_final: 0.9487 (mmmm) REVERT: C 89 ASN cc_start: 0.9530 (m-40) cc_final: 0.9212 (m-40) REVERT: D 34 TYR cc_start: 0.9302 (m-80) cc_final: 0.9012 (m-10) REVERT: D 59 MET cc_start: 0.9809 (mmm) cc_final: 0.9549 (mmp) REVERT: D 65 ASP cc_start: 0.9324 (t70) cc_final: 0.9033 (t0) REVERT: D 73 GLU cc_start: 0.9706 (mm-30) cc_final: 0.9478 (mm-30) REVERT: D 79 HIS cc_start: 0.9723 (t-90) cc_final: 0.9488 (t-90) REVERT: E 84 PHE cc_start: 0.9513 (m-80) cc_final: 0.9255 (m-80) REVERT: E 106 ASP cc_start: 0.9415 (m-30) cc_final: 0.8991 (m-30) REVERT: E 120 MET cc_start: 0.9207 (mtp) cc_final: 0.8824 (mtt) REVERT: F 68 ASP cc_start: 0.9490 (m-30) cc_final: 0.9061 (t70) REVERT: F 91 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9231 (mmmm) REVERT: G 64 GLU cc_start: 0.9544 (tt0) cc_final: 0.8957 (tp30) REVERT: G 71 ARG cc_start: 0.9400 (tmm-80) cc_final: 0.9042 (tmm-80) REVERT: G 72 ASP cc_start: 0.9104 (m-30) cc_final: 0.8781 (m-30) REVERT: G 73 ASN cc_start: 0.9187 (t0) cc_final: 0.8957 (t0) REVERT: G 75 LYS cc_start: 0.9177 (mttt) cc_final: 0.8801 (mttt) REVERT: G 85 LEU cc_start: 0.9333 (mt) cc_final: 0.8988 (tt) REVERT: G 104 GLN cc_start: 0.9526 (mp10) cc_final: 0.9297 (mp10) REVERT: G 112 GLN cc_start: 0.9073 (mp10) cc_final: 0.8424 (mp10) REVERT: H 59 MET cc_start: 0.9738 (mmm) cc_final: 0.9357 (mmm) REVERT: H 65 ASP cc_start: 0.9743 (t70) cc_final: 0.9484 (t70) REVERT: H 69 ARG cc_start: 0.9551 (mtp85) cc_final: 0.9318 (mtp85) REVERT: H 79 HIS cc_start: 0.9805 (t-90) cc_final: 0.9600 (t-90) REVERT: H 96 ARG cc_start: 0.9572 (mmm-85) cc_final: 0.9106 (tpp80) REVERT: H 105 LYS cc_start: 0.9769 (mmtp) cc_final: 0.9406 (mmmt) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.3491 time to fit residues: 209.1295 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 : 0.567 ------------------------------------------------------------------------------- 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: 5.9990 chunk 20 optimal weight: 0.0770 chunk 5 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 109 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 286 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 = 0.2835 r_free = 0.2835 target = 0.044757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.035114 restraints weight = 299798.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.037136 restraints weight = 109034.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038396 restraints weight = 55085.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.039245 restraints weight = 33807.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.039709 restraints weight = 23824.971| |-----------------------------------------------------------------------------| r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16670 Z= 0.168 Angle : 0.646 8.303 23791 Z= 0.409 Chirality : 0.041 0.283 2700 Planarity : 0.004 0.052 1988 Dihedral : 28.529 176.979 4597 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.78 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: 0.48 (0.24), residues: 1196 helix: 1.28 (0.19), residues: 777 sheet: -2.14 (0.54), residues: 68 loop : -1.28 (0.31), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 99 TYR 0.023 0.002 TYR F 51 PHE 0.012 0.001 PHE H 67 TRP 0.004 0.001 TRP K 110 HIS 0.005 0.001 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.17 (16670) covalent geometry : angle 0.64638 / 0.41 (23791) hydrogen bonds : bond 0.05296 / 3.55 ( 897) hydrogen bonds : angle 3.97118 / 2.79 ( 2330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5911.37 seconds wall clock time: 101 minutes 30.17 seconds (6090.17 seconds total)