Starting phenix.real_space_refine on Mon Aug 25 14:43:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7otq_13065/08_2025/7otq_13065.cif Found real_map, /net/cci-nas-00/data/ceres_data/7otq_13065/08_2025/7otq_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_13065/08_2025/7otq_13065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7otq_13065/08_2025/7otq_13065.map" model { file = "/net/cci-nas-00/data/ceres_data/7otq_13065/08_2025/7otq_13065.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7otq_13065/08_2025/7otq_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-2.0-5787/lib/python3.9/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: 6.69, per 1000 atoms: 0.23 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: 3.20 Conformation dependent library (CDL) restraints added in 956.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 5.52 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: 6.64 Time building geometry restraints manager: 4.34 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=" N LYS B 16 " pdb=" CA LYS B 16 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" N THR K 42 " pdb=" CA THR K 42 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.89e+00 bond pdb=" N ASN F 25 " pdb=" CA ASN F 25 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N THR H 29 " pdb=" CA THR H 29 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.86e+00 bond pdb=" N HIS E 39 " pdb=" CA HIS E 39 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.85e+00 ... (remaining 30030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 51661 1.64 - 3.27: 2619 3.27 - 4.91: 124 4.91 - 6.55: 10 6.55 - 8.18: 1 Bond angle restraints: 54415 Sorted by residual: angle pdb=" O3' DC I 35 " pdb=" C3' DC I 35 " pdb=" C2' DC I 35 " ideal model delta sigma weight residual 111.50 117.23 -5.73 1.50e+00 4.44e-01 1.46e+01 angle pdb=" O3' DG J 20 " pdb=" C3' DG J 20 " pdb=" C2' DG J 20 " ideal model delta sigma weight residual 111.50 106.16 5.34 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C4' DC I -18 " pdb=" O4' DC I -18 " pdb=" C1' DC I -18 " ideal model delta sigma weight residual 109.70 104.43 5.27 1.50e+00 4.44e-01 1.24e+01 angle pdb=" C4' DA I 73 " pdb=" O4' DA I 73 " pdb=" C1' DA I 73 " ideal model delta sigma weight residual 109.70 104.47 5.23 1.50e+00 4.44e-01 1.22e+01 angle pdb=" N GLY K 427 " pdb=" CA GLY K 427 " pdb=" C GLY K 427 " ideal model delta sigma weight residual 113.18 121.36 -8.18 2.37e+00 1.78e-01 1.19e+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 - 0.047: 1951 0.047 - 0.094: 556 0.094 - 0.141: 169 0.141 - 0.189: 21 0.189 - 0.236: 3 Chirality restraints: 2700 Sorted by residual: chirality pdb=" C1' DA I 73 " pdb=" O4' DA I 73 " pdb=" C2' DA I 73 " pdb=" N9 DA I 73 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.24 2.00e-01 2.50e+01 1.39e+00 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 -2.66 -2.45 -0.21 2.00e-01 2.50e+01 1.08e+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 -2.66 -2.47 -0.19 2.00e-01 2.50e+01 8.91e-01 ... (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: 7.810 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: 0.190 Extract box with map and model: 0.320 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 34.050 Find NCS groups from input model: 0.200 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: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.004 0.050 16670 Z= 0.199 Angle : 0.758 8.183 23791 Z= 0.480 Chirality : 0.048 0.236 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 aren 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 covalent geometry : bond 0.00424 (16670) covalent geometry : angle 0.75820 (23791) hydrogen bonds : bond 0.20980 ( 897) hydrogen bonds : angle 8.60311 ( 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 : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 72 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.5094 (tp30) REVERT: K 100 ILE cc_start: 0.9610 (mt) cc_final: 0.9406 (tp) REVERT: K 110 TRP cc_start: 0.9739 (t-100) cc_final: 0.9500 (t-100) REVERT: K 194 SER cc_start: 0.9396 (t) cc_final: 0.9156 (p) REVERT: K 372 MET cc_start: 0.8868 (mtm) cc_final: 0.8547 (pmm) REVERT: A 60 LEU cc_start: 0.8760 (mt) cc_final: 0.8042 (mt) REVERT: A 63 ARG cc_start: 0.9287 (mmt180) cc_final: 0.9054 (mmm-85) REVERT: A 67 PHE cc_start: 0.9629 (t80) cc_final: 0.9164 (t80) REVERT: A 84 PHE cc_start: 0.9386 (m-80) cc_final: 0.8908 (m-80) REVERT: A 103 LEU cc_start: 0.9835 (tp) cc_final: 0.9624 (mt) REVERT: A 105 GLU cc_start: 0.9641 (mt-10) cc_final: 0.9327 (mm-30) REVERT: A 108 ASN cc_start: 0.9613 (t0) cc_final: 0.9249 (t0) REVERT: A 119 ILE cc_start: 0.9709 (pt) cc_final: 0.9171 (tp) REVERT: A 120 MET cc_start: 0.7712 (mtm) cc_final: 0.7130 (mpp) REVERT: A 123 ASP cc_start: 0.9633 (m-30) cc_final: 0.9377 (m-30) REVERT: A 125 GLN cc_start: 0.9733 (mt0) cc_final: 0.9477 (mm110) REVERT: A 129 ARG cc_start: 0.9493 (tpt90) cc_final: 0.9258 (tpt90) REVERT: B 64 ASN cc_start: 0.9516 (m-40) cc_final: 0.9218 (t0) REVERT: B 72 TYR cc_start: 0.9261 (m-80) cc_final: 0.8885 (m-80) REVERT: B 74 GLU cc_start: 0.9751 (tt0) cc_final: 0.9432 (tp30) REVERT: C 90 ASP cc_start: 0.9107 (t0) cc_final: 0.8888 (t0) REVERT: C 92 GLU cc_start: 0.9657 (pm20) cc_final: 0.9395 (tt0) REVERT: D 45 VAL cc_start: 0.9276 (m) cc_final: 0.8934 (p) REVERT: D 59 MET cc_start: 0.9782 (mmm) cc_final: 0.9455 (mmp) REVERT: D 65 ASP cc_start: 0.9503 (t70) cc_final: 0.9026 (t0) REVERT: D 79 HIS cc_start: 0.9702 (t70) cc_final: 0.9478 (t-90) REVERT: E 64 LYS cc_start: 0.9648 (mtmm) cc_final: 0.9373 (mtmm) REVERT: E 81 ASP cc_start: 0.9554 (m-30) cc_final: 0.9211 (p0) REVERT: F 62 LEU cc_start: 0.9691 (mt) cc_final: 0.9470 (mt) REVERT: F 68 ASP cc_start: 0.9477 (m-30) cc_final: 0.9011 (t0) REVERT: F 72 TYR cc_start: 0.9469 (m-80) cc_final: 0.9176 (m-80) REVERT: F 77 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9306 (mmmm) REVERT: G 25 PHE cc_start: 0.9260 (m-80) cc_final: 0.8880 (m-10) REVERT: G 64 GLU cc_start: 0.9561 (tt0) cc_final: 0.9266 (pt0) REVERT: G 81 ARG cc_start: 0.9433 (tpt170) cc_final: 0.9159 (tpt170) REVERT: G 84 GLN cc_start: 0.9740 (tp40) cc_final: 0.9539 (tp-100) REVERT: G 110 ASN cc_start: 0.9646 (t0) cc_final: 0.9389 (t0) REVERT: G 112 GLN cc_start: 0.8356 (mp10) cc_final: 0.7874 (mp10) REVERT: H 65 ASP cc_start: 0.9593 (t0) cc_final: 0.9217 (t70) REVERT: H 69 ARG cc_start: 0.8982 (mtt180) cc_final: 0.8768 (mmm-85) REVERT: H 79 HIS cc_start: 0.9748 (t-90) cc_final: 0.9544 (t-90) REVERT: H 86 ILE cc_start: 0.9337 (mm) cc_final: 0.8952 (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: 0.3082 time to fit residues: 210.9703 Evaluate side-chains 437 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 429 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 187 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 371 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.043780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.034279 restraints weight = 309205.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.036318 restraints weight = 113636.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.037572 restraints weight = 57006.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.038349 restraints weight = 34586.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2657 r_free = 0.2657 target = 0.038913 restraints weight = 24648.982| |-----------------------------------------------------------------------------| r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16670 Z= 0.261 Angle : 0.740 6.978 23791 Z= 0.454 Chirality : 0.047 0.222 2700 Planarity : 0.007 0.092 1988 Dihedral : 28.334 172.834 4597 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 0.10 % Allowed : 2.04 % Favored : 97.86 % 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 aren not related in a simple way. whole: -0.15 (0.23), residues: 1196 helix: 0.40 (0.17), residues: 782 sheet: -0.86 (0.63), residues: 68 loop : -0.85 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG A 42 TYR 0.015 0.002 TYR K 214 PHE 0.025 0.002 PHE B 100 TRP 0.004 0.001 TRP K 110 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00542 (16670) covalent geometry : angle 0.74040 (23791) hydrogen bonds : bond 0.08080 ( 897) hydrogen bonds : angle 4.63284 ( 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 475 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 474 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 110 TRP cc_start: 0.9708 (t-100) cc_final: 0.9445 (t-100) REVERT: K 174 ASP cc_start: 0.9138 (t0) cc_final: 0.8790 (t0) REVERT: K 194 SER cc_start: 0.9409 (t) cc_final: 0.9179 (p) REVERT: K 210 LEU cc_start: 0.9505 (pt) cc_final: 0.9272 (pt) REVERT: K 310 LYS cc_start: 0.9717 (mmtm) cc_final: 0.8957 (pttt) REVERT: K 428 MET cc_start: 0.9062 (mtm) cc_final: 0.8764 (mtm) REVERT: K 491 ASN cc_start: 0.9560 (t0) cc_final: 0.9178 (p0) REVERT: A 62 ILE cc_start: 0.9236 (mm) cc_final: 0.8989 (mm) REVERT: A 63 ARG cc_start: 0.9390 (mmt180) cc_final: 0.9000 (mmm-85) REVERT: A 67 PHE cc_start: 0.9573 (t80) cc_final: 0.9351 (t80) REVERT: A 73 GLU cc_start: 0.9690 (mt-10) cc_final: 0.9308 (mt-10) REVERT: A 84 PHE cc_start: 0.9172 (m-80) cc_final: 0.8889 (m-80) REVERT: A 103 LEU cc_start: 0.9861 (tp) cc_final: 0.9506 (mt) REVERT: A 105 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9141 (mm-30) REVERT: A 108 ASN cc_start: 0.9621 (t0) cc_final: 0.9354 (t0) REVERT: A 119 ILE cc_start: 0.9708 (pt) cc_final: 0.9011 (tp) REVERT: A 120 MET cc_start: 0.7858 (mtm) cc_final: 0.6905 (mpp) REVERT: A 129 ARG cc_start: 0.9580 (tpt90) cc_final: 0.8918 (tpt90) REVERT: B 50 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8325 (tp) REVERT: B 68 ASP cc_start: 0.9677 (m-30) cc_final: 0.9445 (m-30) REVERT: B 74 GLU cc_start: 0.9743 (tt0) cc_final: 0.9450 (tp30) REVERT: C 90 ASP cc_start: 0.9346 (t0) cc_final: 0.9139 (t0) REVERT: C 108 LEU cc_start: 0.9578 (tp) cc_final: 0.9274 (tt) REVERT: D 59 MET cc_start: 0.9840 (mmm) cc_final: 0.9528 (mmp) REVERT: D 65 ASP cc_start: 0.9619 (t70) cc_final: 0.9412 (t0) REVERT: E 60 LEU cc_start: 0.8700 (mm) cc_final: 0.8470 (mm) REVERT: E 81 ASP cc_start: 0.9583 (m-30) cc_final: 0.9236 (p0) REVERT: E 90 MET cc_start: 0.9711 (mtm) cc_final: 0.9313 (mmm) REVERT: E 122 LYS cc_start: 0.9371 (ptmt) cc_final: 0.9097 (pttm) REVERT: F 62 LEU cc_start: 0.9682 (mt) cc_final: 0.9456 (mt) REVERT: F 67 ARG cc_start: 0.9583 (ttm-80) cc_final: 0.9373 (ttp80) REVERT: F 68 ASP cc_start: 0.9512 (m-30) cc_final: 0.9178 (t70) REVERT: F 77 LYS cc_start: 0.9670 (mmtt) cc_final: 0.9352 (mmmm) REVERT: F 100 PHE cc_start: 0.7624 (m-80) cc_final: 0.6752 (m-80) REVERT: G 36 LYS cc_start: 0.9725 (mmmt) cc_final: 0.9412 (mmmt) REVERT: G 85 LEU cc_start: 0.9465 (mt) cc_final: 0.9054 (tt) REVERT: G 110 ASN cc_start: 0.9528 (t0) cc_final: 0.9252 (t0) REVERT: G 112 GLN cc_start: 0.8890 (mp10) cc_final: 0.8403 (mp10) REVERT: H 39 TYR cc_start: 0.9395 (t80) cc_final: 0.9094 (t80) REVERT: H 59 MET cc_start: 0.9846 (mmm) cc_final: 0.9420 (mmm) REVERT: H 73 GLU cc_start: 0.9334 (tp30) cc_final: 0.8554 (tp30) REVERT: H 96 ARG cc_start: 0.9599 (mmm-85) cc_final: 0.9293 (tpp80) REVERT: H 97 LEU cc_start: 0.9575 (mt) cc_final: 0.9249 (tp) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.2974 time to fit residues: 189.9199 Evaluate side-chains 425 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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: 9.9990 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS B 75 HIS D 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.043101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.033781 restraints weight = 306939.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.035749 restraints weight = 111216.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.037006 restraints weight = 56446.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.037851 restraints weight = 34287.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.038339 restraints weight = 23805.842| |-----------------------------------------------------------------------------| r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16670 Z= 0.249 Angle : 0.689 6.763 23791 Z= 0.423 Chirality : 0.045 0.199 2700 Planarity : 0.006 0.068 1988 Dihedral : 28.453 175.422 4597 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.60 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % 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 aren not related in a simple way. whole: 0.07 (0.23), residues: 1196 helix: 0.73 (0.18), residues: 776 sheet: -1.36 (0.61), residues: 68 loop : -1.05 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 95 TYR 0.031 0.002 TYR D 80 PHE 0.022 0.002 PHE G 25 TRP 0.002 0.001 TRP K 168 HIS 0.010 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00512 (16670) covalent geometry : angle 0.68914 (23791) hydrogen bonds : bond 0.07174 ( 897) hydrogen bonds : angle 4.36343 ( 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 458 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.482 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: K 73 MET cc_start: 0.8184 (pmm) cc_final: 0.7700 (pmm) REVERT: K 194 SER cc_start: 0.9417 (t) cc_final: 0.9188 (p) REVERT: K 310 LYS cc_start: 0.9694 (mmtm) cc_final: 0.9046 (pttt) REVERT: K 426 VAL cc_start: 0.8387 (m) cc_final: 0.8095 (m) REVERT: K 428 MET cc_start: 0.9038 (mtm) cc_final: 0.8753 (mpp) REVERT: A 63 ARG cc_start: 0.9381 (mmt180) cc_final: 0.8948 (mmm-85) REVERT: A 77 ASP cc_start: 0.9159 (m-30) cc_final: 0.8942 (m-30) REVERT: A 97 GLU cc_start: 0.9733 (mt-10) cc_final: 0.9459 (mt-10) REVERT: A 105 GLU cc_start: 0.9580 (mt-10) cc_final: 0.9137 (mm-30) REVERT: A 108 ASN cc_start: 0.9629 (t0) cc_final: 0.9351 (t0) REVERT: A 119 ILE cc_start: 0.9585 (pt) cc_final: 0.9284 (tp) REVERT: A 120 MET cc_start: 0.7364 (mpp) cc_final: 0.6895 (mpp) REVERT: A 123 ASP cc_start: 0.9420 (m-30) cc_final: 0.9004 (m-30) REVERT: B 74 GLU cc_start: 0.9737 (tt0) cc_final: 0.9454 (tp30) REVERT: B 84 MET cc_start: 0.9426 (mmm) cc_final: 0.9200 (mmm) REVERT: C 108 LEU cc_start: 0.9572 (tp) cc_final: 0.9300 (tt) REVERT: D 44 GLN cc_start: 0.9498 (tm-30) cc_final: 0.9292 (tm-30) REVERT: E 48 LEU cc_start: 0.9634 (mp) cc_final: 0.9425 (mp) REVERT: E 62 ILE cc_start: 0.9421 (mp) cc_final: 0.8610 (mp) REVERT: E 81 ASP cc_start: 0.9627 (m-30) cc_final: 0.9289 (p0) REVERT: E 90 MET cc_start: 0.9712 (mtm) cc_final: 0.9384 (mmp) REVERT: E 97 GLU cc_start: 0.9510 (tt0) cc_final: 0.9204 (tt0) REVERT: E 106 ASP cc_start: 0.9493 (m-30) cc_final: 0.9049 (m-30) REVERT: E 122 LYS cc_start: 0.9363 (ptmt) cc_final: 0.9096 (pttp) REVERT: F 44 LYS cc_start: 0.9298 (tttt) cc_final: 0.9043 (tppt) REVERT: F 68 ASP cc_start: 0.9589 (m-30) cc_final: 0.8978 (t70) REVERT: F 72 TYR cc_start: 0.9283 (m-80) cc_final: 0.8222 (m-10) REVERT: F 77 LYS cc_start: 0.9679 (mmtt) cc_final: 0.9369 (mmmm) REVERT: G 61 GLU cc_start: 0.9572 (tp30) cc_final: 0.9311 (mm-30) REVERT: G 73 ASN cc_start: 0.9314 (t0) cc_final: 0.9015 (t0) REVERT: G 85 LEU cc_start: 0.9399 (mt) cc_final: 0.9056 (tt) REVERT: G 110 ASN cc_start: 0.9513 (t0) cc_final: 0.9256 (t0) REVERT: G 112 GLN cc_start: 0.8808 (mp10) cc_final: 0.8356 (mp10) REVERT: H 39 TYR cc_start: 0.9367 (t80) cc_final: 0.9084 (t80) REVERT: H 73 GLU cc_start: 0.9379 (tp30) cc_final: 0.8570 (tp30) REVERT: H 90 GLU cc_start: 0.9236 (mm-30) cc_final: 0.8474 (mm-30) REVERT: H 96 ARG cc_start: 0.9584 (mmm-85) cc_final: 0.9236 (tpp80) REVERT: H 97 LEU cc_start: 0.9550 (mt) cc_final: 0.9321 (tp) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.2946 time to fit residues: 183.3688 Evaluate side-chains 414 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 13 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.044615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.034971 restraints weight = 294776.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.036966 restraints weight = 107546.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.038234 restraints weight = 54182.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.039075 restraints weight = 33247.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.039551 restraints weight = 23352.885| |-----------------------------------------------------------------------------| r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 16670 Z= 0.182 Angle : 0.641 5.250 23791 Z= 0.395 Chirality : 0.041 0.191 2700 Planarity : 0.005 0.084 1988 Dihedral : 28.309 171.437 4597 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.59 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 aren not related in a simple way. whole: 0.62 (0.24), residues: 1196 helix: 1.26 (0.18), residues: 779 sheet: -1.59 (0.58), residues: 69 loop : -1.01 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 92 TYR 0.020 0.002 TYR B 72 PHE 0.011 0.001 PHE H 67 TRP 0.009 0.001 TRP K 110 HIS 0.006 0.001 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00387 (16670) covalent geometry : angle 0.64052 (23791) hydrogen bonds : bond 0.05175 ( 897) hydrogen bonds : angle 3.98242 ( 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 453 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7772 (pmm) cc_final: 0.7169 (pmm) REVERT: K 194 SER cc_start: 0.9483 (t) cc_final: 0.9278 (p) REVERT: K 426 VAL cc_start: 0.8375 (m) cc_final: 0.8155 (m) REVERT: K 428 MET cc_start: 0.9092 (mtm) cc_final: 0.8798 (mpp) REVERT: A 63 ARG cc_start: 0.9303 (mmt180) cc_final: 0.8868 (mmm-85) REVERT: A 67 PHE cc_start: 0.9435 (t80) cc_final: 0.9168 (t80) REVERT: A 77 ASP cc_start: 0.9142 (m-30) cc_final: 0.8796 (m-30) REVERT: A 106 ASP cc_start: 0.8905 (t0) cc_final: 0.8550 (m-30) REVERT: A 108 ASN cc_start: 0.9563 (t0) cc_final: 0.9303 (t0) REVERT: A 119 ILE cc_start: 0.9570 (pt) cc_final: 0.9144 (tp) REVERT: A 123 ASP cc_start: 0.9406 (m-30) cc_final: 0.8807 (m-30) REVERT: B 46 ILE cc_start: 0.9653 (mm) cc_final: 0.9448 (mp) REVERT: B 74 GLU cc_start: 0.9729 (tt0) cc_final: 0.9400 (tp30) REVERT: B 84 MET cc_start: 0.9364 (mmm) cc_final: 0.9129 (mmm) REVERT: C 36 LYS cc_start: 0.9733 (mmmm) cc_final: 0.9530 (mmmm) REVERT: C 89 ASN cc_start: 0.9473 (m-40) cc_final: 0.9125 (m-40) REVERT: D 65 ASP cc_start: 0.9683 (t0) cc_final: 0.9342 (t0) REVERT: E 62 ILE cc_start: 0.9422 (mp) cc_final: 0.8635 (mp) REVERT: E 81 ASP cc_start: 0.9559 (m-30) cc_final: 0.9193 (p0) REVERT: E 90 MET cc_start: 0.9769 (mtm) cc_final: 0.9380 (mmp) REVERT: E 97 GLU cc_start: 0.9481 (tt0) cc_final: 0.9239 (tt0) REVERT: E 105 GLU cc_start: 0.9433 (tm-30) cc_final: 0.9188 (tm-30) REVERT: E 106 ASP cc_start: 0.9505 (m-30) cc_final: 0.9055 (m-30) REVERT: E 122 LYS cc_start: 0.9368 (ptmt) cc_final: 0.9081 (pttp) REVERT: F 44 LYS cc_start: 0.9287 (tttt) cc_final: 0.9048 (tppt) REVERT: F 68 ASP cc_start: 0.9546 (m-30) cc_final: 0.8992 (t70) REVERT: F 72 TYR cc_start: 0.9251 (m-80) cc_final: 0.8066 (m-10) REVERT: F 98 TYR cc_start: 0.8503 (m-10) cc_final: 0.7864 (m-10) REVERT: G 54 VAL cc_start: 0.9778 (t) cc_final: 0.9444 (t) REVERT: G 64 GLU cc_start: 0.9505 (tt0) cc_final: 0.8956 (tp30) REVERT: G 65 LEU cc_start: 0.9577 (mp) cc_final: 0.9364 (mp) REVERT: G 71 ARG cc_start: 0.9393 (tmm-80) cc_final: 0.9034 (tmm-80) REVERT: G 72 ASP cc_start: 0.9149 (m-30) cc_final: 0.8820 (m-30) REVERT: G 73 ASN cc_start: 0.9311 (t0) cc_final: 0.9003 (t0) REVERT: G 85 LEU cc_start: 0.9375 (mt) cc_final: 0.9052 (tt) REVERT: G 110 ASN cc_start: 0.9499 (t0) cc_final: 0.9228 (t0) REVERT: G 112 GLN cc_start: 0.8844 (mp10) cc_final: 0.8425 (mp10) REVERT: G 116 LEU cc_start: 0.9165 (mm) cc_final: 0.8919 (mm) REVERT: H 77 LEU cc_start: 0.9269 (mt) cc_final: 0.8954 (mt) REVERT: H 96 ARG cc_start: 0.9594 (mmm-85) cc_final: 0.9305 (tpp80) REVERT: H 110 GLU cc_start: 0.9541 (tp30) cc_final: 0.8926 (tm-30) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.2919 time to fit residues: 179.9960 Evaluate side-chains 413 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.585 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 25 optimal weight: 0.0060 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.043164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.033785 restraints weight = 307515.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.035726 restraints weight = 114793.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.036938 restraints weight = 58896.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.037755 restraints weight = 36562.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.038237 restraints weight = 25954.330| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16670 Z= 0.251 Angle : 0.654 6.251 23791 Z= 0.404 Chirality : 0.045 0.174 2700 Planarity : 0.005 0.056 1988 Dihedral : 28.271 173.861 4597 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % 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 aren not related in a simple way. whole: 0.39 (0.24), residues: 1196 helix: 1.10 (0.18), residues: 779 sheet: -1.46 (0.70), residues: 49 loop : -1.25 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.018 0.002 TYR B 72 PHE 0.018 0.002 PHE A 104 TRP 0.004 0.001 TRP K 110 HIS 0.007 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00516 (16670) covalent geometry : angle 0.65378 (23791) hydrogen bonds : bond 0.06540 ( 897) hydrogen bonds : angle 4.12869 ( 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 436 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7581 (pmm) cc_final: 0.6850 (pmm) REVERT: K 113 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8922 (mt-10) REVERT: K 422 ARG cc_start: 0.9470 (ttm-80) cc_final: 0.9107 (mtp85) REVERT: K 426 VAL cc_start: 0.8538 (m) cc_final: 0.8322 (m) REVERT: A 63 ARG cc_start: 0.9360 (mmt180) cc_final: 0.8900 (mmm-85) REVERT: A 67 PHE cc_start: 0.9410 (t80) cc_final: 0.9167 (t80) REVERT: A 77 ASP cc_start: 0.9178 (m-30) cc_final: 0.8925 (m-30) REVERT: A 103 LEU cc_start: 0.9896 (tp) cc_final: 0.9600 (mt) REVERT: A 105 GLU cc_start: 0.9500 (tm-30) cc_final: 0.9018 (tm-30) REVERT: A 106 ASP cc_start: 0.9247 (t0) cc_final: 0.8645 (m-30) REVERT: A 108 ASN cc_start: 0.9591 (t0) cc_final: 0.9313 (t0) REVERT: A 119 ILE cc_start: 0.9538 (pt) cc_final: 0.9107 (tp) REVERT: A 120 MET cc_start: 0.7444 (mpp) cc_final: 0.7227 (mpp) REVERT: A 123 ASP cc_start: 0.9491 (m-30) cc_final: 0.8288 (t70) REVERT: B 74 GLU cc_start: 0.9733 (tt0) cc_final: 0.9428 (tp30) REVERT: B 84 MET cc_start: 0.9401 (mmm) cc_final: 0.9117 (mmm) REVERT: C 36 LYS cc_start: 0.9741 (mmmm) cc_final: 0.9531 (mmmm) REVERT: C 89 ASN cc_start: 0.9529 (m-40) cc_final: 0.9212 (m-40) REVERT: D 65 ASP cc_start: 0.9378 (t0) cc_final: 0.8919 (t0) REVERT: D 68 GLU cc_start: 0.9385 (pp20) cc_final: 0.9145 (pp20) REVERT: D 73 GLU cc_start: 0.9726 (mm-30) cc_final: 0.9505 (mm-30) REVERT: E 51 ILE cc_start: 0.9642 (mt) cc_final: 0.9373 (mt) REVERT: E 62 ILE cc_start: 0.9379 (mp) cc_final: 0.8581 (mp) REVERT: E 64 LYS cc_start: 0.9553 (mtmm) cc_final: 0.9126 (pttm) REVERT: E 81 ASP cc_start: 0.9658 (m-30) cc_final: 0.9239 (p0) REVERT: E 84 PHE cc_start: 0.9572 (m-80) cc_final: 0.9275 (m-80) REVERT: E 90 MET cc_start: 0.9751 (mtm) cc_final: 0.9376 (mmp) REVERT: E 97 GLU cc_start: 0.9492 (tt0) cc_final: 0.9289 (tt0) REVERT: E 105 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8993 (tm-30) REVERT: E 106 ASP cc_start: 0.9584 (m-30) cc_final: 0.9220 (m-30) REVERT: E 122 LYS cc_start: 0.9389 (ptmt) cc_final: 0.9058 (pttm) REVERT: F 68 ASP cc_start: 0.9632 (m-30) cc_final: 0.9045 (t0) REVERT: F 72 TYR cc_start: 0.9338 (m-80) cc_final: 0.8176 (m-10) REVERT: F 98 TYR cc_start: 0.8431 (m-10) cc_final: 0.7872 (m-10) REVERT: G 64 GLU cc_start: 0.9538 (tt0) cc_final: 0.8967 (tp30) REVERT: G 71 ARG cc_start: 0.9416 (tmm-80) cc_final: 0.9020 (tmm-80) REVERT: G 72 ASP cc_start: 0.9139 (m-30) cc_final: 0.8823 (m-30) REVERT: G 73 ASN cc_start: 0.9350 (t0) cc_final: 0.9068 (t0) REVERT: G 85 LEU cc_start: 0.9347 (mt) cc_final: 0.9022 (tt) REVERT: G 110 ASN cc_start: 0.9481 (t0) cc_final: 0.9151 (t0) REVERT: H 39 TYR cc_start: 0.9308 (t80) cc_final: 0.9104 (t80) REVERT: H 66 VAL cc_start: 0.9791 (t) cc_final: 0.9540 (m) REVERT: H 96 ARG cc_start: 0.9585 (mmm-85) cc_final: 0.9125 (tpp80) REVERT: H 105 LYS cc_start: 0.9776 (mmtp) cc_final: 0.9436 (mmmt) outliers start: 0 outliers final: 0 residues processed: 436 average time/residue: 0.2956 time to fit residues: 175.1781 Evaluate side-chains 400 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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: 0.9990 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.046059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.036450 restraints weight = 291307.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.038512 restraints weight = 103313.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.039741 restraints weight = 51355.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.040618 restraints weight = 32130.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.041153 restraints weight = 22441.510| |-----------------------------------------------------------------------------| r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16670 Z= 0.162 Angle : 0.618 4.828 23791 Z= 0.380 Chirality : 0.040 0.157 2700 Planarity : 0.004 0.060 1988 Dihedral : 28.131 170.276 4597 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.76 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.24), residues: 1196 helix: 1.58 (0.19), residues: 780 sheet: -1.42 (0.70), residues: 50 loop : -1.17 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 76 TYR 0.027 0.001 TYR C 39 PHE 0.020 0.001 PHE A 104 TRP 0.002 0.001 TRP K 110 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00342 (16670) covalent geometry : angle 0.61815 (23791) hydrogen bonds : bond 0.04444 ( 897) hydrogen bonds : angle 3.80545 ( 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 441 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.567 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: K 73 MET cc_start: 0.7441 (pmm) cc_final: 0.6716 (pmm) REVERT: K 131 GLU cc_start: 0.9767 (mp0) cc_final: 0.9479 (pm20) REVERT: K 310 LYS cc_start: 0.9641 (mmtm) cc_final: 0.9156 (pttt) REVERT: K 375 MET cc_start: 0.9061 (mmm) cc_final: 0.8860 (mmm) REVERT: K 419 LEU cc_start: 0.9548 (mt) cc_final: 0.9335 (mt) REVERT: K 422 ARG cc_start: 0.9473 (ttm-80) cc_final: 0.9097 (mtp85) REVERT: A 63 ARG cc_start: 0.9286 (mmt180) cc_final: 0.8836 (mmm-85) REVERT: A 67 PHE cc_start: 0.9399 (t80) cc_final: 0.9144 (t80) REVERT: A 70 LEU cc_start: 0.9672 (tt) cc_final: 0.9368 (mt) REVERT: A 84 PHE cc_start: 0.9270 (m-80) cc_final: 0.8777 (m-80) REVERT: A 103 LEU cc_start: 0.9887 (tp) cc_final: 0.9590 (mt) REVERT: A 105 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9120 (tm-30) REVERT: A 106 ASP cc_start: 0.9158 (t0) cc_final: 0.8647 (m-30) REVERT: A 108 ASN cc_start: 0.9490 (t0) cc_final: 0.9236 (t0) REVERT: A 119 ILE cc_start: 0.9604 (pt) cc_final: 0.9164 (tp) REVERT: A 120 MET cc_start: 0.7482 (mpp) cc_final: 0.7192 (mpp) REVERT: A 123 ASP cc_start: 0.9421 (m-30) cc_final: 0.8782 (m-30) REVERT: B 74 GLU cc_start: 0.9699 (tt0) cc_final: 0.9450 (tp30) REVERT: B 84 MET cc_start: 0.9313 (mmm) cc_final: 0.9058 (mmm) REVERT: B 92 ARG cc_start: 0.9374 (ttp80) cc_final: 0.8732 (ttp80) REVERT: C 36 LYS cc_start: 0.9726 (mmmm) cc_final: 0.9492 (mmmm) REVERT: C 89 ASN cc_start: 0.9520 (m-40) cc_final: 0.9191 (m-40) REVERT: D 65 ASP cc_start: 0.9317 (t0) cc_final: 0.8962 (t0) REVERT: D 68 GLU cc_start: 0.9240 (pp20) cc_final: 0.8998 (pp20) REVERT: D 73 GLU cc_start: 0.9690 (mm-30) cc_final: 0.9477 (mm-30) REVERT: E 62 ILE cc_start: 0.9348 (mp) cc_final: 0.8524 (mp) REVERT: E 64 LYS cc_start: 0.9547 (mtmm) cc_final: 0.9103 (pttm) REVERT: E 81 ASP cc_start: 0.9632 (m-30) cc_final: 0.9214 (p0) REVERT: E 84 PHE cc_start: 0.9605 (m-80) cc_final: 0.9323 (m-80) REVERT: E 90 MET cc_start: 0.9728 (mtm) cc_final: 0.9383 (mmp) REVERT: E 97 GLU cc_start: 0.9515 (tt0) cc_final: 0.9312 (tt0) REVERT: E 106 ASP cc_start: 0.9568 (m-30) cc_final: 0.9248 (m-30) REVERT: E 122 LYS cc_start: 0.9388 (ptmt) cc_final: 0.9092 (pttp) REVERT: F 59 LYS cc_start: 0.9631 (tmmt) cc_final: 0.9410 (tppt) REVERT: F 68 ASP cc_start: 0.9616 (m-30) cc_final: 0.9284 (t0) REVERT: F 72 TYR cc_start: 0.9292 (m-80) cc_final: 0.7868 (m-10) REVERT: G 64 GLU cc_start: 0.9525 (tt0) cc_final: 0.8957 (tp30) REVERT: G 65 LEU cc_start: 0.9569 (mp) cc_final: 0.9366 (mp) REVERT: G 71 ARG cc_start: 0.9374 (tmm-80) cc_final: 0.8980 (tmm-80) REVERT: G 72 ASP cc_start: 0.9138 (m-30) cc_final: 0.8813 (m-30) REVERT: G 73 ASN cc_start: 0.9328 (t0) cc_final: 0.9049 (t0) REVERT: G 85 LEU cc_start: 0.9313 (mt) cc_final: 0.9005 (tt) REVERT: G 92 GLU cc_start: 0.9715 (mp0) cc_final: 0.9477 (mp0) REVERT: G 112 GLN cc_start: 0.8695 (mp10) cc_final: 0.8407 (mp10) REVERT: H 39 TYR cc_start: 0.9257 (t80) cc_final: 0.9053 (t80) REVERT: H 66 VAL cc_start: 0.9783 (t) cc_final: 0.9572 (m) REVERT: H 79 HIS cc_start: 0.9806 (t-90) cc_final: 0.9600 (t-90) REVERT: H 83 ARG cc_start: 0.9324 (mpt180) cc_final: 0.8733 (mmp80) REVERT: H 96 ARG cc_start: 0.9560 (mmm-85) cc_final: 0.9057 (tpp80) REVERT: H 105 LYS cc_start: 0.9756 (mmtp) cc_final: 0.9392 (mmmt) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3098 time to fit residues: 183.3299 Evaluate side-chains 398 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 10.0000 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.043701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.034695 restraints weight = 311178.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.036611 restraints weight = 117885.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.037789 restraints weight = 60641.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.038524 restraints weight = 37480.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.039071 restraints weight = 26985.209| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16670 Z= 0.251 Angle : 0.643 4.594 23791 Z= 0.398 Chirality : 0.045 0.196 2700 Planarity : 0.005 0.064 1988 Dihedral : 28.132 172.271 4597 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.68 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.24), residues: 1196 helix: 1.30 (0.18), residues: 780 sheet: -1.71 (0.58), residues: 68 loop : -1.26 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.014 0.002 TYR B 72 PHE 0.019 0.001 PHE A 104 TRP 0.002 0.001 TRP K 110 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00513 (16670) covalent geometry : angle 0.64341 (23791) hydrogen bonds : bond 0.06302 ( 897) hydrogen bonds : angle 4.02147 ( 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 428 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7599 (pmm) cc_final: 0.6941 (pmm) REVERT: K 131 GLU cc_start: 0.9771 (mp0) cc_final: 0.9521 (pm20) REVERT: K 310 LYS cc_start: 0.9634 (mmtm) cc_final: 0.9216 (pttt) REVERT: K 422 ARG cc_start: 0.9457 (ttm-80) cc_final: 0.9108 (mtp85) REVERT: A 63 ARG cc_start: 0.9312 (mmt180) cc_final: 0.8858 (mmm-85) REVERT: A 67 PHE cc_start: 0.9398 (t80) cc_final: 0.9164 (t80) REVERT: A 84 PHE cc_start: 0.9365 (m-80) cc_final: 0.8817 (m-80) REVERT: A 103 LEU cc_start: 0.9907 (tp) cc_final: 0.9606 (mt) REVERT: A 106 ASP cc_start: 0.9248 (t0) cc_final: 0.8955 (m-30) REVERT: A 108 ASN cc_start: 0.9530 (t0) cc_final: 0.9218 (t0) REVERT: A 119 ILE cc_start: 0.9572 (pt) cc_final: 0.9110 (tp) REVERT: A 120 MET cc_start: 0.7653 (mpp) cc_final: 0.7384 (mpp) REVERT: A 123 ASP cc_start: 0.9570 (m-30) cc_final: 0.9240 (m-30) REVERT: B 29 ILE cc_start: 0.9482 (mp) cc_final: 0.9182 (tp) REVERT: B 43 VAL cc_start: 0.8993 (t) cc_final: 0.8503 (p) REVERT: B 68 ASP cc_start: 0.9494 (m-30) cc_final: 0.9023 (t70) REVERT: B 74 GLU cc_start: 0.9714 (tt0) cc_final: 0.9468 (tp30) REVERT: B 84 MET cc_start: 0.9328 (mmm) cc_final: 0.9021 (mmm) REVERT: C 36 LYS cc_start: 0.9741 (mmmm) cc_final: 0.9513 (mmmm) REVERT: C 89 ASN cc_start: 0.9570 (m-40) cc_final: 0.9249 (m-40) REVERT: D 59 MET cc_start: 0.9851 (mmp) cc_final: 0.9642 (mmp) REVERT: D 63 VAL cc_start: 0.9713 (p) cc_final: 0.9509 (p) REVERT: D 65 ASP cc_start: 0.9330 (t0) cc_final: 0.8987 (t0) REVERT: D 73 GLU cc_start: 0.9719 (mm-30) cc_final: 0.9494 (mm-30) REVERT: E 62 ILE cc_start: 0.9339 (mp) cc_final: 0.8538 (mp) REVERT: E 84 PHE cc_start: 0.9543 (m-80) cc_final: 0.9305 (m-80) REVERT: E 90 MET cc_start: 0.9761 (mtm) cc_final: 0.9390 (mmp) REVERT: E 106 ASP cc_start: 0.9565 (m-30) cc_final: 0.9029 (m-30) REVERT: E 131 ARG cc_start: 0.9551 (mtt90) cc_final: 0.9133 (mtt180) REVERT: F 60 VAL cc_start: 0.9876 (p) cc_final: 0.9513 (p) REVERT: F 62 LEU cc_start: 0.9708 (mt) cc_final: 0.9440 (mt) REVERT: F 64 ASN cc_start: 0.9771 (m-40) cc_final: 0.9293 (m110) REVERT: F 68 ASP cc_start: 0.9588 (m-30) cc_final: 0.9117 (t0) REVERT: F 72 TYR cc_start: 0.9219 (m-80) cc_final: 0.7867 (m-10) REVERT: F 98 TYR cc_start: 0.8585 (m-10) cc_final: 0.8018 (m-10) REVERT: G 64 GLU cc_start: 0.9557 (tt0) cc_final: 0.8949 (tp30) REVERT: G 65 LEU cc_start: 0.9599 (mp) cc_final: 0.9390 (mp) REVERT: G 71 ARG cc_start: 0.9426 (tmm-80) cc_final: 0.9033 (tmm-80) REVERT: G 72 ASP cc_start: 0.9114 (m-30) cc_final: 0.8811 (m-30) REVERT: G 73 ASN cc_start: 0.9387 (t0) cc_final: 0.9114 (t0) REVERT: G 85 LEU cc_start: 0.9329 (mt) cc_final: 0.8998 (tt) REVERT: G 92 GLU cc_start: 0.9633 (mp0) cc_final: 0.9245 (mp0) REVERT: H 39 TYR cc_start: 0.9295 (t80) cc_final: 0.9056 (t80) REVERT: H 79 HIS cc_start: 0.9811 (t-90) cc_final: 0.9608 (t-90) REVERT: H 96 ARG cc_start: 0.9601 (mmm-85) cc_final: 0.9111 (tpp80) REVERT: H 105 LYS cc_start: 0.9779 (mmtp) cc_final: 0.9429 (mmmt) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.3066 time to fit residues: 177.4474 Evaluate side-chains 395 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 0.9980 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.2827 r_free = 0.2827 target = 0.043666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.034579 restraints weight = 310257.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.036491 restraints weight = 118261.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.037689 restraints weight = 61207.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.038484 restraints weight = 37882.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.038945 restraints weight = 26774.431| |-----------------------------------------------------------------------------| r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16670 Z= 0.229 Angle : 0.636 6.487 23791 Z= 0.392 Chirality : 0.043 0.170 2700 Planarity : 0.005 0.056 1988 Dihedral : 28.217 169.837 4597 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.24), residues: 1196 helix: 1.18 (0.18), residues: 781 sheet: -1.90 (0.67), residues: 50 loop : -1.40 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.023 0.002 TYR F 51 PHE 0.019 0.001 PHE A 104 TRP 0.002 0.001 TRP K 110 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00467 (16670) covalent geometry : angle 0.63612 (23791) hydrogen bonds : bond 0.05335 ( 897) hydrogen bonds : angle 4.04258 ( 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 427 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7632 (pmm) cc_final: 0.6981 (pmm) REVERT: K 131 GLU cc_start: 0.9767 (mp0) cc_final: 0.9517 (pm20) REVERT: K 159 ASP cc_start: 0.8123 (p0) cc_final: 0.7919 (p0) REVERT: K 310 LYS cc_start: 0.9615 (mmtm) cc_final: 0.9253 (pttt) REVERT: K 375 MET cc_start: 0.9008 (mmm) cc_final: 0.8754 (mmm) REVERT: K 422 ARG cc_start: 0.9447 (ttm-80) cc_final: 0.9116 (mtp85) REVERT: A 63 ARG cc_start: 0.9335 (mmt180) cc_final: 0.8856 (mmm-85) REVERT: A 67 PHE cc_start: 0.9380 (t80) cc_final: 0.9169 (t80) REVERT: A 78 PHE cc_start: 0.6981 (m-80) cc_final: 0.6776 (m-80) REVERT: A 84 PHE cc_start: 0.9387 (m-80) cc_final: 0.8808 (m-80) REVERT: A 105 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9305 (tm-30) REVERT: A 108 ASN cc_start: 0.9502 (t0) cc_final: 0.9185 (t0) REVERT: A 119 ILE cc_start: 0.9567 (pt) cc_final: 0.9194 (tp) REVERT: A 120 MET cc_start: 0.7692 (mpp) cc_final: 0.7439 (mpp) REVERT: A 123 ASP cc_start: 0.9551 (m-30) cc_final: 0.9163 (m-30) REVERT: B 43 VAL cc_start: 0.9051 (t) cc_final: 0.8814 (p) REVERT: B 74 GLU cc_start: 0.9721 (tt0) cc_final: 0.9420 (tp30) REVERT: B 84 MET cc_start: 0.9298 (mmm) cc_final: 0.9005 (mmm) REVERT: B 92 ARG cc_start: 0.9497 (ttp80) cc_final: 0.8949 (ttp80) REVERT: C 36 LYS cc_start: 0.9744 (mmmm) cc_final: 0.9506 (mmmm) REVERT: D 73 GLU cc_start: 0.9710 (mm-30) cc_final: 0.9475 (mm-30) REVERT: E 84 PHE cc_start: 0.9554 (m-80) cc_final: 0.9343 (m-80) REVERT: E 90 MET cc_start: 0.9764 (mtm) cc_final: 0.9385 (mmp) REVERT: E 106 ASP cc_start: 0.9560 (m-30) cc_final: 0.9192 (m-30) REVERT: E 120 MET cc_start: 0.9287 (mtp) cc_final: 0.8907 (mtt) REVERT: F 62 LEU cc_start: 0.9720 (mt) cc_final: 0.9456 (mt) REVERT: F 68 ASP cc_start: 0.9657 (m-30) cc_final: 0.9202 (t70) REVERT: F 72 TYR cc_start: 0.9242 (m-80) cc_final: 0.8030 (m-10) REVERT: G 64 GLU cc_start: 0.9560 (tt0) cc_final: 0.8922 (tp30) REVERT: G 65 LEU cc_start: 0.9595 (mp) cc_final: 0.9380 (mp) REVERT: G 71 ARG cc_start: 0.9440 (tmm-80) cc_final: 0.9046 (tmm-80) REVERT: G 72 ASP cc_start: 0.9108 (m-30) cc_final: 0.8818 (m-30) REVERT: G 73 ASN cc_start: 0.9390 (t0) cc_final: 0.9113 (t0) REVERT: G 85 LEU cc_start: 0.9312 (mt) cc_final: 0.8966 (tt) REVERT: H 39 TYR cc_start: 0.9300 (t80) cc_final: 0.8980 (t80) REVERT: H 65 ASP cc_start: 0.9726 (t70) cc_final: 0.9460 (t70) REVERT: H 79 HIS cc_start: 0.9818 (t-90) cc_final: 0.9579 (t-90) REVERT: H 96 ARG cc_start: 0.9609 (mmm-85) cc_final: 0.9085 (tpp80) REVERT: H 105 LYS cc_start: 0.9780 (mmtp) cc_final: 0.9429 (mmmt) REVERT: H 110 GLU cc_start: 0.9546 (tp30) cc_final: 0.9164 (tp30) outliers start: 0 outliers final: 0 residues processed: 427 average time/residue: 0.3047 time to fit residues: 175.6964 Evaluate side-chains 394 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 394 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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: 4.9990 chunk 84 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.045027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.035783 restraints weight = 300626.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.037789 restraints weight = 113447.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.039015 restraints weight = 57935.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.039828 restraints weight = 35555.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.040299 restraints weight = 24928.192| |-----------------------------------------------------------------------------| r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16670 Z= 0.163 Angle : 0.608 6.109 23791 Z= 0.373 Chirality : 0.040 0.178 2700 Planarity : 0.004 0.054 1988 Dihedral : 28.108 170.086 4597 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.57 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 aren not related in a simple way. whole: 0.81 (0.25), residues: 1196 helix: 1.55 (0.19), residues: 781 sheet: -1.65 (0.65), residues: 57 loop : -1.36 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 76 TYR 0.054 0.002 TYR E 99 PHE 0.023 0.001 PHE K 417 TRP 0.003 0.001 TRP K 168 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00345 (16670) covalent geometry : angle 0.60849 (23791) hydrogen bonds : bond 0.04285 ( 897) hydrogen bonds : angle 3.77469 ( 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 : 0.371 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: 0.7547 (pmm) cc_final: 0.6858 (pmm) REVERT: K 131 GLU cc_start: 0.9749 (mp0) cc_final: 0.9471 (pm20) REVERT: K 174 ASP cc_start: 0.9008 (t0) cc_final: 0.8779 (t0) REVERT: K 310 LYS cc_start: 0.9590 (mmtm) cc_final: 0.9224 (pttt) REVERT: K 422 ARG cc_start: 0.9451 (ttm-80) cc_final: 0.9118 (mtp85) REVERT: A 63 ARG cc_start: 0.9269 (mmt180) cc_final: 0.8855 (mmm-85) REVERT: A 67 PHE cc_start: 0.9404 (t80) cc_final: 0.9171 (t80) REVERT: A 70 LEU cc_start: 0.9668 (tt) cc_final: 0.9358 (mt) REVERT: A 84 PHE cc_start: 0.9375 (m-80) cc_final: 0.8789 (m-80) REVERT: A 108 ASN cc_start: 0.9466 (t0) cc_final: 0.9214 (t0) REVERT: A 119 ILE cc_start: 0.9590 (pt) cc_final: 0.9158 (tp) REVERT: A 120 MET cc_start: 0.7677 (mpp) cc_final: 0.7420 (mpp) REVERT: A 123 ASP cc_start: 0.9506 (m-30) cc_final: 0.8980 (m-30) REVERT: B 74 GLU cc_start: 0.9691 (tt0) cc_final: 0.9387 (tp30) REVERT: B 84 MET cc_start: 0.9200 (mmm) cc_final: 0.8871 (mmm) REVERT: C 36 LYS cc_start: 0.9729 (mmmm) cc_final: 0.9481 (mmmm) REVERT: D 59 MET cc_start: 0.9840 (mmp) cc_final: 0.9640 (mmp) REVERT: D 65 ASP cc_start: 0.9394 (t0) cc_final: 0.9155 (t0) REVERT: D 73 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9446 (mm-30) REVERT: E 59 GLU cc_start: 0.9287 (mp0) cc_final: 0.9059 (mp0) REVERT: E 70 LEU cc_start: 0.9297 (tp) cc_final: 0.9023 (mm) REVERT: E 84 PHE cc_start: 0.9571 (m-80) cc_final: 0.9367 (m-80) REVERT: E 90 MET cc_start: 0.9755 (mtm) cc_final: 0.9412 (mmp) REVERT: E 106 ASP cc_start: 0.9508 (m-30) cc_final: 0.8907 (m-30) REVERT: E 118 THR cc_start: 0.8778 (m) cc_final: 0.8257 (m) REVERT: E 120 MET cc_start: 0.9324 (mtp) cc_final: 0.8971 (mtt) REVERT: E 131 ARG cc_start: 0.9462 (mtt90) cc_final: 0.8958 (mtt180) REVERT: F 62 LEU cc_start: 0.9714 (mt) cc_final: 0.9496 (mt) REVERT: G 64 GLU cc_start: 0.9551 (tt0) cc_final: 0.8904 (tp30) REVERT: G 65 LEU cc_start: 0.9567 (mp) cc_final: 0.9341 (mp) REVERT: G 71 ARG cc_start: 0.9449 (tmm-80) cc_final: 0.9076 (tmm-80) REVERT: G 72 ASP cc_start: 0.9130 (m-30) cc_final: 0.8834 (m-30) REVERT: G 73 ASN cc_start: 0.9370 (t0) cc_final: 0.9077 (t0) REVERT: G 85 LEU cc_start: 0.9290 (mt) cc_final: 0.8967 (tt) REVERT: G 115 LEU cc_start: 0.9572 (mt) cc_final: 0.9347 (mp) REVERT: H 39 TYR cc_start: 0.9245 (t80) cc_final: 0.9001 (t80) REVERT: H 65 ASP cc_start: 0.9712 (t70) cc_final: 0.9480 (t70) REVERT: H 66 VAL cc_start: 0.9802 (t) cc_final: 0.9592 (m) REVERT: H 79 HIS cc_start: 0.9805 (t-90) cc_final: 0.9562 (t-90) REVERT: H 96 ARG cc_start: 0.9619 (mmm-85) cc_final: 0.9245 (tpp80) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.3044 time to fit residues: 178.4212 Evaluate side-chains 403 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 4.9990 chunk 98 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 106 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 = 0.2778 r_free = 0.2778 target = 0.042067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.032956 restraints weight = 325015.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.034788 restraints weight = 126252.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.035948 restraints weight = 66193.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.036743 restraints weight = 41501.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.037253 restraints weight = 29611.325| |-----------------------------------------------------------------------------| r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.120 16670 Z= 0.396 Angle : 0.719 6.834 23791 Z= 0.442 Chirality : 0.052 0.178 2700 Planarity : 0.005 0.055 1988 Dihedral : 28.300 172.417 4597 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.43 % Favored : 95.40 % 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 aren not related in a simple way. whole: -0.34 (0.23), residues: 1196 helix: 0.57 (0.18), residues: 781 sheet: -2.19 (0.56), residues: 69 loop : -1.50 (0.31), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 76 TYR 0.014 0.002 TYR B 72 PHE 0.015 0.002 PHE K 417 TRP 0.011 0.002 TRP K 110 HIS 0.010 0.002 HIS K 187 Details of bonding type rmsd covalent geometry : bond 0.00808 (16670) covalent geometry : angle 0.71878 (23791) hydrogen bonds : bond 0.08245 ( 897) hydrogen bonds : angle 4.54267 ( 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 420 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 73 MET cc_start: 0.7775 (pmm) cc_final: 0.7282 (pmm) REVERT: K 131 GLU cc_start: 0.9772 (mp0) cc_final: 0.9533 (pm20) REVERT: K 310 LYS cc_start: 0.9612 (mmtm) cc_final: 0.9266 (pttt) REVERT: K 422 ARG cc_start: 0.9484 (ttm-80) cc_final: 0.9130 (mtp85) REVERT: A 63 ARG cc_start: 0.9379 (mmt180) cc_final: 0.8910 (mmm-85) REVERT: A 84 PHE cc_start: 0.9394 (m-80) cc_final: 0.8795 (m-80) REVERT: A 105 GLU cc_start: 0.9596 (tm-30) cc_final: 0.9375 (tm-30) REVERT: B 74 GLU cc_start: 0.9741 (tt0) cc_final: 0.9450 (tp30) REVERT: B 84 MET cc_start: 0.9337 (mmm) cc_final: 0.9015 (mmm) REVERT: B 92 ARG cc_start: 0.9507 (ttp80) cc_final: 0.8953 (ttp80) REVERT: C 36 LYS cc_start: 0.9737 (mmmm) cc_final: 0.9474 (mmmm) REVERT: D 63 VAL cc_start: 0.9772 (p) cc_final: 0.9554 (p) REVERT: D 73 GLU cc_start: 0.9733 (mm-30) cc_final: 0.9337 (mt-10) REVERT: E 70 LEU cc_start: 0.9251 (tp) cc_final: 0.8885 (mm) REVERT: E 90 MET cc_start: 0.9790 (mtm) cc_final: 0.9401 (mmm) REVERT: E 120 MET cc_start: 0.9347 (mtp) cc_final: 0.9021 (mtt) REVERT: F 68 ASP cc_start: 0.9608 (m-30) cc_final: 0.9279 (t70) REVERT: F 72 TYR cc_start: 0.9364 (m-10) cc_final: 0.8985 (m-80) REVERT: G 64 GLU cc_start: 0.9577 (tt0) cc_final: 0.8960 (tp30) REVERT: G 65 LEU cc_start: 0.9591 (mp) cc_final: 0.9375 (mp) REVERT: G 71 ARG cc_start: 0.9473 (tmm-80) cc_final: 0.9077 (tmm-80) REVERT: G 72 ASP cc_start: 0.9073 (m-30) cc_final: 0.8602 (m-30) REVERT: G 73 ASN cc_start: 0.9423 (t0) cc_final: 0.9096 (t0) REVERT: G 85 LEU cc_start: 0.9354 (mt) cc_final: 0.9009 (tt) REVERT: G 115 LEU cc_start: 0.9570 (mt) cc_final: 0.9334 (mp) REVERT: H 39 TYR cc_start: 0.9298 (t80) cc_final: 0.9037 (t80) REVERT: H 65 ASP cc_start: 0.9725 (t70) cc_final: 0.9478 (t70) REVERT: H 79 HIS cc_start: 0.9827 (t-90) cc_final: 0.9596 (t-90) REVERT: H 96 ARG cc_start: 0.9619 (mmm-85) cc_final: 0.9353 (tpp80) REVERT: H 105 LYS cc_start: 0.9795 (mmtp) cc_final: 0.9473 (mmmt) REVERT: H 110 GLU cc_start: 0.9606 (tp30) cc_final: 0.9318 (tp30) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.3056 time to fit residues: 174.0566 Evaluate side-chains 379 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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: 3.9990 chunk 20 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.043715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.034612 restraints weight = 310582.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.036533 restraints weight = 117351.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.037715 restraints weight = 60710.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.038503 restraints weight = 37677.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.038970 restraints weight = 26757.578| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16670 Z= 0.206 Angle : 0.630 5.765 23791 Z= 0.388 Chirality : 0.043 0.168 2700 Planarity : 0.005 0.072 1988 Dihedral : 28.329 170.793 4597 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.51 % Favored : 96.32 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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 aren not related in a simple way. whole: 0.19 (0.24), residues: 1196 helix: 1.04 (0.18), residues: 783 sheet: -1.90 (0.63), residues: 57 loop : -1.51 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.028 0.002 TYR E 99 PHE 0.016 0.002 PHE A 104 TRP 0.005 0.001 TRP K 110 HIS 0.016 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00425 (16670) covalent geometry : angle 0.63014 (23791) hydrogen bonds : bond 0.05322 ( 897) hydrogen bonds : angle 4.09007 ( 2330) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4863.05 seconds wall clock time: 83 minutes 23.66 seconds (5003.66 seconds total)