Starting phenix.real_space_refine on Thu Mar 21 02:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_13065.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_13065.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_13065.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_13065.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7otq_13065/03_2024/7otq_13065.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 13.10, per 1000 atoms: 0.45 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 27.20 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 14.96 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: 12.32 Time building geometry restraints manager: 27.84 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: 98.37 - 105.48: 1414 105.48 - 112.60: 33303 112.60 - 119.71: 8202 119.71 - 126.82: 10645 126.82 - 133.94: 851 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 1.850 nonbonded pdb=" HH TYR K 289 " pdb=" OE1 GLU K 304 " model vdw 1.545 1.850 nonbonded pdb=" OE1 GLN K 450 " pdb="HH21 ARG K 454 " model vdw 1.581 1.850 nonbonded pdb="HH22 ARG E 116 " pdb=" OD2 ASP E 123 " model vdw 1.599 1.850 nonbonded pdb=" O GLY K 70 " pdb="HH11 ARG K 260 " model vdw 1.606 1.850 ... (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 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: 2.880 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: 0.380 Extract box with map and model: 14.190 Check model and map are aligned: 0.400 Set scattering table: 0.280 Process input model: 105.180 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.790 ------------------------------------------------------------------------------- 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= 0.229 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (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 TRP 0.021 0.006 TRP K 168 HIS 0.011 0.003 HIS D 46 PHE 0.016 0.003 PHE K 369 TYR 0.043 0.006 TYR K 237 ARG 0.026 0.003 ARG E 116 *********************** 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 fitting. rotamer outliers: 13 poor density : 501 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 100 ILE cc_start: 0.9610 (mt) cc_final: 0.9409 (tp) REVERT: K 110 TRP cc_start: 0.9739 (t-100) cc_final: 0.9498 (t-100) REVERT: K 174 ASP cc_start: 0.9030 (t0) cc_final: 0.8568 (t0) REVERT: K 194 SER cc_start: 0.9396 (t) cc_final: 0.9158 (p) REVERT: K 372 MET cc_start: 0.8868 (mtm) cc_final: 0.8546 (pmm) REVERT: A 60 LEU cc_start: 0.8760 (mt) cc_final: 0.8040 (mt) REVERT: A 63 ARG cc_start: 0.9287 (mmt180) cc_final: 0.9053 (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: 0.8909 (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: 0.9173 (tp) REVERT: A 120 MET cc_start: 0.7712 (mtm) cc_final: 0.7131 (mpp) REVERT: A 123 ASP cc_start: 0.9633 (m-30) cc_final: 0.9376 (m-30) REVERT: A 125 GLN cc_start: 0.9733 (mt0) cc_final: 0.9477 (mm110) REVERT: A 129 ARG cc_start: 0.9493 (tpt90) cc_final: 0.9257 (tpt90) REVERT: B 64 ASN cc_start: 0.9516 (m-40) cc_final: 0.9220 (t0) REVERT: B 72 TYR cc_start: 0.9261 (m-80) cc_final: 0.8882 (m-80) REVERT: B 74 GLU cc_start: 0.9751 (tt0) cc_final: 0.9433 (tp30) REVERT: C 90 ASP cc_start: 0.9107 (t0) cc_final: 0.8883 (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: 0.8933 (p) REVERT: D 59 MET cc_start: 0.9782 (mmm) cc_final: 0.9455 (mmp) REVERT: D 79 HIS cc_start: 0.9702 (t70) cc_final: 0.9477 (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: 0.9210 (p0) REVERT: F 62 LEU cc_start: 0.9691 (mt) cc_final: 0.9469 (mt) REVERT: F 68 ASP cc_start: 0.9477 (m-30) cc_final: 0.9012 (t0) REVERT: F 72 TYR cc_start: 0.9469 (m-80) cc_final: 0.9182 (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: 0.8894 (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: 0.9180 (tpt170) REVERT: G 84 GLN cc_start: 0.9740 (tp40) cc_final: 0.9522 (tp-100) REVERT: G 110 ASN cc_start: 0.9646 (t0) cc_final: 0.9387 (t0) REVERT: G 112 GLN cc_start: 0.8356 (mp10) cc_final: 0.7872 (mp10) 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: 0.8950 (tp) REVERT: H 96 ARG cc_start: 0.9661 (mmm-85) cc_final: 0.9324 (tpp80) REVERT: H 110 GLU cc_start: 0.9543 (tp30) cc_final: 0.9145 (mm-30) outliers start: 13 outliers final: 7 residues processed: 511 average time/residue: 0.8014 time to fit residues: 550.7108 Evaluate side-chains 430 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 423 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** K 371 GLN A 39 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16670 Z= 0.312 Angle : 0.741 5.889 23791 Z= 0.458 Chirality : 0.047 0.228 2700 Planarity : 0.006 0.046 1988 Dihedral : 28.327 171.695 4597 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.84 % Favored : 96.91 % Rotamer: Outliers : 0.10 % Allowed : 2.33 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.23), residues: 1196 helix: 0.27 (0.17), residues: 781 sheet: -0.52 (0.63), residues: 68 loop : -0.88 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 168 HIS 0.015 0.002 HIS D 106 PHE 0.017 0.002 PHE K 417 TYR 0.015 0.002 TYR K 214 ARG 0.026 0.001 ARG A 42 *********************** 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 465 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 464 time to evaluate : 1.688 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 110 TRP cc_start: 0.9715 (t-100) cc_final: 0.9368 (t-100) REVERT: K 113 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8806 (mt-10) REVERT: K 194 SER cc_start: 0.9379 (t) cc_final: 0.9138 (p) REVERT: K 353 ASP cc_start: 0.9338 (t0) cc_final: 0.9136 (t0) REVERT: K 426 VAL cc_start: 0.8454 (m) cc_final: 0.8211 (m) REVERT: K 428 MET cc_start: 0.9108 (mtm) cc_final: 0.8660 (mpp) REVERT: A 62 ILE cc_start: 0.9366 (mm) cc_final: 0.9043 (mm) REVERT: A 63 ARG cc_start: 0.9400 (mmt180) cc_final: 0.9148 (mmm160) REVERT: A 73 GLU cc_start: 0.9614 (mt-10) cc_final: 0.9204 (mt-10) REVERT: A 103 LEU cc_start: 0.9869 (tp) cc_final: 0.9483 (mt) REVERT: A 105 GLU cc_start: 0.9591 (mt-10) cc_final: 0.9286 (mm-30) REVERT: A 108 ASN cc_start: 0.9665 (t0) cc_final: 0.9369 (t0) REVERT: A 119 ILE cc_start: 0.9686 (pt) cc_final: 0.8918 (tp) REVERT: A 120 MET cc_start: 0.8270 (mtm) cc_final: 0.7117 (mpp) REVERT: A 128 ARG cc_start: 0.9214 (mtp-110) cc_final: 0.8966 (mtp-110) REVERT: B 50 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 68 ASP cc_start: 0.9704 (m-30) cc_final: 0.9466 (m-30) REVERT: B 72 TYR cc_start: 0.9313 (m-80) cc_final: 0.9109 (m-80) REVERT: B 74 GLU cc_start: 0.9778 (tt0) cc_final: 0.9488 (tp30) REVERT: C 83 LEU cc_start: 0.9676 (mt) cc_final: 0.9441 (mm) REVERT: C 90 ASP cc_start: 0.9487 (t0) cc_final: 0.9093 (t0) REVERT: C 108 LEU cc_start: 0.9605 (tp) cc_final: 0.9303 (tt) REVERT: D 43 LYS cc_start: 0.9612 (mmtt) cc_final: 0.9386 (mmmm) REVERT: D 59 MET cc_start: 0.9829 (mmm) cc_final: 0.9601 (mmp) REVERT: D 79 HIS cc_start: 0.9703 (t70) cc_final: 0.9376 (t-90) REVERT: E 60 LEU cc_start: 0.8860 (mm) cc_final: 0.8470 (mm) REVERT: E 81 ASP cc_start: 0.9587 (m-30) cc_final: 0.9221 (p0) REVERT: E 84 PHE cc_start: 0.9623 (m-80) cc_final: 0.9171 (m-80) REVERT: E 90 MET cc_start: 0.9739 (mtm) cc_final: 0.9332 (mmm) REVERT: E 99 TYR cc_start: 0.9060 (t80) cc_final: 0.8783 (t80) REVERT: F 62 LEU cc_start: 0.9680 (mt) cc_final: 0.9451 (mt) REVERT: F 77 LYS cc_start: 0.9662 (mmtt) cc_final: 0.9340 (mmmm) REVERT: G 36 LYS cc_start: 0.9751 (mmmt) cc_final: 0.9435 (mmmt) REVERT: G 75 LYS cc_start: 0.9211 (mttt) cc_final: 0.8980 (mmmt) REVERT: G 110 ASN cc_start: 0.9596 (t0) cc_final: 0.9276 (t0) REVERT: G 112 GLN cc_start: 0.8992 (mp10) cc_final: 0.8737 (mp10) REVERT: H 39 TYR cc_start: 0.9367 (t80) cc_final: 0.9090 (t80) REVERT: H 59 MET cc_start: 0.9811 (mmm) cc_final: 0.9345 (mmm) REVERT: H 65 ASP cc_start: 0.9767 (t0) cc_final: 0.9549 (t70) REVERT: H 73 GLU cc_start: 0.9440 (tp30) cc_final: 0.8715 (tp30) REVERT: H 79 HIS cc_start: 0.9791 (t-90) cc_final: 0.9577 (t-90) REVERT: H 96 ARG cc_start: 0.9663 (mmm-85) cc_final: 0.9349 (tpp80) outliers start: 1 outliers final: 0 residues processed: 464 average time/residue: 0.7578 time to fit residues: 471.6637 Evaluate side-chains 421 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 420 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 116 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** B 75 HIS G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16670 Z= 0.270 Angle : 0.674 5.342 23791 Z= 0.417 Chirality : 0.044 0.204 2700 Planarity : 0.005 0.044 1988 Dihedral : 28.376 174.922 4597 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.09 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1196 helix: 0.75 (0.18), residues: 779 sheet: -0.74 (0.61), residues: 66 loop : -1.05 (0.32), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 168 HIS 0.010 0.001 HIS D 106 PHE 0.017 0.002 PHE F 100 TYR 0.030 0.002 TYR B 88 ARG 0.007 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 113 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8901 (mt-10) REVERT: K 174 ASP cc_start: 0.8871 (t0) cc_final: 0.8642 (t0) REVERT: K 194 SER cc_start: 0.9398 (t) cc_final: 0.9167 (p) REVERT: K 310 LYS cc_start: 0.9713 (mptt) cc_final: 0.9336 (pttt) REVERT: K 426 VAL cc_start: 0.8592 (m) cc_final: 0.8387 (m) REVERT: K 428 MET cc_start: 0.9069 (mtm) cc_final: 0.8785 (mpp) REVERT: A 63 ARG cc_start: 0.9411 (mmt180) cc_final: 0.8981 (mmm-85) REVERT: A 77 ASP cc_start: 0.9161 (m-30) cc_final: 0.8818 (m-30) REVERT: A 84 PHE cc_start: 0.8752 (m-80) cc_final: 0.8116 (m-80) REVERT: A 89 VAL cc_start: 0.9765 (t) cc_final: 0.9458 (p) REVERT: A 97 GLU cc_start: 0.9755 (mt-10) cc_final: 0.9516 (mt-10) REVERT: A 103 LEU cc_start: 0.9865 (tp) cc_final: 0.9626 (mt) REVERT: A 105 GLU cc_start: 0.9571 (mt-10) cc_final: 0.9145 (mm-30) REVERT: A 108 ASN cc_start: 0.9671 (t0) cc_final: 0.9351 (t0) REVERT: A 119 ILE cc_start: 0.9556 (pt) cc_final: 0.9235 (tp) REVERT: A 120 MET cc_start: 0.7755 (mpp) cc_final: 0.7178 (mpp) REVERT: B 43 VAL cc_start: 0.9062 (t) cc_final: 0.8746 (t) REVERT: B 74 GLU cc_start: 0.9774 (tt0) cc_final: 0.9491 (tp30) REVERT: B 84 MET cc_start: 0.9500 (mmm) cc_final: 0.9244 (mmm) REVERT: C 108 LEU cc_start: 0.9618 (tp) cc_final: 0.9338 (tt) REVERT: D 79 HIS cc_start: 0.9735 (t70) cc_final: 0.9401 (t-90) REVERT: E 64 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9167 (mtmm) REVERT: E 81 ASP cc_start: 0.9602 (m-30) cc_final: 0.9232 (p0) REVERT: E 84 PHE cc_start: 0.9591 (m-80) cc_final: 0.9268 (m-80) REVERT: E 105 GLU cc_start: 0.9163 (tm-30) cc_final: 0.8897 (tm-30) REVERT: E 106 ASP cc_start: 0.9383 (m-30) cc_final: 0.8897 (m-30) REVERT: E 120 MET cc_start: 0.8854 (mtp) cc_final: 0.8353 (mtt) REVERT: F 68 ASP cc_start: 0.9616 (m-30) cc_final: 0.9008 (t70) REVERT: F 72 TYR cc_start: 0.9403 (m-80) cc_final: 0.8384 (m-10) REVERT: F 77 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9354 (mmmm) REVERT: G 42 ARG cc_start: 0.9407 (mtp-110) cc_final: 0.8924 (mtp85) REVERT: G 54 VAL cc_start: 0.9784 (t) cc_final: 0.9366 (t) REVERT: G 64 GLU cc_start: 0.9494 (tt0) cc_final: 0.9206 (mt-10) REVERT: G 75 LYS cc_start: 0.9285 (mttt) cc_final: 0.9075 (mmmt) REVERT: G 116 LEU cc_start: 0.9118 (mm) cc_final: 0.8878 (mm) REVERT: H 39 TYR cc_start: 0.9363 (t80) cc_final: 0.9068 (t80) REVERT: H 45 VAL cc_start: 0.8610 (m) cc_final: 0.8346 (m) REVERT: H 79 HIS cc_start: 0.9808 (t-90) cc_final: 0.9583 (t-90) REVERT: H 96 ARG cc_start: 0.9648 (mmm-85) cc_final: 0.9267 (tpp80) REVERT: H 110 GLU cc_start: 0.9527 (tp30) cc_final: 0.8901 (tm-30) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.7327 time to fit residues: 448.6372 Evaluate side-chains 407 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 16670 Z= 0.315 Angle : 0.679 5.156 23791 Z= 0.422 Chirality : 0.046 0.207 2700 Planarity : 0.005 0.048 1988 Dihedral : 28.373 173.028 4597 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.84 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.23), residues: 1196 helix: 0.55 (0.18), residues: 779 sheet: -1.00 (0.62), residues: 66 loop : -1.23 (0.30), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 110 HIS 0.007 0.001 HIS D 106 PHE 0.022 0.002 PHE G 25 TYR 0.017 0.002 TYR B 72 ARG 0.007 0.001 ARG D 76 *********************** 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 433 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 194 SER cc_start: 0.9449 (t) cc_final: 0.9245 (p) REVERT: K 210 LEU cc_start: 0.9529 (pt) cc_final: 0.9199 (pt) REVERT: K 422 ARG cc_start: 0.9466 (ttm-80) cc_final: 0.9150 (mtp85) REVERT: K 426 VAL cc_start: 0.8567 (m) cc_final: 0.8360 (m) REVERT: A 63 ARG cc_start: 0.9424 (mmt180) cc_final: 0.9005 (mmm-85) REVERT: A 64 LYS cc_start: 0.9393 (mtmm) cc_final: 0.9132 (mtmm) REVERT: A 77 ASP cc_start: 0.9200 (m-30) cc_final: 0.8855 (m-30) REVERT: A 84 PHE cc_start: 0.8941 (m-80) cc_final: 0.8400 (m-80) REVERT: A 89 VAL cc_start: 0.9777 (t) cc_final: 0.9475 (p) REVERT: A 97 GLU cc_start: 0.9753 (mt-10) cc_final: 0.9478 (mt-10) REVERT: A 103 LEU cc_start: 0.9847 (tp) cc_final: 0.9599 (mt) REVERT: A 105 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9278 (mm-30) REVERT: A 108 ASN cc_start: 0.9661 (t0) cc_final: 0.9376 (t0) REVERT: A 119 ILE cc_start: 0.9526 (pt) cc_final: 0.9115 (tp) REVERT: A 120 MET cc_start: 0.7729 (mpp) cc_final: 0.7233 (mpp) REVERT: A 123 ASP cc_start: 0.9654 (m-30) cc_final: 0.9353 (m-30) REVERT: B 46 ILE cc_start: 0.9615 (mm) cc_final: 0.9404 (mp) REVERT: B 74 GLU cc_start: 0.9787 (tt0) cc_final: 0.9501 (tp30) REVERT: B 84 MET cc_start: 0.9489 (mmm) cc_final: 0.9256 (mmm) REVERT: B 100 PHE cc_start: 0.9317 (m-80) cc_final: 0.9032 (m-80) REVERT: C 108 LEU cc_start: 0.9623 (tp) cc_final: 0.9357 (tt) REVERT: D 79 HIS cc_start: 0.9709 (t70) cc_final: 0.9364 (t-90) REVERT: E 62 ILE cc_start: 0.9416 (mp) cc_final: 0.8599 (mp) REVERT: E 64 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9121 (mtmm) REVERT: E 81 ASP cc_start: 0.9646 (m-30) cc_final: 0.9265 (p0) REVERT: E 84 PHE cc_start: 0.9617 (m-80) cc_final: 0.9336 (m-80) REVERT: E 97 GLU cc_start: 0.9497 (tt0) cc_final: 0.9286 (tt0) REVERT: E 106 ASP cc_start: 0.9395 (m-30) cc_final: 0.9070 (m-30) REVERT: E 120 MET cc_start: 0.8899 (mtp) cc_final: 0.8419 (mtt) REVERT: F 64 ASN cc_start: 0.9782 (m-40) cc_final: 0.9482 (m-40) REVERT: F 68 ASP cc_start: 0.9603 (m-30) cc_final: 0.9110 (t70) REVERT: F 72 TYR cc_start: 0.9416 (m-80) cc_final: 0.8360 (m-10) REVERT: F 77 LYS cc_start: 0.9696 (mmtt) cc_final: 0.9392 (mmmm) REVERT: G 39 TYR cc_start: 0.9450 (m-80) cc_final: 0.9231 (m-80) REVERT: G 71 ARG cc_start: 0.9444 (tmm-80) cc_final: 0.9063 (tmm-80) REVERT: G 72 ASP cc_start: 0.9146 (m-30) cc_final: 0.8766 (m-30) REVERT: G 75 LYS cc_start: 0.9286 (mttt) cc_final: 0.9074 (mmmt) REVERT: G 116 LEU cc_start: 0.9086 (mm) cc_final: 0.8831 (mm) REVERT: H 39 TYR cc_start: 0.9360 (t80) cc_final: 0.8975 (t80) REVERT: H 65 ASP cc_start: 0.9756 (t70) cc_final: 0.9499 (t70) REVERT: H 73 GLU cc_start: 0.9284 (tp30) cc_final: 0.8681 (tp30) REVERT: H 79 HIS cc_start: 0.9811 (t-90) cc_final: 0.9587 (t-90) REVERT: H 96 ARG cc_start: 0.9637 (mmm-85) cc_final: 0.9199 (tpp80) REVERT: H 105 LYS cc_start: 0.9782 (mmtp) cc_final: 0.9441 (mmmt) outliers start: 0 outliers final: 0 residues processed: 433 average time/residue: 0.7642 time to fit residues: 456.2534 Evaluate side-chains 398 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16670 Z= 0.287 Angle : 0.663 7.224 23791 Z= 0.411 Chirality : 0.045 0.193 2700 Planarity : 0.005 0.053 1988 Dihedral : 28.358 172.904 4597 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.01 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.23), residues: 1196 helix: 0.68 (0.18), residues: 779 sheet: -1.40 (0.66), residues: 49 loop : -1.30 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 110 HIS 0.006 0.001 HIS D 106 PHE 0.016 0.001 PHE A 67 TYR 0.018 0.002 TYR B 72 ARG 0.006 0.001 ARG G 42 *********************** 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 432 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 1.768 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: K 194 SER cc_start: 0.9465 (t) cc_final: 0.9259 (p) REVERT: K 422 ARG cc_start: 0.9447 (ttm-80) cc_final: 0.9130 (mtp85) REVERT: A 63 ARG cc_start: 0.9420 (mmt180) cc_final: 0.8976 (mmm-85) REVERT: A 64 LYS cc_start: 0.9415 (mtmm) cc_final: 0.9155 (mtmm) REVERT: A 77 ASP cc_start: 0.9200 (m-30) cc_final: 0.8840 (m-30) REVERT: A 84 PHE cc_start: 0.8931 (m-80) cc_final: 0.8416 (m-80) REVERT: A 89 VAL cc_start: 0.9781 (t) cc_final: 0.9471 (p) REVERT: A 97 GLU cc_start: 0.9755 (mt-10) cc_final: 0.9455 (mt-10) REVERT: A 103 LEU cc_start: 0.9849 (tp) cc_final: 0.9596 (mt) REVERT: A 105 GLU cc_start: 0.9609 (mt-10) cc_final: 0.9154 (mm-30) REVERT: A 106 ASP cc_start: 0.9111 (m-30) cc_final: 0.8902 (m-30) REVERT: A 108 ASN cc_start: 0.9648 (t0) cc_final: 0.9398 (t0) REVERT: A 119 ILE cc_start: 0.9485 (pt) cc_final: 0.9064 (tp) REVERT: A 120 MET cc_start: 0.8100 (mpp) cc_final: 0.7464 (mpp) REVERT: B 74 GLU cc_start: 0.9783 (tt0) cc_final: 0.9503 (tp30) REVERT: B 84 MET cc_start: 0.9446 (mmm) cc_final: 0.9139 (mmm) REVERT: B 92 ARG cc_start: 0.9414 (ttp80) cc_final: 0.8980 (ttp80) REVERT: C 36 LYS cc_start: 0.9724 (mmmm) cc_final: 0.9521 (mmmm) REVERT: D 79 HIS cc_start: 0.9717 (t70) cc_final: 0.9419 (t-90) REVERT: E 62 ILE cc_start: 0.9423 (mp) cc_final: 0.8651 (mp) REVERT: E 81 ASP cc_start: 0.9627 (m-30) cc_final: 0.9228 (p0) REVERT: E 84 PHE cc_start: 0.9635 (m-80) cc_final: 0.9366 (m-80) REVERT: E 90 MET cc_start: 0.9809 (mtm) cc_final: 0.9392 (mmp) REVERT: E 97 GLU cc_start: 0.9499 (tt0) cc_final: 0.9249 (tt0) REVERT: E 105 GLU cc_start: 0.9455 (tm-30) cc_final: 0.9225 (tm-30) REVERT: E 106 ASP cc_start: 0.9469 (m-30) cc_final: 0.9001 (m-30) REVERT: F 64 ASN cc_start: 0.9775 (m-40) cc_final: 0.9506 (m-40) REVERT: F 68 ASP cc_start: 0.9622 (m-30) cc_final: 0.9108 (t0) REVERT: F 72 TYR cc_start: 0.9419 (m-80) cc_final: 0.8295 (m-10) REVERT: F 77 LYS cc_start: 0.9692 (mmtt) cc_final: 0.9374 (mmmm) REVERT: G 71 ARG cc_start: 0.9448 (tmm-80) cc_final: 0.9108 (tmm-80) REVERT: G 72 ASP cc_start: 0.9096 (m-30) cc_final: 0.8749 (m-30) REVERT: G 75 LYS cc_start: 0.9277 (mttt) cc_final: 0.9061 (mmmt) REVERT: G 116 LEU cc_start: 0.9080 (mm) cc_final: 0.8829 (mm) REVERT: H 39 TYR cc_start: 0.9336 (t80) cc_final: 0.8982 (t80) REVERT: H 65 ASP cc_start: 0.9748 (t70) cc_final: 0.9411 (t70) REVERT: H 73 GLU cc_start: 0.9281 (tp30) cc_final: 0.8685 (tp30) REVERT: H 79 HIS cc_start: 0.9811 (t-90) cc_final: 0.9590 (t-90) REVERT: H 96 ARG cc_start: 0.9632 (mmm-85) cc_final: 0.9168 (tpp80) REVERT: H 105 LYS cc_start: 0.9787 (mmtp) cc_final: 0.9443 (mmmt) outliers start: 0 outliers final: 0 residues processed: 432 average time/residue: 0.7542 time to fit residues: 444.2442 Evaluate side-chains 398 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 73 optimal weight: 0.0980 chunk 134 optimal weight: 3.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.5459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 16670 Z= 0.329 Angle : 0.682 5.027 23791 Z= 0.421 Chirality : 0.046 0.182 2700 Planarity : 0.005 0.042 1988 Dihedral : 28.427 172.287 4597 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.01 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.23), residues: 1196 helix: 0.42 (0.18), residues: 778 sheet: -1.95 (0.62), residues: 49 loop : -1.42 (0.29), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 110 HIS 0.007 0.002 HIS D 106 PHE 0.019 0.002 PHE A 104 TYR 0.021 0.002 TYR B 72 ARG 0.007 0.001 ARG C 42 *********************** 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 418 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 1.677 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: K 422 ARG cc_start: 0.9460 (ttm-80) cc_final: 0.9140 (mtp85) REVERT: A 63 ARG cc_start: 0.9442 (mmt180) cc_final: 0.9003 (mmm-85) REVERT: A 84 PHE cc_start: 0.9006 (m-80) cc_final: 0.8326 (m-80) REVERT: A 89 VAL cc_start: 0.9786 (t) cc_final: 0.9480 (p) REVERT: A 97 GLU cc_start: 0.9768 (mt-10) cc_final: 0.9421 (mt-10) REVERT: A 103 LEU cc_start: 0.9851 (tp) cc_final: 0.9613 (mt) REVERT: A 105 GLU cc_start: 0.9598 (mt-10) cc_final: 0.9198 (mm-30) REVERT: A 119 ILE cc_start: 0.9501 (pt) cc_final: 0.9029 (tp) REVERT: A 120 MET cc_start: 0.8212 (mpp) cc_final: 0.7632 (mpp) REVERT: B 46 ILE cc_start: 0.9618 (mm) cc_final: 0.9393 (mp) REVERT: B 74 GLU cc_start: 0.9787 (tt0) cc_final: 0.9518 (tp30) REVERT: B 84 MET cc_start: 0.9453 (mmm) cc_final: 0.9144 (mmm) REVERT: B 92 ARG cc_start: 0.9442 (ttp80) cc_final: 0.9024 (ttp80) REVERT: B 100 PHE cc_start: 0.9351 (m-80) cc_final: 0.9090 (m-80) REVERT: C 36 LYS cc_start: 0.9756 (mmmm) cc_final: 0.9550 (mmmm) REVERT: C 56 GLU cc_start: 0.8764 (tt0) cc_final: 0.8113 (tt0) REVERT: E 62 ILE cc_start: 0.9453 (mp) cc_final: 0.8635 (mp) REVERT: E 81 ASP cc_start: 0.9600 (m-30) cc_final: 0.9200 (p0) REVERT: E 84 PHE cc_start: 0.9603 (m-80) cc_final: 0.9354 (m-80) REVERT: E 90 MET cc_start: 0.9807 (mtm) cc_final: 0.9381 (mmp) REVERT: F 62 LEU cc_start: 0.9620 (mt) cc_final: 0.9401 (mt) REVERT: F 64 ASN cc_start: 0.9765 (m-40) cc_final: 0.9535 (m-40) REVERT: F 68 ASP cc_start: 0.9615 (m-30) cc_final: 0.9176 (t70) REVERT: F 72 TYR cc_start: 0.9441 (m-80) cc_final: 0.8339 (m-10) REVERT: F 77 LYS cc_start: 0.9709 (mmtt) cc_final: 0.9402 (mmmm) REVERT: F 98 TYR cc_start: 0.8379 (m-10) cc_final: 0.8019 (m-10) REVERT: G 71 ARG cc_start: 0.9465 (tmm-80) cc_final: 0.9160 (tmm-80) REVERT: G 72 ASP cc_start: 0.9044 (m-30) cc_final: 0.8715 (m-30) REVERT: G 73 ASN cc_start: 0.9238 (t0) cc_final: 0.8853 (t0) REVERT: G 78 ILE cc_start: 0.9551 (mt) cc_final: 0.9197 (tp) REVERT: H 39 TYR cc_start: 0.9337 (t80) cc_final: 0.9063 (t80) REVERT: H 62 PHE cc_start: 0.9745 (t80) cc_final: 0.9545 (t80) REVERT: H 73 GLU cc_start: 0.9293 (tp30) cc_final: 0.8705 (tp30) REVERT: H 79 HIS cc_start: 0.9813 (t-90) cc_final: 0.9580 (t-90) REVERT: H 96 ARG cc_start: 0.9634 (mmm-85) cc_final: 0.9163 (tpp80) REVERT: H 105 LYS cc_start: 0.9793 (mmtp) cc_final: 0.9448 (mmmt) REVERT: H 110 GLU cc_start: 0.9558 (tp30) cc_final: 0.9239 (tp30) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.7539 time to fit residues: 431.6006 Evaluate side-chains 383 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16670 Z= 0.280 Angle : 0.647 4.867 23791 Z= 0.402 Chirality : 0.044 0.169 2700 Planarity : 0.005 0.091 1988 Dihedral : 28.422 170.729 4597 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.26 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.24), residues: 1196 helix: 0.65 (0.18), residues: 778 sheet: -1.91 (0.56), residues: 66 loop : -1.33 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 56 HIS 0.006 0.001 HIS D 106 PHE 0.029 0.002 PHE K 417 TYR 0.018 0.002 TYR B 72 ARG 0.011 0.001 ARG A 42 *********************** 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 426 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 1.909 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 422 ARG cc_start: 0.9454 (ttm-80) cc_final: 0.9132 (mtp85) REVERT: A 63 ARG cc_start: 0.9426 (mmt180) cc_final: 0.8943 (mmm-85) REVERT: A 84 PHE cc_start: 0.9019 (m-80) cc_final: 0.8495 (m-80) REVERT: A 89 VAL cc_start: 0.9791 (t) cc_final: 0.9480 (p) REVERT: A 97 GLU cc_start: 0.9751 (mt-10) cc_final: 0.9431 (mt-10) REVERT: A 105 GLU cc_start: 0.9610 (mt-10) cc_final: 0.9186 (mm-30) REVERT: A 119 ILE cc_start: 0.9505 (pt) cc_final: 0.9105 (tp) REVERT: A 120 MET cc_start: 0.8282 (mpp) cc_final: 0.7746 (mpp) REVERT: A 123 ASP cc_start: 0.9807 (m-30) cc_final: 0.9478 (m-30) REVERT: B 74 GLU cc_start: 0.9785 (tt0) cc_final: 0.9516 (tp30) REVERT: B 78 ARG cc_start: 0.9218 (mmp80) cc_final: 0.8871 (mmp80) REVERT: B 84 MET cc_start: 0.9425 (mmm) cc_final: 0.9047 (mmm) REVERT: B 88 TYR cc_start: 0.9442 (m-10) cc_final: 0.9155 (m-80) REVERT: B 92 ARG cc_start: 0.9429 (ttp80) cc_final: 0.9065 (ttp80) REVERT: B 100 PHE cc_start: 0.9334 (m-80) cc_final: 0.9042 (m-80) REVERT: C 36 LYS cc_start: 0.9758 (mmmm) cc_final: 0.9531 (mmmm) REVERT: C 56 GLU cc_start: 0.8777 (tt0) cc_final: 0.8102 (tt0) REVERT: D 73 GLU cc_start: 0.9434 (mp0) cc_final: 0.9219 (mp0) REVERT: D 79 HIS cc_start: 0.9734 (t70) cc_final: 0.9426 (t-90) REVERT: E 81 ASP cc_start: 0.9597 (m-30) cc_final: 0.9188 (p0) REVERT: E 84 PHE cc_start: 0.9627 (m-80) cc_final: 0.9415 (m-80) REVERT: E 90 MET cc_start: 0.9815 (mtm) cc_final: 0.9400 (mmp) REVERT: E 106 ASP cc_start: 0.9432 (m-30) cc_final: 0.9145 (m-30) REVERT: F 62 LEU cc_start: 0.9661 (mt) cc_final: 0.9421 (mt) REVERT: F 64 ASN cc_start: 0.9760 (m-40) cc_final: 0.9524 (m-40) REVERT: F 68 ASP cc_start: 0.9599 (m-30) cc_final: 0.9158 (t70) REVERT: F 72 TYR cc_start: 0.9438 (m-80) cc_final: 0.8314 (m-10) REVERT: F 77 LYS cc_start: 0.9706 (mmtt) cc_final: 0.9382 (mmmm) REVERT: F 98 TYR cc_start: 0.8279 (m-10) cc_final: 0.7952 (m-10) REVERT: G 71 ARG cc_start: 0.9466 (tmm-80) cc_final: 0.9160 (tmm-80) REVERT: G 72 ASP cc_start: 0.9015 (m-30) cc_final: 0.8681 (m-30) REVERT: G 73 ASN cc_start: 0.9220 (t0) cc_final: 0.8827 (t0) REVERT: H 39 TYR cc_start: 0.9314 (t80) cc_final: 0.9060 (t80) REVERT: H 59 MET cc_start: 0.9716 (mmm) cc_final: 0.9309 (mmm) REVERT: H 62 PHE cc_start: 0.9737 (t80) cc_final: 0.9514 (t80) REVERT: H 65 ASP cc_start: 0.9785 (t70) cc_final: 0.9566 (t70) REVERT: H 73 GLU cc_start: 0.9319 (tp30) cc_final: 0.8714 (tp30) REVERT: H 79 HIS cc_start: 0.9810 (t-90) cc_final: 0.9582 (t-90) REVERT: H 96 ARG cc_start: 0.9625 (mmm-85) cc_final: 0.9115 (tpp80) REVERT: H 105 LYS cc_start: 0.9787 (mmtp) cc_final: 0.9435 (mmmt) REVERT: H 110 GLU cc_start: 0.9539 (tp30) cc_final: 0.9225 (tp30) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.7437 time to fit residues: 432.0679 Evaluate side-chains 383 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 126 optimal weight: 4.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16670 Z= 0.207 Angle : 0.620 5.449 23791 Z= 0.383 Chirality : 0.041 0.169 2700 Planarity : 0.005 0.066 1988 Dihedral : 28.304 169.977 4597 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.24), residues: 1196 helix: 1.19 (0.19), residues: 778 sheet: -1.42 (0.65), residues: 52 loop : -1.40 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 56 HIS 0.005 0.001 HIS D 106 PHE 0.017 0.001 PHE K 417 TYR 0.025 0.002 TYR C 39 ARG 0.009 0.000 ARG G 42 *********************** 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 428 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 428 time to evaluate : 1.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 419 LEU cc_start: 0.9412 (mt) cc_final: 0.9208 (mt) REVERT: K 422 ARG cc_start: 0.9462 (ttm-80) cc_final: 0.9129 (mtp85) REVERT: A 63 ARG cc_start: 0.9398 (mmt180) cc_final: 0.8938 (mmm-85) REVERT: A 64 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9098 (mtmm) REVERT: A 84 PHE cc_start: 0.9041 (m-80) cc_final: 0.8537 (m-80) REVERT: A 89 VAL cc_start: 0.9775 (t) cc_final: 0.9476 (p) REVERT: A 97 GLU cc_start: 0.9761 (mt-10) cc_final: 0.9433 (mt-10) REVERT: A 105 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9128 (mm-30) REVERT: A 119 ILE cc_start: 0.9575 (pt) cc_final: 0.9160 (tp) REVERT: A 120 MET cc_start: 0.8076 (mpp) cc_final: 0.7634 (mpp) REVERT: A 123 ASP cc_start: 0.9773 (m-30) cc_final: 0.9388 (m-30) REVERT: B 74 GLU cc_start: 0.9762 (tt0) cc_final: 0.9496 (tp30) REVERT: B 78 ARG cc_start: 0.9206 (mmp80) cc_final: 0.8857 (mmp80) REVERT: B 84 MET cc_start: 0.9380 (mmm) cc_final: 0.9019 (mmm) REVERT: B 88 TYR cc_start: 0.9420 (m-10) cc_final: 0.9145 (m-80) REVERT: B 92 ARG cc_start: 0.9441 (ttp80) cc_final: 0.9103 (ttp80) REVERT: C 36 LYS cc_start: 0.9737 (mmmm) cc_final: 0.9506 (mmmm) REVERT: D 59 MET cc_start: 0.9823 (mmp) cc_final: 0.9616 (mmp) REVERT: D 63 VAL cc_start: 0.9747 (p) cc_final: 0.9542 (p) REVERT: D 79 HIS cc_start: 0.9734 (t70) cc_final: 0.9433 (t-90) REVERT: E 59 GLU cc_start: 0.9202 (mp0) cc_final: 0.8966 (mp0) REVERT: E 81 ASP cc_start: 0.9580 (m-30) cc_final: 0.9152 (p0) REVERT: E 84 PHE cc_start: 0.9642 (m-80) cc_final: 0.9440 (m-80) REVERT: E 90 MET cc_start: 0.9791 (mtm) cc_final: 0.9421 (mmp) REVERT: E 105 GLU cc_start: 0.9259 (tm-30) cc_final: 0.9036 (tm-30) REVERT: E 106 ASP cc_start: 0.9454 (m-30) cc_final: 0.9030 (m-30) REVERT: F 68 ASP cc_start: 0.9594 (m-30) cc_final: 0.9007 (t70) REVERT: F 72 TYR cc_start: 0.9424 (m-80) cc_final: 0.8250 (m-80) REVERT: F 77 LYS cc_start: 0.9704 (mmtt) cc_final: 0.9370 (mmmm) REVERT: F 98 TYR cc_start: 0.8397 (m-10) cc_final: 0.8103 (m-10) REVERT: G 64 GLU cc_start: 0.9526 (tt0) cc_final: 0.8875 (tp30) REVERT: G 65 LEU cc_start: 0.9578 (mp) cc_final: 0.9334 (mp) REVERT: G 75 LYS cc_start: 0.9307 (mttt) cc_final: 0.9074 (mmmt) REVERT: G 112 GLN cc_start: 0.8979 (mp10) cc_final: 0.8576 (mp10) REVERT: H 34 TYR cc_start: 0.9007 (m-80) cc_final: 0.8401 (m-80) REVERT: H 39 TYR cc_start: 0.9275 (t80) cc_final: 0.9006 (t80) REVERT: H 64 ASN cc_start: 0.9663 (m110) cc_final: 0.9380 (m110) REVERT: H 65 ASP cc_start: 0.9783 (t70) cc_final: 0.9249 (t70) REVERT: H 69 ARG cc_start: 0.9269 (ptp-110) cc_final: 0.8921 (ptp-170) REVERT: H 79 HIS cc_start: 0.9794 (t-90) cc_final: 0.9554 (t-90) REVERT: H 102 GLU cc_start: 0.9383 (pm20) cc_final: 0.9179 (pm20) outliers start: 0 outliers final: 0 residues processed: 428 average time/residue: 0.7336 time to fit residues: 431.7337 Evaluate side-chains 391 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.125 16670 Z= 0.414 Angle : 0.707 6.910 23791 Z= 0.437 Chirality : 0.050 0.169 2700 Planarity : 0.005 0.046 1988 Dihedral : 28.491 172.362 4597 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.85 % Favored : 94.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1196 helix: 0.38 (0.18), residues: 778 sheet: -2.15 (0.55), residues: 68 loop : -1.54 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 110 HIS 0.005 0.002 HIS K 177 PHE 0.019 0.002 PHE A 67 TYR 0.025 0.002 TYR C 50 ARG 0.017 0.001 ARG K 454 *********************** 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 418 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 418 time to evaluate : 1.704 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: K 164 LYS cc_start: 0.8803 (mttt) cc_final: 0.8426 (mtpt) REVERT: K 419 LEU cc_start: 0.9460 (mt) cc_final: 0.9253 (mt) REVERT: K 422 ARG cc_start: 0.9481 (ttm-80) cc_final: 0.9148 (mtp85) REVERT: A 63 ARG cc_start: 0.9449 (mmt180) cc_final: 0.9039 (mmm-85) REVERT: A 84 PHE cc_start: 0.9133 (m-80) cc_final: 0.8440 (m-80) REVERT: A 89 VAL cc_start: 0.9810 (t) cc_final: 0.9500 (p) REVERT: A 105 GLU cc_start: 0.9671 (mt-10) cc_final: 0.9197 (mm-30) REVERT: A 106 ASP cc_start: 0.9217 (m-30) cc_final: 0.8947 (m-30) REVERT: A 120 MET cc_start: 0.8288 (mpp) cc_final: 0.7953 (mpp) REVERT: A 123 ASP cc_start: 0.9786 (m-30) cc_final: 0.9586 (m-30) REVERT: B 74 GLU cc_start: 0.9793 (tt0) cc_final: 0.9537 (tp30) REVERT: B 78 ARG cc_start: 0.9236 (mmp80) cc_final: 0.8846 (mmp80) REVERT: B 84 MET cc_start: 0.9450 (mmm) cc_final: 0.9021 (mmm) REVERT: B 88 TYR cc_start: 0.9507 (m-10) cc_final: 0.9172 (m-80) REVERT: B 92 ARG cc_start: 0.9482 (ttp80) cc_final: 0.9160 (ttp80) REVERT: B 100 PHE cc_start: 0.9350 (m-80) cc_final: 0.9084 (m-80) REVERT: C 36 LYS cc_start: 0.9766 (mmmm) cc_final: 0.9558 (mmmm) REVERT: D 59 MET cc_start: 0.9835 (mmp) cc_final: 0.9633 (mmp) REVERT: D 79 HIS cc_start: 0.9738 (t70) cc_final: 0.9469 (t-90) REVERT: D 92 GLN cc_start: 0.9488 (tt0) cc_final: 0.9206 (tp40) REVERT: E 70 LEU cc_start: 0.9316 (tp) cc_final: 0.9008 (mm) REVERT: E 90 MET cc_start: 0.9814 (mtm) cc_final: 0.9349 (mmm) REVERT: E 106 ASP cc_start: 0.9429 (m-30) cc_final: 0.9125 (m-30) REVERT: E 120 MET cc_start: 0.8998 (mtp) cc_final: 0.8751 (mtt) REVERT: F 62 LEU cc_start: 0.9743 (mt) cc_final: 0.9513 (mt) REVERT: F 68 ASP cc_start: 0.9589 (m-30) cc_final: 0.9097 (t70) REVERT: F 72 TYR cc_start: 0.9481 (m-80) cc_final: 0.8320 (m-80) REVERT: F 77 LYS cc_start: 0.9718 (mmtt) cc_final: 0.9399 (mmmm) REVERT: F 91 LYS cc_start: 0.9733 (mtpt) cc_final: 0.9379 (mmtp) REVERT: G 73 ASN cc_start: 0.9295 (t0) cc_final: 0.8904 (t0) REVERT: H 34 TYR cc_start: 0.9051 (m-80) cc_final: 0.8656 (m-80) REVERT: H 59 MET cc_start: 0.9727 (mmm) cc_final: 0.9255 (mmm) REVERT: H 65 ASP cc_start: 0.9771 (t70) cc_final: 0.9568 (t70) REVERT: H 73 GLU cc_start: 0.9351 (tp30) cc_final: 0.8762 (tp30) REVERT: H 79 HIS cc_start: 0.9821 (t-90) cc_final: 0.9606 (t-90) REVERT: H 105 LYS cc_start: 0.9791 (mmtp) cc_final: 0.9458 (mmmt) REVERT: H 110 GLU cc_start: 0.9593 (tp30) cc_final: 0.9315 (tp30) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.7260 time to fit residues: 417.7411 Evaluate side-chains 373 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 114 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.6181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16670 Z= 0.206 Angle : 0.629 5.741 23791 Z= 0.386 Chirality : 0.041 0.172 2700 Planarity : 0.005 0.053 1988 Dihedral : 28.391 170.406 4597 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.76 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.24), residues: 1196 helix: 1.10 (0.18), residues: 779 sheet: -1.72 (0.60), residues: 57 loop : -1.44 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 110 HIS 0.009 0.001 HIS A 113 PHE 0.018 0.002 PHE F 61 TYR 0.021 0.002 TYR F 51 ARG 0.009 0.001 ARG A 42 ********************** 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 421 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 421 time to evaluate : 1.930 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: K 422 ARG cc_start: 0.9463 (ttm-80) cc_final: 0.9124 (mtp85) REVERT: A 63 ARG cc_start: 0.9380 (mmt180) cc_final: 0.9035 (mmm-85) REVERT: A 64 LYS cc_start: 0.9391 (mtmm) cc_final: 0.9074 (mtmm) REVERT: A 84 PHE cc_start: 0.9087 (m-80) cc_final: 0.8559 (m-80) REVERT: A 89 VAL cc_start: 0.9792 (t) cc_final: 0.9491 (p) REVERT: A 119 ILE cc_start: 0.9567 (pt) cc_final: 0.9204 (tp) REVERT: A 120 MET cc_start: 0.8128 (mpp) cc_final: 0.7635 (mpp) REVERT: A 123 ASP cc_start: 0.9739 (m-30) cc_final: 0.9278 (m-30) REVERT: B 74 GLU cc_start: 0.9766 (tt0) cc_final: 0.9502 (tp30) REVERT: B 84 MET cc_start: 0.9428 (mmm) cc_final: 0.9023 (mmm) REVERT: B 88 TYR cc_start: 0.9491 (m-10) cc_final: 0.9206 (m-80) REVERT: B 92 ARG cc_start: 0.9406 (ttp80) cc_final: 0.9171 (ttp80) REVERT: C 36 LYS cc_start: 0.9752 (mmmm) cc_final: 0.9522 (mmmm) REVERT: D 73 GLU cc_start: 0.9442 (mp0) cc_final: 0.9218 (mp0) REVERT: D 92 GLN cc_start: 0.9462 (tt0) cc_final: 0.9155 (tp40) REVERT: E 59 GLU cc_start: 0.9221 (mp0) cc_final: 0.9004 (mp0) REVERT: E 70 LEU cc_start: 0.9257 (tp) cc_final: 0.8929 (mm) REVERT: E 81 ASP cc_start: 0.9635 (m-30) cc_final: 0.9172 (p0) REVERT: E 90 MET cc_start: 0.9791 (mtm) cc_final: 0.9401 (mmp) REVERT: E 106 ASP cc_start: 0.9450 (m-30) cc_final: 0.9122 (m-30) REVERT: E 120 MET cc_start: 0.9019 (mtp) cc_final: 0.8796 (mtt) REVERT: F 62 LEU cc_start: 0.9762 (mt) cc_final: 0.9514 (mt) REVERT: F 68 ASP cc_start: 0.9602 (m-30) cc_final: 0.9037 (t70) REVERT: F 72 TYR cc_start: 0.9439 (m-80) cc_final: 0.8217 (m-80) REVERT: F 77 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9355 (mmmm) REVERT: G 64 GLU cc_start: 0.9528 (tt0) cc_final: 0.8882 (tp30) REVERT: G 65 LEU cc_start: 0.9574 (mp) cc_final: 0.9343 (mp) REVERT: G 75 LYS cc_start: 0.9315 (mttt) cc_final: 0.9096 (mmmt) REVERT: G 85 LEU cc_start: 0.9345 (mt) cc_final: 0.8937 (tt) REVERT: G 112 GLN cc_start: 0.9086 (mp10) cc_final: 0.8637 (mp10) REVERT: H 34 TYR cc_start: 0.8998 (m-80) cc_final: 0.8424 (m-80) REVERT: H 64 ASN cc_start: 0.9656 (m110) cc_final: 0.9396 (m110) REVERT: H 79 HIS cc_start: 0.9800 (t-90) cc_final: 0.9564 (t-90) REVERT: H 97 LEU cc_start: 0.9411 (tp) cc_final: 0.9150 (tp) REVERT: H 105 LYS cc_start: 0.9766 (mmtp) cc_final: 0.9393 (mmmt) outliers start: 0 outliers final: 0 residues processed: 421 average time/residue: 0.7145 time to fit residues: 415.3042 Evaluate side-chains 382 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 382 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.2994 ------------------------------------------------------------------------------- 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 = 0.045783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.036306 restraints weight = 304445.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.038264 restraints weight = 114320.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.039481 restraints weight = 59230.521| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16670 Z= 0.213 Angle : 0.616 6.265 23791 Z= 0.379 Chirality : 0.041 0.163 2700 Planarity : 0.004 0.052 1988 Dihedral : 28.281 170.976 4597 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.01 % Favored : 96.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1196 helix: 1.40 (0.19), residues: 778 sheet: -1.76 (0.60), residues: 57 loop : -1.43 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 110 HIS 0.005 0.001 HIS G 31 PHE 0.021 0.001 PHE G 25 TYR 0.035 0.002 TYR C 39 ARG 0.009 0.001 ARG K 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9534.87 seconds wall clock time: 167 minutes 30.75 seconds (10050.75 seconds total)