Starting phenix.real_space_refine on Wed Feb 14 16:49:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4p_21044/02_2024/6v4p_21044.pdb" } resolution = 2.8 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= 0.012 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 Ca 6 9.91 5 Mg 1 5.21 5 S 41 5.16 5 C 6131 2.51 5 N 1636 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 77": "NH1" <-> "NH2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "B ARG 62": "NH1" <-> "NH2" Residue "B ARG 360": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9717 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3467 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 27, 'TRANS': 424} Chain: "B" Number of atoms: 2927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2927 Classifications: {'peptide': 375} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 356} Chain: "C" Number of atoms: 1665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1665 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain: "D" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1651 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 4, 'PTRANS': 6, 'TRANS': 203} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.56, per 1000 atoms: 0.57 Number of scatterers: 9717 At special positions: 0 Unit cell: (99, 150, 76, 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) Ca 6 19.99 S 41 16.00 Mg 1 11.99 O 1902 8.00 N 1636 7.00 C 6131 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.61 Conformation dependent library (CDL) restraints added in 2.0 seconds 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2308 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 24 sheets defined 12.5% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'B' and resid 121 through 125 Processing helix chain 'B' and resid 126 through 131 removed outlier: 3.763A pdb=" N SER B 130 " --> pdb=" O ASP B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 142 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.665A pdb=" N LEU B 173 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 179 removed outlier: 4.311A pdb=" N ASP B 179 " --> pdb=" O PRO B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 209 removed outlier: 3.765A pdb=" N ASN B 204 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 259 through 264 Processing helix chain 'B' and resid 291 through 302 Processing helix chain 'B' and resid 314 through 323 Processing helix chain 'B' and resid 339 through 352 Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.501A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.505A pdb=" N SER C 91 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 194 Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'D' and resid 121 through 127 removed outlier: 3.936A pdb=" N SER D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 189 removed outlier: 4.083A pdb=" N HIS D 189 " --> pdb=" O ASP D 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 removed outlier: 8.111A pdb=" N GLY A 63 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE A 10 " --> pdb=" O GLY A 63 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLN A 7 " --> pdb=" O ARG A 449 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ARG A 449 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 removed outlier: 4.338A pdb=" N VAL A 53 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 79 removed outlier: 3.583A pdb=" N GLN A 82 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 316 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.748A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.521A pdb=" N GLY A 398 " --> pdb=" O GLN A 395 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 65 removed outlier: 6.503A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197 removed outlier: 6.161A pdb=" N PHE B 153 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR B 195 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 151 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 197 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU B 149 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N HIS B 244 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 307 " --> pdb=" O HIS B 244 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU B 246 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA B 309 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE B 248 " --> pdb=" O ALA B 309 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR B 311 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR B 250 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B 333 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL B 310 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.351A pdb=" N MET C 34 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 10 through 11 Processing sheet with id=AB8, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.593A pdb=" N LYS C 148 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N TYR C 181 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 174 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 155 through 159 removed outlier: 4.480A pdb=" N TYR C 199 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU D 33 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LYS D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.824A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 114 through 118 removed outlier: 4.928A pdb=" N SER D 131 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU D 181 " --> pdb=" O SER D 131 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 133 " --> pdb=" O LEU D 179 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 179 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N LEU D 135 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N SER D 177 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN D 137 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 175 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 147 through 150 347 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1634 1.32 - 1.44: 2738 1.44 - 1.57: 5507 1.57 - 1.69: 0 1.69 - 1.81: 59 Bond restraints: 9938 Sorted by residual: bond pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.32e-02 5.74e+03 1.23e+01 bond pdb=" CA ASN D 32 " pdb=" C ASN D 32 " ideal model delta sigma weight residual 1.523 1.478 0.045 1.34e-02 5.57e+03 1.12e+01 bond pdb=" C ILE D 29 " pdb=" O ILE D 29 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.19e-02 7.06e+03 8.62e+00 bond pdb=" C SER D 30 " pdb=" O SER D 30 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.11e+00 bond pdb=" C ASN D 32 " pdb=" O ASN D 32 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.26e-02 6.30e+03 7.78e+00 ... (remaining 9933 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.37: 313 106.37 - 113.27: 5373 113.27 - 120.17: 3321 120.17 - 127.08: 4388 127.08 - 133.98: 119 Bond angle restraints: 13514 Sorted by residual: angle pdb=" C LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta sigma weight residual 109.61 117.10 -7.49 1.58e+00 4.01e-01 2.25e+01 angle pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " pdb=" CG LEU B 375 " ideal model delta sigma weight residual 116.30 102.78 13.52 3.50e+00 8.16e-02 1.49e+01 angle pdb=" C CYS B 374 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " ideal model delta sigma weight residual 121.31 126.33 -5.02 1.49e+00 4.50e-01 1.13e+01 angle pdb=" N SER D 30 " pdb=" CA SER D 30 " pdb=" C SER D 30 " ideal model delta sigma weight residual 110.80 117.64 -6.84 2.13e+00 2.20e-01 1.03e+01 angle pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta sigma weight residual 121.54 127.38 -5.84 1.91e+00 2.74e-01 9.34e+00 ... (remaining 13509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 5514 16.69 - 33.39: 297 33.39 - 50.08: 77 50.08 - 66.77: 25 66.77 - 83.47: 9 Dihedral angle restraints: 5922 sinusoidal: 2300 harmonic: 3622 Sorted by residual: dihedral pdb=" CA LEU B 375 " pdb=" C LEU B 375 " pdb=" N ASN B 376 " pdb=" CA ASN B 376 " ideal model delta harmonic sigma weight residual -180.00 -151.79 -28.21 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA THR D 39 " pdb=" C THR D 39 " pdb=" N SER D 40 " pdb=" CA SER D 40 " ideal model delta harmonic sigma weight residual -180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" C LEU B 375 " pdb=" N LEU B 375 " pdb=" CA LEU B 375 " pdb=" CB LEU B 375 " ideal model delta harmonic sigma weight residual -122.60 -133.94 11.34 0 2.50e+00 1.60e-01 2.06e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1328 0.073 - 0.146: 162 0.146 - 0.218: 2 0.218 - 0.291: 2 0.291 - 0.364: 2 Chirality restraints: 1496 Sorted by residual: chirality pdb=" CA LEU B 375 " pdb=" N LEU B 375 " pdb=" C LEU B 375 " pdb=" CB LEU B 375 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CG LEU B 375 " pdb=" CB LEU B 375 " pdb=" CD1 LEU B 375 " pdb=" CD2 LEU B 375 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CA SER D 30 " pdb=" N SER D 30 " pdb=" C SER D 30 " pdb=" CB SER D 30 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 1493 not shown) Planarity restraints: 1758 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 375 " 0.019 2.00e-02 2.50e+03 4.07e-02 1.66e+01 pdb=" C LEU B 375 " -0.070 2.00e-02 2.50e+03 pdb=" O LEU B 375 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 376 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 29 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.17e+00 pdb=" C ILE D 29 " 0.039 2.00e-02 2.50e+03 pdb=" O ILE D 29 " -0.015 2.00e-02 2.50e+03 pdb=" N SER D 30 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 153 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 154 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 1755 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 209 2.65 - 3.21: 8814 3.21 - 3.77: 15823 3.77 - 4.34: 23593 4.34 - 4.90: 38440 Nonbonded interactions: 86879 Sorted by model distance: nonbonded pdb=" OE2 GLU B 220 " pdb="MG MG B 701 " model vdw 2.084 2.170 nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP B 259 " model vdw 2.197 2.440 nonbonded pdb=" NZ LYS B 417 " pdb=" O PHE B 421 " model vdw 2.204 2.520 nonbonded pdb=" OH TYR B 178 " pdb=" OD2 ASP C 57 " model vdw 2.233 2.440 nonbonded pdb=" O ASP D 82 " pdb=" OH TYR D 86 " model vdw 2.241 2.440 ... (remaining 86874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.300 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.880 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 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 : 0.005 0.046 9938 Z= 0.310 Angle : 0.600 13.516 13514 Z= 0.335 Chirality : 0.047 0.364 1496 Planarity : 0.004 0.042 1758 Dihedral : 12.282 83.466 3584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.07 % Favored : 95.69 % Rotamer: Outliers : 3.16 % Allowed : 7.72 % Favored : 89.12 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 13.43 % 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: -2.71 (0.21), residues: 1254 helix: -2.93 (0.33), residues: 116 sheet: -1.38 (0.22), residues: 448 loop : -1.87 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.005 0.001 HIS A 291 PHE 0.017 0.002 PHE A 19 TYR 0.014 0.002 TYR D 50 ARG 0.004 0.001 ARG B 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 187 time to evaluate : 1.166 Fit side-chains REVERT: A 23 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8841 (pp) REVERT: A 77 ARG cc_start: 0.7045 (mpt180) cc_final: 0.6137 (ttt-90) REVERT: A 120 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 125 THR cc_start: 0.9011 (p) cc_final: 0.8534 (p) REVERT: A 166 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7124 (m-80) REVERT: A 208 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7667 (mmt180) REVERT: A 386 ARG cc_start: 0.8120 (mtm180) cc_final: 0.7845 (mtm180) REVERT: A 401 SER cc_start: 0.8835 (p) cc_final: 0.8554 (m) REVERT: B 93 ARG cc_start: 0.7249 (ptm160) cc_final: 0.6320 (ttt180) REVERT: B 108 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7484 (pt0) REVERT: B 137 LYS cc_start: 0.8387 (mttt) cc_final: 0.7989 (mtmt) REVERT: B 187 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.7806 (tmm) REVERT: B 277 SER cc_start: 0.8844 (p) cc_final: 0.8592 (m) REVERT: B 323 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7710 (mt-10) REVERT: B 365 GLU cc_start: 0.8079 (mp0) cc_final: 0.7709 (pm20) REVERT: B 387 MET cc_start: 0.7990 (mtm) cc_final: 0.7682 (mtm) REVERT: B 400 GLU cc_start: 0.7933 (tt0) cc_final: 0.7546 (tt0) REVERT: B 402 LYS cc_start: 0.6772 (mtpt) cc_final: 0.6169 (mptt) REVERT: B 426 ILE cc_start: 0.9085 (mt) cc_final: 0.8833 (mm) REVERT: B 428 GLN cc_start: 0.8446 (mt0) cc_final: 0.8242 (mt0) REVERT: C 3 GLN cc_start: 0.7627 (tt0) cc_final: 0.7057 (mm-40) REVERT: C 32 TYR cc_start: 0.7811 (m-80) cc_final: 0.7391 (m-80) REVERT: C 100 ASP cc_start: 0.8450 (p0) cc_final: 0.8171 (p0) REVERT: C 122 LYS cc_start: 0.7556 (tttt) cc_final: 0.7218 (tttm) REVERT: D 70 ASP cc_start: 0.8047 (t70) cc_final: 0.7825 (t70) REVERT: D 103 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.7978 (ttpp) REVERT: D 105 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7111 (mt-10) outliers start: 34 outliers final: 10 residues processed: 209 average time/residue: 1.1412 time to fit residues: 256.8465 Evaluate side-chains 159 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 chunk 72 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 85 GLN A 134 GLN B 267 GLN B 280 HIS C 3 GLN D 32 ASN D 92 ASN D 124 GLN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 155 GLN D 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 9938 Z= 0.288 Angle : 0.572 8.623 13514 Z= 0.302 Chirality : 0.046 0.147 1496 Planarity : 0.004 0.039 1758 Dihedral : 7.434 57.912 1396 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 4.19 % Allowed : 12.37 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.77 (0.22), residues: 1254 helix: -1.84 (0.40), residues: 121 sheet: -0.91 (0.23), residues: 448 loop : -1.17 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.005 0.001 HIS A 215 PHE 0.017 0.002 PHE C 105 TYR 0.012 0.002 TYR D 50 ARG 0.007 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 1.190 Fit side-chains REVERT: A 76 THR cc_start: 0.8947 (t) cc_final: 0.8668 (m) REVERT: A 77 ARG cc_start: 0.7108 (mpt180) cc_final: 0.6549 (ttt-90) REVERT: A 120 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 125 THR cc_start: 0.8976 (p) cc_final: 0.8536 (p) REVERT: A 166 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.7154 (m-80) REVERT: A 208 ARG cc_start: 0.8042 (mpt180) cc_final: 0.7756 (mmt-90) REVERT: A 355 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8336 (mtt180) REVERT: A 386 ARG cc_start: 0.8151 (mtm180) cc_final: 0.7932 (mtm180) REVERT: A 400 ARG cc_start: 0.7754 (mmt180) cc_final: 0.7298 (mmt90) REVERT: A 401 SER cc_start: 0.8746 (p) cc_final: 0.8543 (m) REVERT: B 93 ARG cc_start: 0.7190 (ptm160) cc_final: 0.6236 (ttt180) REVERT: B 108 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 137 LYS cc_start: 0.8369 (mttt) cc_final: 0.7959 (mtmt) REVERT: B 187 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: B 234 GLU cc_start: 0.7341 (pm20) cc_final: 0.7140 (pm20) REVERT: B 277 SER cc_start: 0.8827 (p) cc_final: 0.8582 (m) REVERT: B 323 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7658 (mt-10) REVERT: B 365 GLU cc_start: 0.8117 (mp0) cc_final: 0.7800 (pm20) REVERT: B 387 MET cc_start: 0.8069 (mtm) cc_final: 0.7640 (mtm) REVERT: B 400 GLU cc_start: 0.7869 (tt0) cc_final: 0.7480 (tt0) REVERT: B 402 LYS cc_start: 0.6877 (mtpt) cc_final: 0.6649 (tttm) REVERT: C 3 GLN cc_start: 0.7624 (tt0) cc_final: 0.7054 (mm-40) REVERT: C 32 TYR cc_start: 0.7827 (m-80) cc_final: 0.7416 (m-80) REVERT: C 69 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8128 (tttt) REVERT: C 122 LYS cc_start: 0.7614 (tttt) cc_final: 0.7255 (tttm) REVERT: C 202 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6681 (m110) REVERT: D 55 MET cc_start: 0.8519 (mmm) cc_final: 0.8198 (mmm) REVERT: D 63 SER cc_start: 0.8572 (m) cc_final: 0.8365 (p) REVERT: D 79 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.7663 (mm-30) REVERT: D 81 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: D 175 LEU cc_start: 0.7408 (tt) cc_final: 0.7181 (tt) outliers start: 45 outliers final: 21 residues processed: 179 average time/residue: 1.2028 time to fit residues: 231.7507 Evaluate side-chains 168 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 204 ASN ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 9938 Z= 0.412 Angle : 0.610 8.542 13514 Z= 0.321 Chirality : 0.047 0.150 1496 Planarity : 0.004 0.039 1758 Dihedral : 7.289 58.932 1390 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.47 % Allowed : 13.58 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.39 (0.23), residues: 1254 helix: -1.41 (0.42), residues: 120 sheet: -0.74 (0.24), residues: 445 loop : -0.87 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 33 HIS 0.006 0.001 HIS A 291 PHE 0.021 0.002 PHE C 105 TYR 0.022 0.002 TYR C 150 ARG 0.008 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 137 time to evaluate : 1.088 Fit side-chains REVERT: A 77 ARG cc_start: 0.7285 (mpt180) cc_final: 0.6434 (ttt-90) REVERT: A 120 GLU cc_start: 0.7575 (mt-10) cc_final: 0.6955 (mt-10) REVERT: A 166 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.7147 (m-80) REVERT: A 355 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8315 (mtt180) REVERT: A 401 SER cc_start: 0.8819 (p) cc_final: 0.8584 (m) REVERT: B 93 ARG cc_start: 0.7179 (ptm160) cc_final: 0.6159 (ttt180) REVERT: B 137 LYS cc_start: 0.8341 (mttt) cc_final: 0.7902 (mtmt) REVERT: B 187 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.7848 (tmm) REVERT: B 234 GLU cc_start: 0.7371 (pm20) cc_final: 0.7120 (pm20) REVERT: B 277 SER cc_start: 0.8831 (p) cc_final: 0.8588 (m) REVERT: B 387 MET cc_start: 0.8116 (mtm) cc_final: 0.7644 (mtm) REVERT: B 400 GLU cc_start: 0.7906 (tt0) cc_final: 0.7438 (tt0) REVERT: B 402 LYS cc_start: 0.6783 (mtpt) cc_final: 0.6514 (tptp) REVERT: C 3 GLN cc_start: 0.7551 (tt0) cc_final: 0.7003 (mm-40) REVERT: C 19 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8945 (ttpp) REVERT: C 32 TYR cc_start: 0.7809 (m-80) cc_final: 0.7442 (m-80) REVERT: C 67 LYS cc_start: 0.8479 (tppt) cc_final: 0.8205 (tppt) REVERT: C 69 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8102 (tttt) REVERT: C 122 LYS cc_start: 0.7653 (tttt) cc_final: 0.7296 (tttm) REVERT: C 202 ASN cc_start: 0.7312 (OUTLIER) cc_final: 0.7092 (m110) REVERT: D 38 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: D 63 SER cc_start: 0.8571 (m) cc_final: 0.8356 (p) REVERT: D 81 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: D 103 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7918 (ttpp) REVERT: D 105 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7105 (mt-10) outliers start: 48 outliers final: 22 residues processed: 165 average time/residue: 1.2469 time to fit residues: 220.8168 Evaluate side-chains 163 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 132 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 202 ASN Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 108 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 137 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9938 Z= 0.277 Angle : 0.552 9.031 13514 Z= 0.291 Chirality : 0.045 0.142 1496 Planarity : 0.004 0.038 1758 Dihedral : 7.087 58.152 1390 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.65 % Allowed : 13.77 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.12 (0.23), residues: 1254 helix: -1.03 (0.44), residues: 121 sheet: -0.57 (0.24), residues: 446 loop : -0.71 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 PHE 0.016 0.002 PHE A 19 TYR 0.012 0.002 TYR D 50 ARG 0.008 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 139 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7362 (mpt180) cc_final: 0.6527 (ttt-90) REVERT: A 120 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 125 THR cc_start: 0.8939 (p) cc_final: 0.8522 (p) REVERT: A 166 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 180 GLU cc_start: 0.7737 (mp0) cc_final: 0.7467 (mp0) REVERT: A 192 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 401 SER cc_start: 0.8798 (p) cc_final: 0.8573 (m) REVERT: B 62 ARG cc_start: 0.7826 (mtp-110) cc_final: 0.7487 (mtm110) REVERT: B 93 ARG cc_start: 0.7171 (ptm160) cc_final: 0.6122 (ttt180) REVERT: B 137 LYS cc_start: 0.8373 (mttt) cc_final: 0.7974 (mtmt) REVERT: B 187 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.7842 (tmm) REVERT: B 234 GLU cc_start: 0.7352 (pm20) cc_final: 0.7009 (pm20) REVERT: B 277 SER cc_start: 0.8775 (p) cc_final: 0.8558 (m) REVERT: B 365 GLU cc_start: 0.8055 (mp0) cc_final: 0.7770 (pm20) REVERT: B 387 MET cc_start: 0.8102 (mtm) cc_final: 0.7602 (mtm) REVERT: B 400 GLU cc_start: 0.7855 (tt0) cc_final: 0.7426 (tt0) REVERT: B 402 LYS cc_start: 0.6849 (mtpt) cc_final: 0.6566 (tptp) REVERT: B 422 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8224 (pttp) REVERT: C 3 GLN cc_start: 0.7555 (tt0) cc_final: 0.7042 (mm-40) REVERT: C 19 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8936 (ttpp) REVERT: C 32 TYR cc_start: 0.7802 (m-80) cc_final: 0.7419 (m-80) REVERT: C 67 LYS cc_start: 0.8495 (tppt) cc_final: 0.8251 (tppt) REVERT: C 122 LYS cc_start: 0.7665 (tttt) cc_final: 0.7315 (tttm) REVERT: D 55 MET cc_start: 0.8516 (mmm) cc_final: 0.8270 (mmm) REVERT: D 81 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: D 103 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7892 (ttpp) outliers start: 50 outliers final: 27 residues processed: 172 average time/residue: 1.1930 time to fit residues: 220.4642 Evaluate side-chains 167 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 133 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 150 TYR Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9938 Z= 0.330 Angle : 0.575 12.231 13514 Z= 0.303 Chirality : 0.046 0.143 1496 Planarity : 0.004 0.048 1758 Dihedral : 7.075 58.895 1390 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 5.02 % Allowed : 14.70 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.07 (0.23), residues: 1254 helix: -0.86 (0.45), residues: 120 sheet: -0.55 (0.23), residues: 464 loop : -0.69 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 PHE 0.019 0.002 PHE C 105 TYR 0.015 0.002 TYR D 50 ARG 0.008 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 134 time to evaluate : 1.172 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7438 (mpt180) cc_final: 0.6642 (ttt180) REVERT: A 120 GLU cc_start: 0.7468 (mt-10) cc_final: 0.7087 (mt-10) REVERT: A 166 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.7201 (m-80) REVERT: A 180 GLU cc_start: 0.7717 (mp0) cc_final: 0.7475 (mp0) REVERT: A 192 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 401 SER cc_start: 0.8803 (p) cc_final: 0.8587 (m) REVERT: B 62 ARG cc_start: 0.7804 (mtp-110) cc_final: 0.7490 (mtm110) REVERT: B 93 ARG cc_start: 0.6998 (ptm160) cc_final: 0.5913 (ttt180) REVERT: B 137 LYS cc_start: 0.8367 (mttt) cc_final: 0.7961 (mtmt) REVERT: B 187 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.7856 (tmm) REVERT: B 234 GLU cc_start: 0.7364 (pm20) cc_final: 0.6995 (pm20) REVERT: B 278 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7563 (p0) REVERT: B 365 GLU cc_start: 0.8025 (mp0) cc_final: 0.7814 (pm20) REVERT: B 387 MET cc_start: 0.8119 (mtm) cc_final: 0.7596 (mtm) REVERT: B 400 GLU cc_start: 0.7849 (tt0) cc_final: 0.7534 (tt0) REVERT: B 402 LYS cc_start: 0.6844 (mtpt) cc_final: 0.6498 (mptt) REVERT: B 422 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8258 (pttp) REVERT: C 3 GLN cc_start: 0.7565 (tt0) cc_final: 0.7060 (mm-40) REVERT: C 32 TYR cc_start: 0.7799 (m-80) cc_final: 0.7420 (m-80) REVERT: C 69 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: C 122 LYS cc_start: 0.7651 (tttt) cc_final: 0.7301 (tttm) REVERT: D 27 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7507 (ptm160) REVERT: D 81 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: D 85 MET cc_start: 0.8447 (tpt) cc_final: 0.8098 (tpt) REVERT: D 103 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.7828 (ttpp) outliers start: 54 outliers final: 27 residues processed: 171 average time/residue: 1.1760 time to fit residues: 216.2625 Evaluate side-chains 167 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 278 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 116 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.8182 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9938 Z= 0.271 Angle : 0.547 11.369 13514 Z= 0.287 Chirality : 0.045 0.141 1496 Planarity : 0.004 0.039 1758 Dihedral : 6.926 58.974 1388 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 4.37 % Allowed : 15.91 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.93 (0.23), residues: 1254 helix: -0.70 (0.45), residues: 120 sheet: -0.46 (0.23), residues: 459 loop : -0.61 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 PHE 0.016 0.002 PHE A 19 TYR 0.012 0.002 TYR D 50 ARG 0.009 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 1.144 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7379 (mpt180) cc_final: 0.6644 (ttt180) REVERT: A 125 THR cc_start: 0.8941 (p) cc_final: 0.8528 (p) REVERT: A 166 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: A 180 GLU cc_start: 0.7701 (mp0) cc_final: 0.7472 (mp0) REVERT: A 192 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 248 LEU cc_start: 0.8834 (mp) cc_final: 0.8603 (mt) REVERT: A 400 ARG cc_start: 0.7815 (mmt180) cc_final: 0.7387 (mmt90) REVERT: A 401 SER cc_start: 0.8703 (p) cc_final: 0.8496 (m) REVERT: B 62 ARG cc_start: 0.7751 (mtp-110) cc_final: 0.7446 (mtm110) REVERT: B 93 ARG cc_start: 0.6959 (ptm160) cc_final: 0.5858 (ttt180) REVERT: B 137 LYS cc_start: 0.8364 (mttt) cc_final: 0.7978 (mtmt) REVERT: B 187 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.7834 (tmm) REVERT: B 234 GLU cc_start: 0.7353 (pm20) cc_final: 0.6920 (pm20) REVERT: B 365 GLU cc_start: 0.8019 (mp0) cc_final: 0.7806 (pm20) REVERT: B 387 MET cc_start: 0.8136 (mtm) cc_final: 0.7605 (mtm) REVERT: B 400 GLU cc_start: 0.7805 (tt0) cc_final: 0.7456 (tt0) REVERT: B 402 LYS cc_start: 0.6734 (mtpt) cc_final: 0.6394 (mptt) REVERT: B 422 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8252 (pttp) REVERT: C 32 TYR cc_start: 0.7796 (m-80) cc_final: 0.7390 (m-80) REVERT: C 67 LYS cc_start: 0.8434 (tppt) cc_final: 0.8118 (tppt) REVERT: C 69 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8021 (tttt) REVERT: C 122 LYS cc_start: 0.7675 (tttt) cc_final: 0.7331 (tttm) REVERT: D 27 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7517 (ptm160) REVERT: D 81 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: D 85 MET cc_start: 0.8461 (tpt) cc_final: 0.8089 (tpt) REVERT: D 103 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7692 (ttpp) outliers start: 47 outliers final: 23 residues processed: 164 average time/residue: 1.1742 time to fit residues: 207.8832 Evaluate side-chains 155 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 124 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 413 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 74 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.8171 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 9938 Z= 0.246 Angle : 0.529 11.733 13514 Z= 0.278 Chirality : 0.044 0.140 1496 Planarity : 0.004 0.042 1758 Dihedral : 6.832 59.680 1388 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 3.81 % Allowed : 16.56 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.81 (0.23), residues: 1254 helix: -0.51 (0.46), residues: 120 sheet: -0.33 (0.23), residues: 468 loop : -0.59 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 PHE 0.015 0.002 PHE A 19 TYR 0.017 0.002 TYR C 150 ARG 0.009 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 131 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7283 (mpt180) cc_final: 0.6587 (ttt180) REVERT: A 125 THR cc_start: 0.8936 (p) cc_final: 0.8499 (p) REVERT: A 166 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7279 (m-80) REVERT: A 192 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8313 (mp) REVERT: A 241 VAL cc_start: 0.8621 (m) cc_final: 0.8404 (m) REVERT: A 400 ARG cc_start: 0.7819 (mmt180) cc_final: 0.7409 (mmt90) REVERT: B 62 ARG cc_start: 0.7718 (mtp-110) cc_final: 0.7439 (mtm110) REVERT: B 93 ARG cc_start: 0.6956 (ptm160) cc_final: 0.5794 (ttt180) REVERT: B 137 LYS cc_start: 0.8381 (mttt) cc_final: 0.7992 (mtmt) REVERT: B 187 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7830 (tmm) REVERT: B 234 GLU cc_start: 0.7374 (pm20) cc_final: 0.6936 (pm20) REVERT: B 365 GLU cc_start: 0.8025 (mp0) cc_final: 0.7817 (pm20) REVERT: B 387 MET cc_start: 0.8145 (mtm) cc_final: 0.7579 (mtm) REVERT: B 400 GLU cc_start: 0.7790 (tt0) cc_final: 0.7449 (tt0) REVERT: B 402 LYS cc_start: 0.6731 (mtpt) cc_final: 0.6417 (mptt) REVERT: B 422 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8244 (pttp) REVERT: C 3 GLN cc_start: 0.7499 (tt0) cc_final: 0.7045 (mm-40) REVERT: C 32 TYR cc_start: 0.7793 (m-80) cc_final: 0.7398 (m-80) REVERT: C 69 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8001 (tttt) REVERT: C 122 LYS cc_start: 0.7639 (tttt) cc_final: 0.7323 (tttp) REVERT: D 27 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7527 (ptm160) REVERT: D 81 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: D 103 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7786 (ttpp) outliers start: 41 outliers final: 23 residues processed: 163 average time/residue: 1.1522 time to fit residues: 202.4753 Evaluate side-chains 157 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 76 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9938 Z= 0.223 Angle : 0.522 11.995 13514 Z= 0.273 Chirality : 0.044 0.149 1496 Planarity : 0.004 0.042 1758 Dihedral : 6.759 58.253 1387 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.28 % Allowed : 16.56 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.71 (0.24), residues: 1254 helix: -0.38 (0.47), residues: 121 sheet: -0.29 (0.23), residues: 467 loop : -0.52 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 33 HIS 0.006 0.001 HIS A 215 PHE 0.015 0.002 PHE A 19 TYR 0.011 0.001 TYR D 50 ARG 0.010 0.000 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 132 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7261 (mpt180) cc_final: 0.6614 (ttt-90) REVERT: A 125 THR cc_start: 0.8896 (OUTLIER) cc_final: 0.8517 (p) REVERT: A 192 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8306 (mp) REVERT: A 241 VAL cc_start: 0.8583 (m) cc_final: 0.8326 (m) REVERT: A 400 ARG cc_start: 0.7829 (mmt180) cc_final: 0.7420 (mmt90) REVERT: B 62 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7302 (mtm110) REVERT: B 93 ARG cc_start: 0.7010 (ptm160) cc_final: 0.5816 (ttt180) REVERT: B 137 LYS cc_start: 0.8368 (mttt) cc_final: 0.7986 (mtmt) REVERT: B 187 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: B 234 GLU cc_start: 0.7381 (pm20) cc_final: 0.6932 (pm20) REVERT: B 365 GLU cc_start: 0.8019 (mp0) cc_final: 0.7795 (pm20) REVERT: B 387 MET cc_start: 0.8146 (mtm) cc_final: 0.7581 (mtm) REVERT: B 400 GLU cc_start: 0.7703 (tt0) cc_final: 0.7336 (tt0) REVERT: B 402 LYS cc_start: 0.6727 (mtpt) cc_final: 0.6392 (mptt) REVERT: B 422 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8246 (pttp) REVERT: C 32 TYR cc_start: 0.7793 (m-80) cc_final: 0.7399 (m-80) REVERT: C 67 LYS cc_start: 0.8330 (tppt) cc_final: 0.7994 (tppt) REVERT: C 122 LYS cc_start: 0.7622 (tttt) cc_final: 0.7341 (tttp) REVERT: D 27 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7524 (ptm160) REVERT: D 81 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: D 103 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7780 (ttpp) REVERT: D 205 VAL cc_start: 0.5985 (OUTLIER) cc_final: 0.5675 (p) outliers start: 46 outliers final: 23 residues processed: 167 average time/residue: 1.0967 time to fit residues: 198.1400 Evaluate side-chains 160 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 101 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- 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: 0.8222 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 9938 Z= 0.451 Angle : 0.622 15.790 13514 Z= 0.325 Chirality : 0.048 0.210 1496 Planarity : 0.004 0.045 1758 Dihedral : 7.093 59.304 1387 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.81 % Allowed : 17.40 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.74 (0.23), residues: 1254 helix: -0.60 (0.46), residues: 120 sheet: -0.36 (0.24), residues: 446 loop : -0.46 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 33 HIS 0.008 0.001 HIS A 215 PHE 0.022 0.002 PHE C 105 TYR 0.027 0.002 TYR C 150 ARG 0.010 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 130 time to evaluate : 1.121 Fit side-chains REVERT: A 77 ARG cc_start: 0.7443 (mpt180) cc_final: 0.6658 (ttt-90) REVERT: A 120 GLU cc_start: 0.7592 (mt-10) cc_final: 0.7157 (mt-10) REVERT: A 166 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: A 192 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 355 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8298 (mtt180) REVERT: B 62 ARG cc_start: 0.7723 (mtp-110) cc_final: 0.7323 (mtm110) REVERT: B 93 ARG cc_start: 0.6871 (ptm160) cc_final: 0.5764 (ttt180) REVERT: B 108 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7073 (mm-30) REVERT: B 137 LYS cc_start: 0.8333 (mttt) cc_final: 0.7917 (mtmt) REVERT: B 187 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.7849 (tmm) REVERT: B 234 GLU cc_start: 0.7401 (pm20) cc_final: 0.6859 (pm20) REVERT: B 365 GLU cc_start: 0.8003 (mp0) cc_final: 0.7730 (pm20) REVERT: B 387 MET cc_start: 0.8136 (mtm) cc_final: 0.7553 (mtm) REVERT: B 400 GLU cc_start: 0.7797 (tt0) cc_final: 0.7461 (tt0) REVERT: B 402 LYS cc_start: 0.6863 (mtpt) cc_final: 0.6478 (mptt) REVERT: B 422 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8309 (pttp) REVERT: C 3 GLN cc_start: 0.7518 (tt0) cc_final: 0.7048 (mm-40) REVERT: C 32 TYR cc_start: 0.7809 (m-80) cc_final: 0.7428 (m-80) REVERT: C 67 LYS cc_start: 0.8431 (tppt) cc_final: 0.8136 (tppt) REVERT: C 69 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8047 (tttt) REVERT: C 122 LYS cc_start: 0.7701 (tttt) cc_final: 0.7368 (tttm) REVERT: D 27 ARG cc_start: 0.8482 (OUTLIER) cc_final: 0.7496 (ptm160) REVERT: D 81 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: D 103 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7863 (ttpp) REVERT: D 105 GLU cc_start: 0.7453 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 205 VAL cc_start: 0.6015 (OUTLIER) cc_final: 0.5679 (p) outliers start: 41 outliers final: 24 residues processed: 158 average time/residue: 1.1871 time to fit residues: 201.4995 Evaluate side-chains 162 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 128 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 143 GLU Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 78 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9938 Z= 0.271 Angle : 0.551 13.526 13514 Z= 0.287 Chirality : 0.045 0.164 1496 Planarity : 0.004 0.044 1758 Dihedral : 6.952 58.722 1387 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.16 % Allowed : 18.14 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.71 (0.23), residues: 1254 helix: -0.45 (0.47), residues: 120 sheet: -0.32 (0.24), residues: 457 loop : -0.47 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 PHE 0.016 0.002 PHE A 19 TYR 0.014 0.002 TYR A 432 ARG 0.009 0.000 ARG B 91 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2508 Ramachandran restraints generated. 1254 Oldfield, 0 Emsley, 1254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 127 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 77 ARG cc_start: 0.7393 (mpt180) cc_final: 0.6622 (ttt-90) REVERT: A 120 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7031 (mt-10) REVERT: A 125 THR cc_start: 0.8917 (p) cc_final: 0.8486 (p) REVERT: A 166 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.7272 (m-80) REVERT: A 192 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 62 ARG cc_start: 0.7623 (mtp-110) cc_final: 0.7284 (mtm110) REVERT: B 72 LYS cc_start: 0.8067 (ptmm) cc_final: 0.7772 (ptmm) REVERT: B 93 ARG cc_start: 0.6777 (ptm160) cc_final: 0.5739 (ttt180) REVERT: B 137 LYS cc_start: 0.8378 (mttt) cc_final: 0.7977 (mtmt) REVERT: B 187 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.7821 (tmm) REVERT: B 234 GLU cc_start: 0.7422 (pm20) cc_final: 0.6884 (pm20) REVERT: B 365 GLU cc_start: 0.8013 (mp0) cc_final: 0.7789 (pm20) REVERT: B 387 MET cc_start: 0.8171 (mtm) cc_final: 0.7602 (mtm) REVERT: B 400 GLU cc_start: 0.7706 (tt0) cc_final: 0.7302 (tt0) REVERT: B 402 LYS cc_start: 0.6799 (mtpt) cc_final: 0.6413 (mptt) REVERT: B 422 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8286 (pttp) REVERT: C 32 TYR cc_start: 0.7799 (m-80) cc_final: 0.7433 (m-80) REVERT: C 67 LYS cc_start: 0.8382 (tppt) cc_final: 0.8130 (tppt) REVERT: C 122 LYS cc_start: 0.7646 (tttt) cc_final: 0.7316 (tttm) REVERT: D 27 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.7531 (ptm160) REVERT: D 81 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: D 85 MET cc_start: 0.8474 (tpt) cc_final: 0.8270 (mmt) REVERT: D 103 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7774 (ttpp) REVERT: D 205 VAL cc_start: 0.6013 (OUTLIER) cc_final: 0.5680 (p) outliers start: 34 outliers final: 22 residues processed: 153 average time/residue: 1.2523 time to fit residues: 206.0848 Evaluate side-chains 156 residues out of total 1075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 126 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 167 CYS Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 144 LYS Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 422 LYS Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 98 LEU Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 174 VAL Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 81 GLU Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 205 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 41 optimal weight: 0.0170 chunk 101 optimal weight: 30.0000 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.149777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.104389 restraints weight = 9707.998| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.05 r_work: 0.2700 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9938 Z= 0.209 Angle : 0.517 12.632 13514 Z= 0.271 Chirality : 0.044 0.162 1496 Planarity : 0.004 0.046 1758 Dihedral : 6.812 59.685 1387 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.98 % Allowed : 18.14 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.43 % 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: -0.55 (0.24), residues: 1254 helix: -0.30 (0.47), residues: 121 sheet: -0.14 (0.24), residues: 463 loop : -0.43 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 33 HIS 0.007 0.001 HIS A 215 PHE 0.015 0.001 PHE A 19 TYR 0.033 0.002 TYR C 150 ARG 0.010 0.000 ARG B 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4014.89 seconds wall clock time: 72 minutes 8.71 seconds (4328.71 seconds total)