Starting phenix.real_space_refine on Fri Nov 15 08:27:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkz_36384/11_2024/8jkz_36384.cif" } resolution = 3.6 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= 0.002 sd= 0.027 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 33 5.16 5 C 5404 2.51 5 N 1443 2.21 5 O 1562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8444 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4674 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 23, 'TRANS': 560} Chain: "B" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3726 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 28, 'TRANS': 440} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.11, per 1000 atoms: 0.61 Number of scatterers: 8444 At special positions: 0 Unit cell: (78.12, 98.28, 122.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 33 16.00 P 2 15.00 O 1562 8.00 N 1443 7.00 C 5404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.50 Conformation dependent library (CDL) restraints added in 989.0 milliseconds 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1976 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 11 sheets defined 41.5% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 removed outlier: 3.550A pdb=" N GLN A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N HIS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR A 13 " --> pdb=" O PHE A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 removed outlier: 3.621A pdb=" N THR A 28 " --> pdb=" O GLY A 25 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 29 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 30 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N SER A 31 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 33 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.600A pdb=" N SER A 69 " --> pdb=" O HIS A 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 98 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 176 removed outlier: 3.826A pdb=" N SER A 172 " --> pdb=" O TYR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'A' and resid 257 through 261 Processing helix chain 'A' and resid 262 through 276 Processing helix chain 'A' and resid 286 through 297 removed outlier: 4.075A pdb=" N GLN A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.547A pdb=" N ARG A 310 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 366 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.965A pdb=" N SER A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 517 through 529 Processing helix chain 'A' and resid 532 through 548 removed outlier: 3.574A pdb=" N GLN A 538 " --> pdb=" O GLN A 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 60 through 71 removed outlier: 3.837A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 removed outlier: 3.699A pdb=" N ARG B 106 " --> pdb=" O GLU B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 119 removed outlier: 3.948A pdb=" N VAL B 116 " --> pdb=" O GLU B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.602A pdb=" N ALA B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 164 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.118A pdb=" N LEU B 188 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.547A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY B 199 " --> pdb=" O ASN B 195 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA B 203 " --> pdb=" O GLY B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 276 through 295 Processing helix chain 'B' and resid 312 through 321 removed outlier: 3.514A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 4.150A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 458 removed outlier: 3.624A pdb=" N VAL B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 458 " --> pdb=" O ASP B 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 184 removed outlier: 6.404A pdb=" N VAL A 138 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N MET A 20 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N PHE A 139 " --> pdb=" O MET A 20 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TRP A 22 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 252 removed outlier: 6.546A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 removed outlier: 3.610A pdb=" N ALA A 330 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 345 " --> pdb=" O ALA A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.550A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 380 removed outlier: 3.611A pdb=" N CYS A 345 " --> pdb=" O TYR A 402 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 559 through 561 removed outlier: 3.548A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.331A pdb=" N ILE B 303 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL B 332 " --> pdb=" O ILE B 303 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE B 305 " --> pdb=" O VAL B 332 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE B 334 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS B 307 " --> pdb=" O ILE B 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.748A pdb=" N ARG B 25 " --> pdb=" O PHE B 21 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 6.669A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 51 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LEU B 147 " --> pdb=" O ARG B 51 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA B 53 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N TYR B 149 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU B 55 " --> pdb=" O TYR B 149 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 146 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 265 through 267 346 hydrogen bonds defined for protein. 990 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: 2.51 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1378 1.31 - 1.43: 2382 1.43 - 1.56: 4838 1.56 - 1.68: 8 1.68 - 1.81: 51 Bond restraints: 8657 Sorted by residual: bond pdb=" C2D NAD A 601 " pdb=" C3D NAD A 601 " ideal model delta sigma weight residual 1.531 1.243 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4B NAD A 601 " pdb=" O4B NAD A 601 " ideal model delta sigma weight residual 1.433 1.681 -0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" C3B NAD A 601 " pdb=" C4B NAD A 601 " ideal model delta sigma weight residual 1.523 1.281 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C4D NAD A 601 " pdb=" O4D NAD A 601 " ideal model delta sigma weight residual 1.445 1.274 0.171 2.00e-02 2.50e+03 7.31e+01 bond pdb=" C7N NAD A 601 " pdb=" N7N NAD A 601 " ideal model delta sigma weight residual 1.328 1.473 -0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 8652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11571 2.64 - 5.28: 154 5.28 - 7.93: 15 7.93 - 10.57: 5 10.57 - 13.21: 3 Bond angle restraints: 11748 Sorted by residual: angle pdb=" C ILE A 390 " pdb=" N PHE A 391 " pdb=" CA PHE A 391 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" O1A NAD A 601 " pdb=" PA NAD A 601 " pdb=" O2A NAD A 601 " ideal model delta sigma weight residual 122.64 109.43 13.21 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C ALA B 9 " pdb=" CA ALA B 9 " pdb=" CB ALA B 9 " ideal model delta sigma weight residual 116.34 110.45 5.89 1.40e+00 5.10e-01 1.77e+01 angle pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " pdb=" O5D NAD A 601 " ideal model delta sigma weight residual 98.00 109.75 -11.75 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O1N NAD A 601 " pdb=" PN NAD A 601 " pdb=" O2N NAD A 601 " ideal model delta sigma weight residual 120.02 109.43 10.59 3.00e+00 1.11e-01 1.25e+01 ... (remaining 11743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4401 17.98 - 35.96: 593 35.96 - 53.95: 154 53.95 - 71.93: 32 71.93 - 89.91: 15 Dihedral angle restraints: 5195 sinusoidal: 2120 harmonic: 3075 Sorted by residual: dihedral pdb=" CA LEU B 46 " pdb=" C LEU B 46 " pdb=" N PRO B 47 " pdb=" CA PRO B 47 " ideal model delta harmonic sigma weight residual 180.00 152.47 27.53 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA TYR A 374 " pdb=" C TYR A 374 " pdb=" N THR A 375 " pdb=" CA THR A 375 " ideal model delta harmonic sigma weight residual 180.00 161.19 18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA MET A 132 " pdb=" C MET A 132 " pdb=" N ASN A 133 " pdb=" CA ASN A 133 " ideal model delta harmonic sigma weight residual -180.00 -161.98 -18.02 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1141 0.070 - 0.140: 130 0.140 - 0.210: 8 0.210 - 0.280: 1 0.280 - 0.351: 1 Chirality restraints: 1281 Sorted by residual: chirality pdb=" C3D NAD A 601 " pdb=" C2D NAD A 601 " pdb=" C4D NAD A 601 " pdb=" O3D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.73 -2.38 -0.35 2.00e-01 2.50e+01 3.07e+00 chirality pdb=" C3B NAD A 601 " pdb=" C2B NAD A 601 " pdb=" C4B NAD A 601 " pdb=" O3B NAD A 601 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C2D NAD A 601 " pdb=" C1D NAD A 601 " pdb=" C3D NAD A 601 " pdb=" O2D NAD A 601 " both_signs ideal model delta sigma weight residual False -2.56 -2.37 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 1278 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 206 " 0.187 9.50e-02 1.11e+02 8.39e-02 4.33e+00 pdb=" NE ARG A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 206 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 206 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 206 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 391 " -0.011 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE A 391 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 391 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 391 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 391 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 391 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 391 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 390 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.81e+00 pdb=" C ILE A 390 " -0.029 2.00e-02 2.50e+03 pdb=" O ILE A 390 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE A 391 " 0.010 2.00e-02 2.50e+03 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1203 2.76 - 3.29: 8017 3.29 - 3.83: 13547 3.83 - 4.36: 15536 4.36 - 4.90: 27371 Nonbonded interactions: 65674 Sorted by model distance: nonbonded pdb=" OH TYR B 83 " pdb=" O ASN B 436 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR B 277 " pdb=" OD2 ASP B 321 " model vdw 2.231 3.040 nonbonded pdb=" OG1 THR A 333 " pdb=" O ALA A 578 " model vdw 2.233 3.040 nonbonded pdb=" OE2 GLU B 330 " pdb=" NH1 ARG B 411 " model vdw 2.267 3.120 nonbonded pdb=" ND2 ASN B 389 " pdb=" OE1 GLN B 392 " model vdw 2.267 3.120 ... (remaining 65669 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 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: 1.490 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.930 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 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 : 0.007 0.288 8657 Z= 0.369 Angle : 0.735 13.209 11748 Z= 0.398 Chirality : 0.045 0.351 1281 Planarity : 0.004 0.084 1505 Dihedral : 17.975 89.910 3219 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 1.00 % Allowed : 26.00 % Favored : 73.01 % 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: -1.21 (0.27), residues: 1049 helix: 0.80 (0.27), residues: 388 sheet: -0.76 (0.40), residues: 189 loop : -2.25 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 198 HIS 0.007 0.001 HIS A 52 PHE 0.035 0.002 PHE A 391 TYR 0.013 0.001 TYR B 149 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 92 average time/residue: 0.2730 time to fit residues: 33.2520 Evaluate side-chains 78 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 257 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 26 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.0906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8657 Z= 0.178 Angle : 0.562 8.625 11748 Z= 0.296 Chirality : 0.041 0.154 1281 Planarity : 0.004 0.038 1505 Dihedral : 7.096 64.174 1212 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.53 % Favored : 90.37 % Rotamer: Outliers : 3.32 % Allowed : 24.45 % Favored : 72.23 % 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: -0.94 (0.27), residues: 1049 helix: 1.15 (0.28), residues: 389 sheet: -0.67 (0.39), residues: 186 loop : -2.20 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.030 0.001 PHE A 391 TYR 0.014 0.001 TYR B 366 ARG 0.004 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7614 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 112 LEU cc_start: 0.4399 (OUTLIER) cc_final: 0.4060 (tt) REVERT: B 49 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: B 98 LEU cc_start: 0.8912 (tt) cc_final: 0.8477 (tt) outliers start: 30 outliers final: 11 residues processed: 109 average time/residue: 0.2132 time to fit residues: 32.2230 Evaluate side-chains 88 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 chunk 94 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 45 ASN B 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8657 Z= 0.214 Angle : 0.562 8.258 11748 Z= 0.295 Chirality : 0.042 0.153 1281 Planarity : 0.004 0.037 1505 Dihedral : 6.592 61.111 1209 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.82 % Favored : 90.09 % Rotamer: Outliers : 4.31 % Allowed : 23.23 % Favored : 72.46 % 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: -0.85 (0.27), residues: 1049 helix: 1.29 (0.28), residues: 389 sheet: -0.72 (0.39), residues: 187 loop : -2.16 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.013 0.001 PHE A 328 TYR 0.013 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 77 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7221 (t80) REVERT: A 112 LEU cc_start: 0.4541 (OUTLIER) cc_final: 0.4208 (tt) REVERT: A 275 LYS cc_start: 0.7948 (tmtt) cc_final: 0.7747 (tppt) REVERT: B 188 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8546 (mt) REVERT: B 197 MET cc_start: 0.9014 (mmp) cc_final: 0.8696 (mmm) REVERT: B 373 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7665 (mp0) outliers start: 39 outliers final: 20 residues processed: 111 average time/residue: 0.2027 time to fit residues: 32.0212 Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.0770 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 83 optimal weight: 5.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8657 Z= 0.197 Angle : 0.551 8.487 11748 Z= 0.287 Chirality : 0.041 0.176 1281 Planarity : 0.003 0.036 1505 Dihedral : 6.364 56.639 1209 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 3.65 % Allowed : 24.89 % Favored : 71.46 % 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: -0.80 (0.27), residues: 1049 helix: 1.35 (0.28), residues: 389 sheet: -0.65 (0.40), residues: 185 loop : -2.17 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 377 HIS 0.006 0.001 HIS A 52 PHE 0.052 0.002 PHE A 391 TYR 0.012 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 77 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: A 93 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7266 (t80) REVERT: A 112 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4212 (tt) REVERT: A 275 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7739 (tppt) REVERT: B 197 MET cc_start: 0.9009 (mmp) cc_final: 0.8752 (mmm) REVERT: B 373 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7723 (mp0) outliers start: 33 outliers final: 20 residues processed: 105 average time/residue: 0.2232 time to fit residues: 32.6421 Evaluate side-chains 93 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS B 339 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8657 Z= 0.271 Angle : 0.578 8.142 11748 Z= 0.304 Chirality : 0.042 0.189 1281 Planarity : 0.004 0.036 1505 Dihedral : 6.404 52.579 1209 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.39 % Favored : 89.51 % Rotamer: Outliers : 4.20 % Allowed : 24.56 % Favored : 71.24 % 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: -0.86 (0.27), residues: 1049 helix: 1.34 (0.28), residues: 387 sheet: -0.74 (0.40), residues: 187 loop : -2.21 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 377 HIS 0.007 0.001 HIS A 52 PHE 0.016 0.002 PHE A 9 TYR 0.014 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 77 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7893 (mp10) REVERT: A 93 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7348 (t80) REVERT: A 112 LEU cc_start: 0.4444 (OUTLIER) cc_final: 0.4128 (tt) REVERT: A 275 LYS cc_start: 0.7944 (tmtt) cc_final: 0.7709 (tppt) REVERT: A 372 LEU cc_start: 0.8909 (mt) cc_final: 0.8531 (mp) REVERT: A 496 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.6683 (tp30) REVERT: B 197 MET cc_start: 0.9055 (mmp) cc_final: 0.8850 (mmm) outliers start: 38 outliers final: 25 residues processed: 108 average time/residue: 0.2109 time to fit residues: 31.9415 Evaluate side-chains 103 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 308 LYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 373 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 448 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 2.9990 chunk 19 optimal weight: 0.1980 chunk 59 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 97 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8657 Z= 0.151 Angle : 0.533 8.163 11748 Z= 0.279 Chirality : 0.040 0.158 1281 Planarity : 0.003 0.034 1505 Dihedral : 6.134 50.344 1209 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.15 % Favored : 90.75 % Rotamer: Outliers : 3.54 % Allowed : 25.77 % Favored : 70.69 % 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: -0.68 (0.27), residues: 1049 helix: 1.45 (0.28), residues: 388 sheet: -0.53 (0.40), residues: 185 loop : -2.12 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 377 HIS 0.005 0.001 HIS A 46 PHE 0.034 0.001 PHE A 391 TYR 0.011 0.001 TYR B 366 ARG 0.004 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7349 (t80) REVERT: A 112 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.4193 (tt) REVERT: A 372 LEU cc_start: 0.8743 (mt) cc_final: 0.8366 (mp) REVERT: A 403 TYR cc_start: 0.7097 (m-80) cc_final: 0.6862 (m-80) REVERT: A 496 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.6560 (tp30) outliers start: 32 outliers final: 18 residues processed: 107 average time/residue: 0.2174 time to fit residues: 32.2560 Evaluate side-chains 92 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 8657 Z= 0.151 Angle : 0.545 8.468 11748 Z= 0.282 Chirality : 0.041 0.217 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.980 51.607 1209 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.25 % Favored : 90.66 % Rotamer: Outliers : 3.43 % Allowed : 25.88 % Favored : 70.69 % 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: -0.58 (0.27), residues: 1049 helix: 1.46 (0.28), residues: 389 sheet: -0.35 (0.41), residues: 185 loop : -2.06 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 377 HIS 0.004 0.001 HIS A 52 PHE 0.010 0.001 PHE B 137 TYR 0.011 0.001 TYR B 366 ARG 0.005 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 84 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7780 (OUTLIER) cc_final: 0.7399 (t80) REVERT: A 112 LEU cc_start: 0.4488 (OUTLIER) cc_final: 0.4175 (tt) REVERT: A 372 LEU cc_start: 0.8861 (mt) cc_final: 0.8472 (mp) REVERT: A 403 TYR cc_start: 0.7095 (m-80) cc_final: 0.6841 (m-80) REVERT: B 146 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (tt) REVERT: B 321 ASP cc_start: 0.8220 (m-30) cc_final: 0.7979 (m-30) outliers start: 31 outliers final: 19 residues processed: 111 average time/residue: 0.2086 time to fit residues: 32.4645 Evaluate side-chains 97 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8657 Z= 0.184 Angle : 0.556 7.967 11748 Z= 0.288 Chirality : 0.041 0.147 1281 Planarity : 0.003 0.034 1505 Dihedral : 6.022 52.203 1209 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.44 % Favored : 90.47 % Rotamer: Outliers : 3.21 % Allowed : 26.00 % Favored : 70.80 % 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 (0.27), residues: 1049 helix: 1.50 (0.28), residues: 388 sheet: -0.37 (0.41), residues: 185 loop : -2.05 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.036 0.001 PHE A 391 TYR 0.011 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7373 (t80) REVERT: A 112 LEU cc_start: 0.4382 (OUTLIER) cc_final: 0.4092 (tt) REVERT: A 372 LEU cc_start: 0.8808 (mt) cc_final: 0.8440 (mp) REVERT: A 403 TYR cc_start: 0.7080 (m-80) cc_final: 0.6829 (m-80) REVERT: B 146 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 397 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7839 (mt-10) outliers start: 29 outliers final: 22 residues processed: 102 average time/residue: 0.2386 time to fit residues: 34.4050 Evaluate side-chains 100 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 93 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8657 Z= 0.165 Angle : 0.554 8.781 11748 Z= 0.285 Chirality : 0.041 0.209 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.934 53.998 1209 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.87 % Favored : 91.04 % Rotamer: Outliers : 2.99 % Allowed : 26.44 % Favored : 70.58 % 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: -0.53 (0.27), residues: 1049 helix: 1.51 (0.28), residues: 389 sheet: -0.39 (0.41), residues: 185 loop : -2.00 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 377 HIS 0.004 0.001 HIS A 52 PHE 0.009 0.001 PHE B 471 TYR 0.011 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7794 (OUTLIER) cc_final: 0.7418 (t80) REVERT: A 112 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3808 (tt) REVERT: A 372 LEU cc_start: 0.8830 (mt) cc_final: 0.8455 (mp) REVERT: B 49 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7498 (mm-40) REVERT: B 146 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8450 (tt) REVERT: B 321 ASP cc_start: 0.8247 (m-30) cc_final: 0.8020 (m-30) REVERT: B 397 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7768 (mt-10) outliers start: 27 outliers final: 21 residues processed: 102 average time/residue: 0.2090 time to fit residues: 30.2182 Evaluate side-chains 103 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.9980 chunk 68 optimal weight: 20.0000 chunk 103 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 63 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 65 optimal weight: 0.0870 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8657 Z= 0.157 Angle : 0.545 7.621 11748 Z= 0.281 Chirality : 0.040 0.168 1281 Planarity : 0.003 0.034 1505 Dihedral : 5.883 55.054 1209 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.87 % Favored : 90.94 % Rotamer: Outliers : 3.43 % Allowed : 26.00 % Favored : 70.58 % 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: -0.48 (0.27), residues: 1049 helix: 1.57 (0.28), residues: 388 sheet: -0.38 (0.41), residues: 185 loop : -1.98 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 377 HIS 0.004 0.001 HIS A 52 PHE 0.053 0.001 PHE A 391 TYR 0.011 0.001 TYR B 366 ARG 0.006 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2098 Ramachandran restraints generated. 1049 Oldfield, 0 Emsley, 1049 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 82 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7409 (t80) REVERT: A 112 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3923 (tt) REVERT: A 372 LEU cc_start: 0.8848 (mt) cc_final: 0.8475 (mp) REVERT: B 49 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7479 (mm-40) REVERT: B 146 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 263 ARG cc_start: 0.7358 (tpm170) cc_final: 0.7038 (tpm170) REVERT: B 321 ASP cc_start: 0.8225 (m-30) cc_final: 0.7974 (m-30) REVERT: B 397 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7781 (mt-10) outliers start: 31 outliers final: 21 residues processed: 107 average time/residue: 0.2032 time to fit residues: 31.3024 Evaluate side-chains 104 residues out of total 904 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 GLN Chi-restraints excluded: chain A residue 46 HIS Chi-restraints excluded: chain A residue 69 SER Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 374 TYR Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 541 ASP Chi-restraints excluded: chain A residue 551 ILE Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 185 ASP Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 397 GLU Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 447 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 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 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.154579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.116497 restraints weight = 11850.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.114907 restraints weight = 14674.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116120 restraints weight = 15169.574| |-----------------------------------------------------------------------------| r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8657 Z= 0.182 Angle : 0.564 7.846 11748 Z= 0.290 Chirality : 0.041 0.150 1281 Planarity : 0.003 0.035 1505 Dihedral : 5.930 55.310 1209 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.96 % Favored : 90.85 % Rotamer: Outliers : 3.32 % Allowed : 26.55 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.50 (0.27), residues: 1049 helix: 1.55 (0.28), residues: 389 sheet: -0.43 (0.41), residues: 185 loop : -1.97 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 377 HIS 0.005 0.001 HIS A 52 PHE 0.013 0.001 PHE B 471 TYR 0.017 0.001 TYR A 402 ARG 0.006 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1763.62 seconds wall clock time: 33 minutes 10.81 seconds (1990.81 seconds total)