Starting phenix.real_space_refine on Tue Jan 14 14:37:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.map" model { file = "/net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gqo_51510/01_2025/9gqo_51510.cif" } resolution = 3.46 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= 0.020 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 1 5.49 5 Mg 1 5.21 5 S 34 5.16 5 C 4284 2.51 5 N 1111 2.21 5 O 1284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 880, 6710 Classifications: {'peptide': 880} Link IDs: {'PTRANS': 29, 'TRANS': 850} Chain breaks: 1 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 6 Unusual residues: {' CA': 1, ' MG': 1, 'PO3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.14, per 1000 atoms: 0.62 Number of scatterers: 6716 At special positions: 0 Unit cell: (71.17, 86.698, 142.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 34 16.00 P 1 15.00 Mg 1 11.99 O 1284 8.00 N 1111 7.00 C 4284 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: 1.58 Conformation dependent library (CDL) restraints added in 970.1 milliseconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 50.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 4.251A pdb=" N GLN A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU A 15 " --> pdb=" O THR A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 10 through 15' Processing helix chain 'A' and resid 23 through 35 removed outlier: 3.659A pdb=" N VAL A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N GLU A 32 " --> pdb=" O THR A 28 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 removed outlier: 3.597A pdb=" N THR A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 72 removed outlier: 4.070A pdb=" N LEU A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 69 " --> pdb=" O ILE A 65 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 99 removed outlier: 3.990A pdb=" N LEU A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 213 through 223 removed outlier: 3.590A pdb=" N LEU A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 removed outlier: 4.260A pdb=" N ARG A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS A 235 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 255 removed outlier: 3.879A pdb=" N LEU A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 removed outlier: 3.937A pdb=" N LEU A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 290 removed outlier: 3.670A pdb=" N ASN A 277 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 311 removed outlier: 4.277A pdb=" N SER A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 369 through 380 Processing helix chain 'A' and resid 394 through 407 removed outlier: 3.712A pdb=" N ASN A 407 " --> pdb=" O PHE A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 418 removed outlier: 4.046A pdb=" N ILE A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 458 Processing helix chain 'A' and resid 474 through 488 Processing helix chain 'A' and resid 529 through 541 removed outlier: 4.266A pdb=" N ALA A 533 " --> pdb=" O GLU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 562 removed outlier: 4.866A pdb=" N GLY A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ARG A 561 " --> pdb=" O GLN A 557 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.582A pdb=" N MET A 581 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 removed outlier: 4.328A pdb=" N GLU A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 614 removed outlier: 3.593A pdb=" N ILE A 607 " --> pdb=" O ASN A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 626 No H-bonds generated for 'chain 'A' and resid 624 through 626' Processing helix chain 'A' and resid 627 through 634 Processing helix chain 'A' and resid 644 through 651 Processing helix chain 'A' and resid 660 through 701 removed outlier: 4.292A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 681 " --> pdb=" O ILE A 677 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 682 " --> pdb=" O LYS A 678 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 701 " --> pdb=" O PHE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 720 removed outlier: 3.504A pdb=" N LEU A 713 " --> pdb=" O ALA A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 750 through 776 removed outlier: 4.362A pdb=" N ALA A 756 " --> pdb=" O GLY A 752 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N SER A 759 " --> pdb=" O ARG A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 798 removed outlier: 3.830A pdb=" N ALA A 787 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 788 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 789 " --> pdb=" O ALA A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 817 through 836 removed outlier: 3.664A pdb=" N LEU A 836 " --> pdb=" O GLY A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 877 removed outlier: 3.587A pdb=" N ILE A 871 " --> pdb=" O MET A 867 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 119 Processing sheet with id=AA2, first strand: chain 'A' and resid 136 through 139 removed outlier: 3.958A pdb=" N LEU A 196 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS A 158 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY A 200 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N SER A 156 " --> pdb=" O GLY A 200 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N GLY A 202 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N SER A 154 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 204 " --> pdb=" O PHE A 152 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE A 152 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N VAL A 206 " --> pdb=" O ARG A 150 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG A 150 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 148 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LEU A 157 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 574 removed outlier: 6.457A pdb=" N LEU A 573 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N TYR A 596 " --> pdb=" O THR A 545 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N MET A 547 " --> pdb=" O TYR A 596 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE A 331 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE A 548 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N THR A 333 " --> pdb=" O ILE A 548 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 618 " --> pdb=" O ILE A 636 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N VAL A 638 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N MET A 620 " --> pdb=" O VAL A 638 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET A 640 " --> pdb=" O MET A 620 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY A 622 " --> pdb=" O MET A 640 " (cutoff:3.500A) removed outlier: 8.621A pdb=" N LEU A 655 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ALA A 639 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.181A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 517 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TYR A 497 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 345 through 350 removed outlier: 5.181A pdb=" N VAL A 346 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE A 524 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A 460 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY A 519 " --> pdb=" O TYR A 460 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 894 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: 2.06 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2207 1.35 - 1.46: 1372 1.46 - 1.58: 3169 1.58 - 1.70: 0 1.70 - 1.82: 63 Bond restraints: 6811 Sorted by residual: bond pdb=" O2 PO3 A1002 " pdb=" P PO3 A1002 " ideal model delta sigma weight residual 1.604 1.509 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O1 PO3 A1002 " pdb=" P PO3 A1002 " ideal model delta sigma weight residual 1.604 1.509 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O3 PO3 A1002 " pdb=" P PO3 A1002 " ideal model delta sigma weight residual 1.601 1.510 0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" N ILE A 3 " pdb=" CA ILE A 3 " ideal model delta sigma weight residual 1.461 1.491 -0.030 1.17e-02 7.31e+03 6.40e+00 bond pdb=" N GLU A 2 " pdb=" CA GLU A 2 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.15e+00 ... (remaining 6806 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8962 1.89 - 3.77: 195 3.77 - 5.66: 42 5.66 - 7.55: 10 7.55 - 9.43: 3 Bond angle restraints: 9212 Sorted by residual: angle pdb=" CB LYS A 40 " pdb=" CG LYS A 40 " pdb=" CD LYS A 40 " ideal model delta sigma weight residual 111.30 120.73 -9.43 2.30e+00 1.89e-01 1.68e+01 angle pdb=" N VAL A 378 " pdb=" CA VAL A 378 " pdb=" C VAL A 378 " ideal model delta sigma weight residual 113.42 108.64 4.78 1.17e+00 7.31e-01 1.67e+01 angle pdb=" CA MET A 868 " pdb=" CB MET A 868 " pdb=" CG MET A 868 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" C LEU A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 125.66 131.81 -6.15 1.85e+00 2.92e-01 1.11e+01 angle pdb=" CA TYR A 4 " pdb=" CB TYR A 4 " pdb=" CG TYR A 4 " ideal model delta sigma weight residual 113.90 119.72 -5.82 1.80e+00 3.09e-01 1.04e+01 ... (remaining 9207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3447 17.81 - 35.63: 545 35.63 - 53.44: 128 53.44 - 71.25: 21 71.25 - 89.06: 12 Dihedral angle restraints: 4153 sinusoidal: 1627 harmonic: 2526 Sorted by residual: dihedral pdb=" CA MET A 271 " pdb=" C MET A 271 " pdb=" N ALA A 272 " pdb=" CA ALA A 272 " ideal model delta harmonic sigma weight residual 180.00 155.35 24.65 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CD ARG A 5 " pdb=" NE ARG A 5 " pdb=" CZ ARG A 5 " pdb=" NH1 ARG A 5 " ideal model delta sinusoidal sigma weight residual 0.00 36.04 -36.04 1 1.00e+01 1.00e-02 1.84e+01 dihedral pdb=" CA THR A 165 " pdb=" C THR A 165 " pdb=" N GLY A 166 " pdb=" CA GLY A 166 " ideal model delta harmonic sigma weight residual 180.00 159.10 20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 4150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 850 0.045 - 0.091: 198 0.091 - 0.136: 51 0.136 - 0.182: 2 0.182 - 0.227: 1 Chirality restraints: 1102 Sorted by residual: chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR A 165 " pdb=" N THR A 165 " pdb=" C THR A 165 " pdb=" CB THR A 165 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA MET A 470 " pdb=" N MET A 470 " pdb=" C MET A 470 " pdb=" CB MET A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.64e-01 ... (remaining 1099 not shown) Planarity restraints: 1175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.644 9.50e-02 1.11e+02 2.89e-01 5.08e+01 pdb=" NE ARG A 5 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 178 " 0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO A 179 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 179 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 179 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 391 " -0.007 2.00e-02 2.50e+03 1.44e-02 2.08e+00 pdb=" CD GLU A 391 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLU A 391 " -0.009 2.00e-02 2.50e+03 pdb=" OE2 GLU A 391 " -0.009 2.00e-02 2.50e+03 ... (remaining 1172 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 137 2.65 - 3.21: 6907 3.21 - 3.78: 10744 3.78 - 4.34: 14411 4.34 - 4.90: 22082 Nonbonded interactions: 54281 Sorted by model distance: nonbonded pdb=" OD2 ASP A 334 " pdb="MG MG A1003 " model vdw 2.090 2.170 nonbonded pdb=" O3 PO3 A1002 " pdb="MG MG A1003 " model vdw 2.099 2.170 nonbonded pdb=" O THR A 336 " pdb="MG MG A1003 " model vdw 2.132 2.170 nonbonded pdb=" OG1 THR A 549 " pdb=" O1 PO3 A1002 " model vdw 2.225 3.040 nonbonded pdb=" OG SER A 680 " pdb=" O ALA A 724 " model vdw 2.240 3.040 ... (remaining 54276 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=0.00 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: 0.720 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 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 : 0.003 0.095 6811 Z= 0.240 Angle : 0.714 9.434 9212 Z= 0.386 Chirality : 0.042 0.227 1102 Planarity : 0.009 0.289 1175 Dihedral : 18.403 89.063 2521 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.41 % Allowed : 39.92 % Favored : 59.67 % 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: -1.32 (0.28), residues: 876 helix: -0.53 (0.26), residues: 390 sheet: 0.15 (0.61), residues: 72 loop : -1.35 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 703 HIS 0.002 0.000 HIS A 437 PHE 0.013 0.001 PHE A 707 TYR 0.020 0.001 TYR A 4 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 GLU cc_start: 0.5023 (OUTLIER) cc_final: 0.1506 (pt0) REVERT: A 445 MET cc_start: 0.5896 (tpt) cc_final: 0.5448 (tpp) outliers start: 3 outliers final: 0 residues processed: 85 average time/residue: 0.1942 time to fit residues: 22.1270 Evaluate side-chains 61 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 26 optimal weight: 0.0370 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.051381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.042030 restraints weight = 51587.945| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 8.35 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6811 Z= 0.210 Angle : 0.720 11.811 9212 Z= 0.365 Chirality : 0.043 0.219 1102 Planarity : 0.005 0.048 1175 Dihedral : 5.026 29.103 930 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.73 % Allowed : 35.08 % Favored : 61.19 % 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: -1.06 (0.28), residues: 876 helix: -0.19 (0.26), residues: 388 sheet: 0.15 (0.60), residues: 78 loop : -1.34 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 703 HIS 0.002 0.001 HIS A 552 PHE 0.016 0.001 PHE A 403 TYR 0.014 0.001 TYR A 497 ARG 0.008 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 MET cc_start: 0.4508 (mmm) cc_final: 0.4273 (mmm) REVERT: A 547 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8354 (tmm) REVERT: A 640 MET cc_start: 0.9182 (tpt) cc_final: 0.8950 (tpt) REVERT: A 754 MET cc_start: 0.8021 (mmt) cc_final: 0.7810 (mmp) REVERT: A 862 LEU cc_start: 0.9514 (mt) cc_final: 0.9220 (pp) REVERT: A 867 MET cc_start: 0.8980 (ptt) cc_final: 0.8732 (mmm) outliers start: 27 outliers final: 8 residues processed: 91 average time/residue: 0.1999 time to fit residues: 24.2770 Evaluate side-chains 69 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 77 optimal weight: 0.0030 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 69 optimal weight: 0.0670 chunk 64 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.054888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.047268 restraints weight = 60181.789| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 6.99 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6811 Z= 0.175 Angle : 0.700 9.347 9212 Z= 0.345 Chirality : 0.042 0.191 1102 Planarity : 0.004 0.056 1175 Dihedral : 4.842 18.573 927 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 5.11 % Allowed : 33.98 % Favored : 60.91 % 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: -1.14 (0.28), residues: 876 helix: -0.07 (0.26), residues: 388 sheet: -0.45 (0.59), residues: 83 loop : -1.47 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.014 0.001 PHE A 403 TYR 0.014 0.001 TYR A 497 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 LEU cc_start: 0.9446 (mt) cc_final: 0.9027 (pp) REVERT: A 280 MET cc_start: 0.8931 (mmt) cc_final: 0.8674 (mmt) REVERT: A 397 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9010 (mp0) REVERT: A 433 MET cc_start: 0.8112 (tmm) cc_final: 0.7909 (tmm) REVERT: A 445 MET cc_start: 0.8153 (tpp) cc_final: 0.7726 (tpp) REVERT: A 500 MET cc_start: 0.4870 (mmm) cc_final: 0.4545 (mmm) REVERT: A 523 MET cc_start: 0.8681 (mpp) cc_final: 0.8148 (mmp) REVERT: A 547 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: A 566 MET cc_start: 0.7511 (tpp) cc_final: 0.7255 (tpp) REVERT: A 754 MET cc_start: 0.8306 (mmt) cc_final: 0.7988 (mmt) REVERT: A 786 MET cc_start: 0.7545 (mmm) cc_final: 0.7269 (mmp) REVERT: A 862 LEU cc_start: 0.9516 (mt) cc_final: 0.9192 (pp) REVERT: A 867 MET cc_start: 0.8852 (ptt) cc_final: 0.8575 (mmm) outliers start: 37 outliers final: 21 residues processed: 93 average time/residue: 0.1831 time to fit residues: 23.2953 Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 HIS A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.048650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.040290 restraints weight = 54884.136| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 6.83 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6811 Z= 0.323 Angle : 0.757 9.665 9212 Z= 0.386 Chirality : 0.044 0.169 1102 Planarity : 0.005 0.044 1175 Dihedral : 5.091 21.320 927 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 4.70 % Allowed : 34.25 % Favored : 61.05 % 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 (0.28), residues: 876 helix: 0.07 (0.26), residues: 388 sheet: 0.19 (0.66), residues: 66 loop : -1.40 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 703 HIS 0.003 0.001 HIS A 592 PHE 0.011 0.002 PHE A 152 TYR 0.013 0.002 TYR A 497 ARG 0.003 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.9217 (mmm) cc_final: 0.8957 (mmm) REVERT: A 397 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.8953 (mp0) REVERT: A 433 MET cc_start: 0.8321 (tmm) cc_final: 0.8113 (tmm) REVERT: A 445 MET cc_start: 0.8371 (tpp) cc_final: 0.8021 (tpp) REVERT: A 500 MET cc_start: 0.5305 (mmm) cc_final: 0.4902 (mmm) REVERT: A 523 MET cc_start: 0.8487 (mpp) cc_final: 0.7920 (mmt) REVERT: A 566 MET cc_start: 0.7464 (tpp) cc_final: 0.7226 (tpp) REVERT: A 729 MET cc_start: 0.8651 (mmm) cc_final: 0.8332 (mmm) REVERT: A 754 MET cc_start: 0.8509 (mmt) cc_final: 0.8259 (mmt) REVERT: A 786 MET cc_start: 0.7572 (mmm) cc_final: 0.7150 (mmt) REVERT: A 862 LEU cc_start: 0.9577 (mt) cc_final: 0.9280 (pp) REVERT: A 867 MET cc_start: 0.8932 (ptt) cc_final: 0.8666 (mmm) outliers start: 34 outliers final: 20 residues processed: 85 average time/residue: 0.1864 time to fit residues: 22.0600 Evaluate side-chains 73 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 116 LYS Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 636 ILE Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 3 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 64 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.052028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.044781 restraints weight = 61407.275| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 6.75 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6811 Z= 0.186 Angle : 0.702 12.268 9212 Z= 0.347 Chirality : 0.042 0.176 1102 Planarity : 0.004 0.039 1175 Dihedral : 5.058 19.456 927 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.70 % Allowed : 34.67 % Favored : 60.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.91 (0.28), residues: 876 helix: 0.16 (0.26), residues: 386 sheet: 0.11 (0.63), residues: 72 loop : -1.46 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.003 0.001 HIS A 437 PHE 0.009 0.001 PHE A 204 TYR 0.012 0.001 TYR A 497 ARG 0.020 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 58 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.8361 (tptp) cc_final: 0.8061 (tptp) REVERT: A 344 MET cc_start: 0.8295 (tpp) cc_final: 0.8080 (tpp) REVERT: A 421 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8435 (pt0) REVERT: A 433 MET cc_start: 0.8600 (tmm) cc_final: 0.8223 (tmm) REVERT: A 445 MET cc_start: 0.8776 (tpp) cc_final: 0.8451 (tpp) REVERT: A 454 MET cc_start: 0.8537 (mmp) cc_final: 0.8097 (mmp) REVERT: A 500 MET cc_start: 0.5166 (mmm) cc_final: 0.4831 (mmm) REVERT: A 566 MET cc_start: 0.7972 (tpp) cc_final: 0.7475 (tpp) REVERT: A 729 MET cc_start: 0.8505 (mmm) cc_final: 0.8132 (mmm) REVERT: A 754 MET cc_start: 0.8649 (mmt) cc_final: 0.8420 (mmt) REVERT: A 786 MET cc_start: 0.7951 (mmm) cc_final: 0.7429 (mmt) REVERT: A 862 LEU cc_start: 0.9459 (mt) cc_final: 0.9246 (pp) REVERT: A 867 MET cc_start: 0.9063 (ptt) cc_final: 0.8730 (mmm) outliers start: 34 outliers final: 23 residues processed: 88 average time/residue: 0.1809 time to fit residues: 22.0349 Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 56 optimal weight: 0.0270 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.052526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.045241 restraints weight = 60887.099| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 6.82 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6811 Z= 0.184 Angle : 0.705 12.996 9212 Z= 0.346 Chirality : 0.042 0.170 1102 Planarity : 0.004 0.039 1175 Dihedral : 4.967 19.282 927 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.73 % Allowed : 36.19 % Favored : 60.08 % 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: -1.01 (0.29), residues: 876 helix: 0.12 (0.26), residues: 387 sheet: -0.74 (0.57), residues: 88 loop : -1.41 (0.32), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.003 0.001 HIS A 437 PHE 0.014 0.001 PHE A 685 TYR 0.014 0.001 TYR A 831 ARG 0.005 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 LYS cc_start: 0.8318 (tptp) cc_final: 0.8034 (tptp) REVERT: A 421 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: A 433 MET cc_start: 0.8610 (tmm) cc_final: 0.8212 (tmm) REVERT: A 445 MET cc_start: 0.8794 (tpp) cc_final: 0.8447 (tpp) REVERT: A 500 MET cc_start: 0.5190 (mmm) cc_final: 0.4846 (mmm) REVERT: A 536 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.9253 (mp0) REVERT: A 566 MET cc_start: 0.8258 (tpp) cc_final: 0.7636 (tpp) REVERT: A 653 MET cc_start: 0.8769 (tpt) cc_final: 0.8206 (tpt) REVERT: A 729 MET cc_start: 0.8793 (mmm) cc_final: 0.8496 (mmm) REVERT: A 754 MET cc_start: 0.8654 (mmt) cc_final: 0.8408 (mmt) REVERT: A 786 MET cc_start: 0.7647 (mmm) cc_final: 0.7255 (mmt) REVERT: A 862 LEU cc_start: 0.9458 (mt) cc_final: 0.9241 (pp) REVERT: A 867 MET cc_start: 0.9037 (ptt) cc_final: 0.8701 (mmm) outliers start: 27 outliers final: 23 residues processed: 81 average time/residue: 0.1775 time to fit residues: 20.1815 Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 697 PHE Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.049680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.041005 restraints weight = 55645.521| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 7.51 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6811 Z= 0.238 Angle : 0.738 13.664 9212 Z= 0.366 Chirality : 0.043 0.161 1102 Planarity : 0.004 0.038 1175 Dihedral : 5.038 20.227 927 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.28 % Allowed : 36.05 % Favored : 59.67 % 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: -1.00 (0.28), residues: 876 helix: 0.10 (0.26), residues: 389 sheet: 0.08 (0.65), residues: 65 loop : -1.52 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 703 HIS 0.002 0.001 HIS A 437 PHE 0.013 0.001 PHE A 685 TYR 0.013 0.001 TYR A 831 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 55 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8938 (pmm) cc_final: 0.8617 (pmm) REVERT: A 318 LYS cc_start: 0.8560 (tptp) cc_final: 0.8330 (tptp) REVERT: A 421 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8164 (pt0) REVERT: A 433 MET cc_start: 0.8637 (tmm) cc_final: 0.8167 (tmm) REVERT: A 445 MET cc_start: 0.8644 (tpp) cc_final: 0.8278 (tpp) REVERT: A 500 MET cc_start: 0.5483 (mmm) cc_final: 0.5034 (mmm) REVERT: A 523 MET cc_start: 0.8630 (mmp) cc_final: 0.8429 (mmp) REVERT: A 566 MET cc_start: 0.8134 (tpp) cc_final: 0.7691 (tpp) REVERT: A 729 MET cc_start: 0.9097 (mmm) cc_final: 0.8856 (mmm) REVERT: A 754 MET cc_start: 0.8678 (mmt) cc_final: 0.8446 (mmt) REVERT: A 786 MET cc_start: 0.7562 (mmm) cc_final: 0.7195 (mmt) REVERT: A 862 LEU cc_start: 0.9493 (mt) cc_final: 0.9277 (pp) REVERT: A 867 MET cc_start: 0.8979 (ptt) cc_final: 0.8667 (mmm) outliers start: 31 outliers final: 25 residues processed: 83 average time/residue: 0.1702 time to fit residues: 19.9207 Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.049888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.041271 restraints weight = 55853.419| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 7.56 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6811 Z= 0.198 Angle : 0.722 14.108 9212 Z= 0.359 Chirality : 0.042 0.160 1102 Planarity : 0.004 0.037 1175 Dihedral : 5.040 19.676 927 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.28 % Allowed : 35.64 % Favored : 60.08 % 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: -0.92 (0.29), residues: 876 helix: 0.17 (0.26), residues: 389 sheet: -0.16 (0.63), residues: 71 loop : -1.44 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.003 0.001 HIS A 437 PHE 0.013 0.001 PHE A 685 TYR 0.012 0.001 TYR A 497 ARG 0.003 0.000 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8897 (pmm) cc_final: 0.8488 (pmm) REVERT: A 318 LYS cc_start: 0.8578 (tptp) cc_final: 0.8332 (tptp) REVERT: A 421 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8099 (pt0) REVERT: A 433 MET cc_start: 0.8611 (tmm) cc_final: 0.8104 (tmm) REVERT: A 445 MET cc_start: 0.8788 (tpp) cc_final: 0.8489 (tpp) REVERT: A 500 MET cc_start: 0.5505 (mmm) cc_final: 0.5041 (mmm) REVERT: A 566 MET cc_start: 0.8153 (tpp) cc_final: 0.7640 (tpp) REVERT: A 696 LEU cc_start: 0.9425 (tt) cc_final: 0.9156 (pp) REVERT: A 729 MET cc_start: 0.9125 (mmm) cc_final: 0.8892 (mmm) REVERT: A 754 MET cc_start: 0.8643 (mmt) cc_final: 0.8404 (mmt) REVERT: A 786 MET cc_start: 0.7375 (mmm) cc_final: 0.6992 (mmt) REVERT: A 862 LEU cc_start: 0.9497 (mt) cc_final: 0.9279 (pp) REVERT: A 867 MET cc_start: 0.8944 (ptt) cc_final: 0.8638 (mmm) outliers start: 31 outliers final: 24 residues processed: 83 average time/residue: 0.1728 time to fit residues: 20.4671 Evaluate side-chains 79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 31 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.052252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.045014 restraints weight = 61401.528| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 6.77 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6811 Z= 0.186 Angle : 0.747 14.859 9212 Z= 0.366 Chirality : 0.043 0.172 1102 Planarity : 0.004 0.037 1175 Dihedral : 4.990 19.423 927 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.87 % Allowed : 36.19 % Favored : 59.94 % 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: -0.83 (0.29), residues: 876 helix: 0.23 (0.26), residues: 387 sheet: -0.15 (0.60), residues: 79 loop : -1.37 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.003 0.001 HIS A 313 PHE 0.013 0.001 PHE A 685 TYR 0.011 0.001 TYR A 497 ARG 0.003 0.000 ARG A 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8832 (pmm) cc_final: 0.8385 (pmm) REVERT: A 318 LYS cc_start: 0.8501 (tptp) cc_final: 0.8241 (tptp) REVERT: A 421 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8220 (pt0) REVERT: A 433 MET cc_start: 0.8677 (tmm) cc_final: 0.8135 (tmm) REVERT: A 445 MET cc_start: 0.8819 (tpp) cc_final: 0.8505 (tpp) REVERT: A 500 MET cc_start: 0.5447 (mmm) cc_final: 0.4991 (mmm) REVERT: A 566 MET cc_start: 0.8167 (tpp) cc_final: 0.7542 (tpp) REVERT: A 696 LEU cc_start: 0.9372 (tt) cc_final: 0.9085 (pp) REVERT: A 729 MET cc_start: 0.9135 (mmm) cc_final: 0.8931 (mmm) REVERT: A 754 MET cc_start: 0.8630 (mmt) cc_final: 0.8377 (mmt) REVERT: A 786 MET cc_start: 0.7291 (mmm) cc_final: 0.6776 (mmt) REVERT: A 862 LEU cc_start: 0.9508 (mt) cc_final: 0.9268 (pp) outliers start: 28 outliers final: 23 residues processed: 85 average time/residue: 0.1716 time to fit residues: 20.6453 Evaluate side-chains 77 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 866 VAL Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 27 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.051655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.043632 restraints weight = 49041.238| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 6.41 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6811 Z= 0.203 Angle : 0.800 14.903 9212 Z= 0.388 Chirality : 0.043 0.172 1102 Planarity : 0.004 0.037 1175 Dihedral : 5.068 26.888 927 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.59 % Allowed : 36.60 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.29), residues: 876 helix: 0.15 (0.26), residues: 393 sheet: -0.12 (0.61), residues: 79 loop : -1.36 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.003 0.001 HIS A 313 PHE 0.013 0.001 PHE A 685 TYR 0.011 0.001 TYR A 497 ARG 0.003 0.000 ARG A 261 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 MET cc_start: 0.8940 (pmm) cc_final: 0.8539 (pmm) REVERT: A 318 LYS cc_start: 0.8505 (tptp) cc_final: 0.8053 (tptt) REVERT: A 421 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8070 (pt0) REVERT: A 433 MET cc_start: 0.8577 (tmm) cc_final: 0.8078 (tmm) REVERT: A 445 MET cc_start: 0.8598 (tpp) cc_final: 0.8322 (tpp) REVERT: A 500 MET cc_start: 0.5484 (mmm) cc_final: 0.5001 (mmm) REVERT: A 566 MET cc_start: 0.8223 (tpp) cc_final: 0.7653 (tpp) REVERT: A 696 LEU cc_start: 0.9359 (tt) cc_final: 0.9066 (pp) REVERT: A 729 MET cc_start: 0.9210 (mmm) cc_final: 0.9007 (mmm) REVERT: A 754 MET cc_start: 0.8585 (mmt) cc_final: 0.8362 (mmt) REVERT: A 862 LEU cc_start: 0.9507 (mt) cc_final: 0.9274 (pp) outliers start: 26 outliers final: 21 residues processed: 79 average time/residue: 0.1683 time to fit residues: 18.7218 Evaluate side-chains 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 105 ASP Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 316 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 592 HIS Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 745 ASN Chi-restraints excluded: chain A residue 808 THR Chi-restraints excluded: chain A residue 873 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.050468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.042648 restraints weight = 50285.580| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 6.25 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6811 Z= 0.240 Angle : 0.803 14.670 9212 Z= 0.395 Chirality : 0.043 0.195 1102 Planarity : 0.004 0.037 1175 Dihedral : 5.112 20.149 927 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.01 % Allowed : 36.19 % Favored : 59.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.29), residues: 876 helix: 0.09 (0.26), residues: 393 sheet: -0.15 (0.68), residues: 66 loop : -1.39 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.003 0.001 HIS A 437 PHE 0.013 0.001 PHE A 685 TYR 0.011 0.001 TYR A 497 ARG 0.003 0.000 ARG A 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.51 seconds wall clock time: 49 minutes 43.79 seconds (2983.79 seconds total)