Starting phenix.real_space_refine on Thu Nov 14 16:39:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_51510.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_51510.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_51510.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_51510.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gqo_51510/11_2024/9gqo_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-5513/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: 4.45, per 1000 atoms: 0.66 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: 1.91 Conformation dependent library (CDL) restraints added in 997.1 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: 0.74 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: 2.17 Time building geometry restraints manager: 2.16 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: 0.830 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.540 ------------------------------------------------------------------------------- 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 : 0.814 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: 0.2075 time to fit residues: 23.7685 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 : 0.853 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 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 : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.5149 (m110) outliers start: 27 outliers final: 8 residues processed: 91 average time/residue: 0.2085 time to fit residues: 25.2556 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 : 0.855 ------------------------------------------------------------------------------- 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 719 ASN 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 44 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 A 798 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6811 Z= 0.192 Angle : 0.707 9.436 9212 Z= 0.349 Chirality : 0.042 0.202 1102 Planarity : 0.004 0.056 1175 Dihedral : 4.886 19.137 927 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 4.97 % Allowed : 34.39 % 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: -1.12 (0.28), residues: 876 helix: -0.03 (0.26), residues: 388 sheet: -0.47 (0.62), residues: 77 loop : -1.45 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.002 0.001 HIS A 552 PHE 0.013 0.001 PHE A 403 TYR 0.014 0.001 TYR A 497 ARG 0.003 0.000 ARG A 528 *********************** 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 98 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 62 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 20 residues processed: 91 average time/residue: 0.1872 time to fit residues: 23.2226 Evaluate side-chains 77 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 116 LYS Chi-restraints excluded: chain A residue 137 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 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 719 ASN 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 873 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 41 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 22 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2351 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= 0.173 Angle : 0.724 11.133 9212 Z= 0.351 Chirality : 0.042 0.162 1102 Planarity : 0.004 0.042 1175 Dihedral : 4.840 18.029 927 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.42 % Allowed : 34.25 % Favored : 61.33 % 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: -1.04 (0.29), residues: 876 helix: 0.01 (0.26), residues: 388 sheet: -0.52 (0.59), residues: 83 loop : -1.38 (0.32), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 703 HIS 0.001 0.000 HIS A 552 PHE 0.010 0.001 PHE A 12 TYR 0.015 0.001 TYR A 497 ARG 0.006 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 96 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7390 (mmm) cc_final: 0.7059 (mmm) REVERT: A 729 MET cc_start: 0.7698 (mmm) cc_final: 0.7407 (mmm) outliers start: 32 outliers final: 22 residues processed: 91 average time/residue: 0.1919 time to fit residues: 23.8349 Evaluate side-chains 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 58 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 114 VAL 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 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 683 TYR Chi-restraints excluded: chain A residue 782 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 58 optimal weight: 0.0470 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6811 Z= 0.181 Angle : 0.721 12.600 9212 Z= 0.348 Chirality : 0.042 0.182 1102 Planarity : 0.004 0.040 1175 Dihedral : 4.795 17.988 927 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.59 % Allowed : 34.94 % Favored : 61.46 % 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: -0.99 (0.29), residues: 876 helix: 0.05 (0.26), residues: 393 sheet: -0.28 (0.59), residues: 84 loop : -1.42 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.002 0.000 HIS A 375 PHE 0.010 0.001 PHE A 12 TYR 0.014 0.001 TYR A 497 ARG 0.003 0.000 ARG A 187 *********************** 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 86 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7392 (mmm) cc_final: 0.7087 (mmm) REVERT: A 729 MET cc_start: 0.7861 (mmm) cc_final: 0.7613 (mmm) outliers start: 26 outliers final: 20 residues processed: 82 average time/residue: 0.1751 time to fit residues: 20.2609 Evaluate side-chains 77 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 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 316 ILE Chi-restraints excluded: chain A residue 332 CYS Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 607 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 860 LEU 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 76 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6811 Z= 0.186 Angle : 0.717 13.110 9212 Z= 0.348 Chirality : 0.042 0.182 1102 Planarity : 0.004 0.039 1175 Dihedral : 4.779 18.194 927 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.73 % Allowed : 36.05 % Favored : 60.22 % 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: -0.99 (0.29), residues: 876 helix: 0.07 (0.26), residues: 398 sheet: -0.38 (0.60), residues: 78 loop : -1.42 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 703 HIS 0.002 0.001 HIS A 375 PHE 0.010 0.001 PHE A 707 TYR 0.013 0.001 TYR A 497 ARG 0.002 0.000 ARG A 187 *********************** 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 : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 MET cc_start: 0.7400 (mmm) cc_final: 0.7184 (mmm) REVERT: A 445 MET cc_start: 0.7194 (tpp) cc_final: 0.6595 (tpp) outliers start: 27 outliers final: 23 residues processed: 80 average time/residue: 0.1720 time to fit residues: 19.4363 Evaluate side-chains 79 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 56 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 252 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 421 GLU Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 VAL 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 789 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 860 LEU 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 9 optimal weight: 0.0370 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 0.0980 chunk 53 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6811 Z= 0.171 Angle : 0.728 13.769 9212 Z= 0.350 Chirality : 0.042 0.169 1102 Planarity : 0.004 0.037 1175 Dihedral : 4.760 18.098 927 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.59 % Allowed : 35.91 % Favored : 60.50 % 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: -0.99 (0.29), residues: 876 helix: 0.08 (0.26), residues: 395 sheet: -0.37 (0.58), residues: 84 loop : -1.44 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.001 0.000 HIS A 437 PHE 0.010 0.001 PHE A 685 TYR 0.013 0.001 TYR A 497 ARG 0.005 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 83 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 MET cc_start: 0.8304 (tpp) cc_final: 0.8086 (tpp) REVERT: A 445 MET cc_start: 0.7608 (tpp) cc_final: 0.6972 (tpp) REVERT: A 719 ASN cc_start: 0.5379 (t0) cc_final: 0.4699 (t0) REVERT: A 789 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7881 (t) outliers start: 26 outliers final: 20 residues processed: 80 average time/residue: 0.1822 time to fit residues: 20.1359 Evaluate side-chains 75 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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 316 ILE Chi-restraints excluded: chain A residue 332 CYS 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 531 VAL Chi-restraints excluded: chain A residue 546 VAL 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 693 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6811 Z= 0.181 Angle : 0.755 14.209 9212 Z= 0.359 Chirality : 0.042 0.166 1102 Planarity : 0.004 0.042 1175 Dihedral : 4.749 18.312 927 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 3.18 % Allowed : 37.71 % Favored : 59.12 % 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: -0.99 (0.29), residues: 876 helix: 0.17 (0.27), residues: 391 sheet: -0.84 (0.57), residues: 85 loop : -1.42 (0.32), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 703 HIS 0.003 0.001 HIS A 313 PHE 0.014 0.001 PHE A 685 TYR 0.013 0.001 TYR A 497 ARG 0.006 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 80 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7641 (tpp) cc_final: 0.7021 (tpp) REVERT: A 523 MET cc_start: 0.6140 (mmp) cc_final: 0.5738 (mmp) REVERT: A 719 ASN cc_start: 0.5386 (t0) cc_final: 0.4642 (t0) outliers start: 23 outliers final: 16 residues processed: 78 average time/residue: 0.1935 time to fit residues: 20.7807 Evaluate side-chains 71 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 316 ILE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 VAL 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 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 79 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.2980 chunk 62 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6811 Z= 0.181 Angle : 0.774 14.904 9212 Z= 0.366 Chirality : 0.042 0.170 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.729 18.972 927 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.90 % Allowed : 37.43 % 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: -0.98 (0.28), residues: 876 helix: 0.15 (0.26), residues: 392 sheet: -0.31 (0.62), residues: 70 loop : -1.48 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 703 HIS 0.001 0.001 HIS A 375 PHE 0.017 0.001 PHE A 403 TYR 0.013 0.001 TYR A 497 ARG 0.005 0.000 ARG A 187 *********************** 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 78 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7696 (tpp) cc_final: 0.6971 (tpp) REVERT: A 523 MET cc_start: 0.6133 (mmp) cc_final: 0.5905 (mmp) REVERT: A 719 ASN cc_start: 0.5460 (t0) cc_final: 0.4860 (t0) outliers start: 21 outliers final: 19 residues processed: 76 average time/residue: 0.1536 time to fit residues: 16.1255 Evaluate side-chains 74 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 316 ILE Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 VAL 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 782 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 80 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 chunk 7 optimal weight: 0.1980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3503 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= 0.178 Angle : 0.800 15.139 9212 Z= 0.377 Chirality : 0.042 0.171 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.749 22.899 927 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.76 % Allowed : 37.57 % 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: -1.01 (0.29), residues: 876 helix: 0.19 (0.26), residues: 392 sheet: -0.87 (0.60), residues: 80 loop : -1.47 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 703 HIS 0.004 0.001 HIS A 313 PHE 0.015 0.001 PHE A 403 TYR 0.013 0.001 TYR A 497 ARG 0.004 0.000 ARG A 187 ********************** 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 76 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 56 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 445 MET cc_start: 0.7712 (tpp) cc_final: 0.6908 (tpp) REVERT: A 500 MET cc_start: 0.3967 (mmm) cc_final: 0.3583 (mmp) REVERT: A 523 MET cc_start: 0.6046 (mmp) cc_final: 0.5785 (mmp) REVERT: A 719 ASN cc_start: 0.5436 (t0) cc_final: 0.4792 (t0) outliers start: 20 outliers final: 18 residues processed: 74 average time/residue: 0.1874 time to fit residues: 19.2572 Evaluate side-chains 73 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.822 ------------------------------------------------------------------------------- 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 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 492 VAL Chi-restraints excluded: chain A residue 531 VAL Chi-restraints excluded: chain A residue 546 VAL 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 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 21 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 69 optimal weight: 0.4980 chunk 29 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 8 optimal weight: 0.0670 chunk 12 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.052606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.043977 restraints weight = 53084.772| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 7.21 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3636 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= 0.176 Angle : 0.793 15.320 9212 Z= 0.371 Chirality : 0.042 0.179 1102 Planarity : 0.004 0.045 1175 Dihedral : 4.680 18.724 927 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.62 % Allowed : 38.12 % Favored : 59.25 % 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: -0.96 (0.29), residues: 876 helix: 0.22 (0.26), residues: 392 sheet: -0.81 (0.61), residues: 80 loop : -1.42 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 703 HIS 0.002 0.001 HIS A 313 PHE 0.015 0.001 PHE A 403 TYR 0.013 0.001 TYR A 497 ARG 0.005 0.000 ARG A 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1494.76 seconds wall clock time: 31 minutes 54.40 seconds (1914.40 seconds total)