Starting phenix.real_space_refine on Fri Aug 7 10:01:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xzl_72361/08_2026/9xzl_72361.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 10 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 6410 2.51 5 N 1738 2.21 5 O 1897 1.98 5 H 10035 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20146 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4393 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 4, 'TRANS': 261} Chain breaks: 1 Chain: "F" Number of atoms: 12969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 12969 Classifications: {'peptide': 805} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain breaks: 1 Chain: "S" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 2532 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 9, 'TRANS': 150} Chain: "X" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 219 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, ' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16324 SG CYS F 889 34.780 83.492 71.552 1.00111.14 S ATOM 16385 SG CYS F 894 36.839 86.092 69.925 1.00116.52 S ATOM 16881 SG CYS F 925 37.255 82.548 68.868 1.00 97.31 S ATOM 16919 SG CYS F 928 38.492 83.477 72.138 1.00126.22 S Time building chain proxies: 3.35, per 1000 atoms: 0.17 Number of scatterers: 20146 At special positions: 0 Unit cell: (80.164, 125.972, 153.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 54 16.00 P 10 15.00 Mg 1 11.99 O 1897 8.00 N 1738 7.00 C 6410 6.00 H 10035 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 414.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F1003 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 925 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 889 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 894 " pdb="ZN ZN F1003 " - pdb=" SG CYS F 928 " Number of angles added : 6 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 6 sheets defined 68.4% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'C' and resid 16 through 33 removed outlier: 3.654A pdb=" N ILE C 20 " --> pdb=" O GLY C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 54 Processing helix chain 'C' and resid 77 through 108 Processing helix chain 'C' and resid 111 through 137 Processing helix chain 'C' and resid 137 through 152 removed outlier: 4.081A pdb=" N VAL C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ARG C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 171 through 193 removed outlier: 4.862A pdb=" N LYS C 177 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N GLN C 178 " --> pdb=" O PRO C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 3.869A pdb=" N ILE C 201 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 232 through 255 Processing helix chain 'C' and resid 256 through 279 Processing helix chain 'C' and resid 282 through 296 removed outlier: 4.651A pdb=" N GLU C 286 " --> pdb=" O SER C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.655A pdb=" N LEU C 300 " --> pdb=" O GLU C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'F' and resid 137 through 141 Processing helix chain 'F' and resid 142 through 151 Processing helix chain 'F' and resid 154 through 161 Processing helix chain 'F' and resid 162 through 165 Processing helix chain 'F' and resid 166 through 175 Processing helix chain 'F' and resid 179 through 190 Processing helix chain 'F' and resid 192 through 206 Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 233 through 242 Processing helix chain 'F' and resid 246 through 258 Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 283 through 295 removed outlier: 3.707A pdb=" N ILE F 287 " --> pdb=" O SER F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 removed outlier: 4.392A pdb=" N THR F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 324 Processing helix chain 'F' and resid 329 through 344 Processing helix chain 'F' and resid 368 through 377 Processing helix chain 'F' and resid 394 through 406 Processing helix chain 'F' and resid 417 through 428 Processing helix chain 'F' and resid 437 through 445 Processing helix chain 'F' and resid 445 through 452 removed outlier: 3.959A pdb=" N TYR F 449 " --> pdb=" O ILE F 445 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 469 removed outlier: 3.579A pdb=" N VAL F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 492 Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 517 through 537 Processing helix chain 'F' and resid 543 through 547 removed outlier: 3.854A pdb=" N GLN F 547 " --> pdb=" O GLU F 544 " (cutoff:3.500A) Processing helix chain 'F' and resid 549 through 560 removed outlier: 3.668A pdb=" N LEU F 554 " --> pdb=" O HIS F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 575 through 578 Processing helix chain 'F' and resid 579 through 588 Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 604 through 608 Processing helix chain 'F' and resid 611 through 616 removed outlier: 3.566A pdb=" N THR F 615 " --> pdb=" O ASN F 611 " (cutoff:3.500A) Processing helix chain 'F' and resid 631 through 647 Processing helix chain 'F' and resid 676 through 689 Processing helix chain 'F' and resid 706 through 718 Processing helix chain 'F' and resid 719 through 727 Processing helix chain 'F' and resid 732 through 738 removed outlier: 3.952A pdb=" N TRP F 738 " --> pdb=" O PHE F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 743 through 755 Processing helix chain 'F' and resid 756 through 770 Processing helix chain 'F' and resid 772 through 784 Processing helix chain 'F' and resid 787 through 791 Processing helix chain 'F' and resid 798 through 802 Processing helix chain 'F' and resid 821 through 828 Proline residue: F 826 - end of helix Processing helix chain 'F' and resid 832 through 836 Processing helix chain 'F' and resid 837 through 850 removed outlier: 3.908A pdb=" N TRP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 858 through 868 removed outlier: 3.748A pdb=" N ALA F 868 " --> pdb=" O ILE F 864 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 882 Processing helix chain 'F' and resid 925 through 934 Processing helix chain 'F' and resid 935 through 940 Processing helix chain 'F' and resid 942 through 948 Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 24 through 34 Processing helix chain 'S' and resid 51 through 65 Processing helix chain 'S' and resid 86 through 93 Processing helix chain 'S' and resid 96 through 111 Processing helix chain 'S' and resid 112 through 128 Processing helix chain 'S' and resid 131 through 140 Processing helix chain 'S' and resid 146 through 158 Processing helix chain 'S' and resid 159 through 161 No H-bonds generated for 'chain 'S' and resid 159 through 161' Processing sheet with id=AA1, first strand: chain 'F' and resid 432 through 436 removed outlier: 6.629A pdb=" N PHE F 411 " --> pdb=" O ILE F 433 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LYS F 435 " --> pdb=" O PHE F 411 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR F 413 " --> pdb=" O LYS F 435 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE F 570 " --> pdb=" O ILE F 594 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N VAL F 596 " --> pdb=" O ILE F 570 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL F 572 " --> pdb=" O VAL F 596 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL F 384 " --> pdb=" O HIS F 620 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N PHE F 622 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LYS F 386 " --> pdb=" O PHE F 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 505 through 507 Processing sheet with id=AA3, first strand: chain 'F' and resid 696 through 698 removed outlier: 6.087A pdb=" N HIS F 697 " --> pdb=" O LEU F 795 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N THR F 797 " --> pdb=" O HIS F 697 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY F 796 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA F 671 " --> pdb=" O HIS F 810 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP F 807 " --> pdb=" O ARG F 854 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE F 856 " --> pdb=" O ASP F 807 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL F 809 " --> pdb=" O ILE F 856 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 873 through 877 removed outlier: 4.409A pdb=" N MET F 906 " --> pdb=" O LEU F 924 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 911 through 912 Processing sheet with id=AA6, first strand: chain 'S' and resid 13 through 17 removed outlier: 9.538A pdb=" N VAL S 45 " --> pdb=" O SER S 3 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LYS S 5 " --> pdb=" O VAL S 45 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1647 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: 4.12 Time building geometry restraints manager: 2.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 10007 1.04 - 1.25: 1380 1.25 - 1.45: 3088 1.45 - 1.65: 5815 1.65 - 1.86: 75 Bond restraints: 20365 Sorted by residual: bond pdb=" O2A AGS F1001 " pdb=" PA AGS F1001 " ideal model delta sigma weight residual 1.505 1.604 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" O2B AGS F1001 " pdb=" PB AGS F1001 " ideal model delta sigma weight residual 1.518 1.603 -0.085 2.00e-02 2.50e+03 1.83e+01 bond pdb=" PG AGS F1001 " pdb=" S1G AGS F1001 " ideal model delta sigma weight residual 1.936 1.858 0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" O3B AGS F1001 " pdb=" PB AGS F1001 " ideal model delta sigma weight residual 1.673 1.598 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" O3A AGS F1001 " pdb=" PA AGS F1001 " ideal model delta sigma weight residual 1.664 1.601 0.063 2.00e-02 2.50e+03 9.83e+00 ... (remaining 20360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 36764 2.58 - 5.16: 71 5.16 - 7.74: 8 7.74 - 10.32: 2 10.32 - 12.90: 3 Bond angle restraints: 36848 Sorted by residual: angle pdb=" O1A AGS F1001 " pdb=" PA AGS F1001 " pdb=" O2A AGS F1001 " ideal model delta sigma weight residual 122.09 109.19 12.90 3.00e+00 1.11e-01 1.85e+01 angle pdb=" N3 DT X 22 " pdb=" C4 DT X 22 " pdb=" O4 DT X 22 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" O3A AGS F1001 " pdb=" PA AGS F1001 " pdb=" O5' AGS F1001 " ideal model delta sigma weight residual 97.67 109.63 -11.96 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O1B AGS F1001 " pdb=" PB AGS F1001 " pdb=" O2B AGS F1001 " ideal model delta sigma weight residual 121.53 109.99 11.54 3.00e+00 1.11e-01 1.48e+01 angle pdb=" O4 DT X 22 " pdb=" C4 DT X 22 " pdb=" C5 DT X 22 " ideal model delta sigma weight residual 124.90 122.38 2.52 7.00e-01 2.04e+00 1.29e+01 ... (remaining 36843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 8928 17.14 - 34.27: 375 34.27 - 51.41: 124 51.41 - 68.55: 68 68.55 - 85.69: 13 Dihedral angle restraints: 9508 sinusoidal: 5258 harmonic: 4250 Sorted by residual: dihedral pdb=" CA LEU F 812 " pdb=" C LEU F 812 " pdb=" N ASP F 813 " pdb=" CA ASP F 813 " ideal model delta harmonic sigma weight residual -180.00 -163.86 -16.14 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" O2' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" O3' AGS F1001 " ideal model delta sinusoidal sigma weight residual 48.13 -37.56 85.69 1 3.00e+01 1.11e-03 9.86e+00 dihedral pdb=" C1' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" O3' AGS F1001 " ideal model delta sinusoidal sigma weight residual 164.95 79.88 85.07 1 3.00e+01 1.11e-03 9.75e+00 ... (remaining 9505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1460 0.073 - 0.147: 107 0.147 - 0.220: 4 0.220 - 0.294: 1 0.294 - 0.367: 1 Chirality restraints: 1573 Sorted by residual: chirality pdb=" C3' AGS F1001 " pdb=" C2' AGS F1001 " pdb=" C4' AGS F1001 " pdb=" O3' AGS F1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.74 0.37 2.00e-01 2.50e+01 3.38e+00 chirality pdb=" C4' AGS F1001 " pdb=" C3' AGS F1001 " pdb=" C5' AGS F1001 " pdb=" O4' AGS F1001 " both_signs ideal model delta sigma weight residual False -2.41 -2.66 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' DA X 19 " pdb=" C4' DA X 19 " pdb=" O3' DA X 19 " pdb=" C2' DA X 19 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1570 not shown) Planarity restraints: 2950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET F 303 " 0.023 5.00e-02 4.00e+02 3.46e-02 1.91e+00 pdb=" N PRO F 304 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO F 304 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO F 304 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 173 " 0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO C 174 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO C 174 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 174 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 461 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO F 462 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO F 462 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO F 462 " -0.018 5.00e-02 4.00e+02 ... (remaining 2947 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.42: 9561 2.42 - 2.96: 47889 2.96 - 3.51: 53733 3.51 - 4.05: 70007 4.05 - 4.60: 107679 Nonbonded interactions: 288869 Sorted by model distance: nonbonded pdb=" HG SER S 24 " pdb=" H ILE S 27 " model vdw 1.872 2.100 nonbonded pdb=" H THR F 393 " pdb=" HG1 THR F 393 " model vdw 1.904 2.100 nonbonded pdb=" H THR F 849 " pdb=" HG1 THR F 849 " model vdw 1.910 2.100 nonbonded pdb=" HD1 TYR C 139 " pdb="HH21 ARG C 142 " model vdw 1.924 2.100 nonbonded pdb=" H THR F 625 " pdb=" HG1 THR F 625 " model vdw 1.935 2.100 ... (remaining 288864 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 10.400 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: 0.140 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.860 Find NCS groups from input model: 0.190 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 10334 Z= 0.214 Angle : 0.517 12.898 14015 Z= 0.268 Chirality : 0.040 0.367 1573 Planarity : 0.004 0.035 1761 Dihedral : 11.567 85.685 3911 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.25), residues: 1221 helix: 2.19 (0.19), residues: 752 sheet: 0.41 (0.61), residues: 74 loop : 0.48 (0.35), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 321 TYR 0.014 0.001 TYR F 553 PHE 0.007 0.001 PHE S 92 TRP 0.010 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (10330) covalent geometry : angle 0.51431 / 0.27 (14009) hydrogen bonds : bond 0.12792 / 8.62 ( 572) hydrogen bonds : angle 5.37479 / 4.09 ( 1647) metal coordination : bond 0.04740 / 2.79 ( 4) metal coordination : angle 2.51381 / 1.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 244 TYR cc_start: 0.8205 (m-80) cc_final: 0.7947 (m-10) REVERT: C 294 VAL cc_start: 0.8723 (t) cc_final: 0.8418 (p) REVERT: F 522 LEU cc_start: 0.9461 (mt) cc_final: 0.9152 (mt) REVERT: F 790 PHE cc_start: 0.8897 (m-10) cc_final: 0.8611 (m-10) REVERT: F 951 ARG cc_start: 0.8343 (ttt180) cc_final: 0.8132 (ttt90) REVERT: S 152 GLN cc_start: 0.9160 (tp40) cc_final: 0.8518 (tp-100) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 1.8196 time to fit residues: 270.3541 Evaluate side-chains 77 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.087757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063617 restraints weight = 60671.675| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.51 r_work: 0.2697 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10334 Z= 0.162 Angle : 0.509 6.754 14015 Z= 0.275 Chirality : 0.038 0.143 1573 Planarity : 0.005 0.077 1761 Dihedral : 10.146 67.869 1448 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.36 % Allowed : 8.00 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.25), residues: 1221 helix: 2.04 (0.19), residues: 756 sheet: 0.32 (0.61), residues: 74 loop : 0.31 (0.35), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 724 TYR 0.021 0.001 TYR C 260 PHE 0.007 0.001 PHE F 336 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (10330) covalent geometry : angle 0.50603 / 0.28 (14009) hydrogen bonds : bond 0.04747 / 3.10 ( 572) hydrogen bonds : angle 4.67763 / 3.50 ( 1647) metal coordination : bond 0.00767 / 0.45 ( 4) metal coordination : angle 2.68183 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 530 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8242 (tmm-80) REVERT: F 679 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8872 (t0) REVERT: F 760 GLU cc_start: 0.9002 (tt0) cc_final: 0.8120 (tm-30) REVERT: F 813 ASP cc_start: 0.8218 (m-30) cc_final: 0.8017 (m-30) REVERT: S 152 GLN cc_start: 0.9154 (tp40) cc_final: 0.8613 (tp-100) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 1.5659 time to fit residues: 137.2246 Evaluate side-chains 70 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 679 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.087034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.061474 restraints weight = 60877.006| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 2.67 r_work: 0.2685 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10334 Z= 0.172 Angle : 0.501 7.332 14015 Z= 0.271 Chirality : 0.038 0.150 1573 Planarity : 0.005 0.093 1761 Dihedral : 9.429 68.358 1448 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.73 % Allowed : 8.36 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.25), residues: 1221 helix: 1.95 (0.19), residues: 758 sheet: 0.19 (0.61), residues: 74 loop : 0.26 (0.34), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 724 TYR 0.016 0.001 TYR F 553 PHE 0.009 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10330) covalent geometry : angle 0.49677 / 0.27 (14009) hydrogen bonds : bond 0.04432 / 2.88 ( 572) hydrogen bonds : angle 4.56336 / 3.39 ( 1647) metal coordination : bond 0.00494 / 0.28 ( 4) metal coordination : angle 3.05583 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 296 ILE cc_start: 0.5838 (tt) cc_final: 0.5435 (pp) REVERT: F 453 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8469 (tmmt) REVERT: F 530 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8236 (tmm-80) REVERT: F 760 GLU cc_start: 0.8985 (tt0) cc_final: 0.8099 (tm-30) REVERT: F 813 ASP cc_start: 0.8281 (m-30) cc_final: 0.8075 (m-30) REVERT: S 152 GLN cc_start: 0.9177 (tp40) cc_final: 0.8840 (tp40) outliers start: 8 outliers final: 2 residues processed: 80 average time/residue: 1.4913 time to fit residues: 128.0135 Evaluate side-chains 72 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 72 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.063774 restraints weight = 60988.911| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.54 r_work: 0.2694 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10334 Z= 0.170 Angle : 0.486 5.973 14015 Z= 0.261 Chirality : 0.038 0.156 1573 Planarity : 0.005 0.102 1761 Dihedral : 8.914 68.964 1448 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.36 % Allowed : 8.55 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.25), residues: 1221 helix: 1.96 (0.19), residues: 759 sheet: 0.07 (0.61), residues: 74 loop : 0.25 (0.34), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 724 TYR 0.020 0.001 TYR C 260 PHE 0.008 0.001 PHE F 336 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (10330) covalent geometry : angle 0.48191 / 0.26 (14009) hydrogen bonds : bond 0.04157 / 2.70 ( 572) hydrogen bonds : angle 4.48241 / 3.32 ( 1647) metal coordination : bond 0.00494 / 0.28 ( 4) metal coordination : angle 3.17277 / 1.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8818 (mmmm) cc_final: 0.8423 (tmmt) REVERT: F 530 ARG cc_start: 0.8466 (ttp80) cc_final: 0.8245 (tmm-80) REVERT: F 679 ASN cc_start: 0.9154 (OUTLIER) cc_final: 0.8717 (t0) REVERT: F 760 GLU cc_start: 0.8978 (tt0) cc_final: 0.8089 (tm-30) REVERT: S 152 GLN cc_start: 0.9170 (tp40) cc_final: 0.8599 (tp-100) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 1.3924 time to fit residues: 111.6023 Evaluate side-chains 70 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 679 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 73 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.087654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.063642 restraints weight = 59961.574| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.50 r_work: 0.2694 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10334 Z= 0.172 Angle : 0.479 5.951 14015 Z= 0.258 Chirality : 0.038 0.166 1573 Planarity : 0.005 0.106 1761 Dihedral : 8.597 69.503 1448 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 8.18 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.25), residues: 1221 helix: 1.98 (0.19), residues: 760 sheet: -0.04 (0.62), residues: 74 loop : 0.27 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 724 TYR 0.022 0.001 TYR C 260 PHE 0.008 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10330) covalent geometry : angle 0.47389 / 0.26 (14009) hydrogen bonds : bond 0.04080 / 2.65 ( 572) hydrogen bonds : angle 4.43034 / 3.28 ( 1647) metal coordination : bond 0.00500 / 0.29 ( 4) metal coordination : angle 3.25138 / 1.64 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8809 (mmmm) cc_final: 0.8420 (tmmt) REVERT: F 530 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8278 (tmm-80) REVERT: F 679 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8777 (t0) REVERT: F 760 GLU cc_start: 0.8996 (tt0) cc_final: 0.8089 (tm-30) REVERT: S 152 GLN cc_start: 0.9165 (tp40) cc_final: 0.8591 (tp-100) outliers start: 7 outliers final: 3 residues processed: 75 average time/residue: 1.4955 time to fit residues: 120.8018 Evaluate side-chains 75 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Chi-restraints excluded: chain F residue 679 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 94 optimal weight: 0.5980 chunk 110 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.088442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.064495 restraints weight = 60325.745| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.51 r_work: 0.2704 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10334 Z= 0.135 Angle : 0.463 5.507 14015 Z= 0.250 Chirality : 0.038 0.167 1573 Planarity : 0.005 0.114 1761 Dihedral : 8.390 69.710 1448 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.64 % Allowed : 8.27 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.25), residues: 1221 helix: 2.03 (0.19), residues: 760 sheet: -0.14 (0.62), residues: 74 loop : 0.34 (0.35), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 724 TYR 0.025 0.001 TYR C 260 PHE 0.009 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (10330) covalent geometry : angle 0.45924 / 0.25 (14009) hydrogen bonds : bond 0.03900 / 2.53 ( 572) hydrogen bonds : angle 4.37284 / 3.23 ( 1647) metal coordination : bond 0.00336 / 0.19 ( 4) metal coordination : angle 3.03146 / 1.55 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8792 (mmmm) cc_final: 0.8415 (tmmt) REVERT: F 530 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8261 (tmm-80) REVERT: F 724 ARG cc_start: 0.8944 (mmm160) cc_final: 0.8320 (tpm-80) REVERT: F 760 GLU cc_start: 0.9002 (tt0) cc_final: 0.8079 (tm-30) REVERT: S 152 GLN cc_start: 0.9170 (tp40) cc_final: 0.8600 (tp-100) outliers start: 7 outliers final: 3 residues processed: 78 average time/residue: 1.5018 time to fit residues: 126.1674 Evaluate side-chains 73 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 120 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.065696 restraints weight = 61108.516| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.50 r_work: 0.2711 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10334 Z= 0.126 Angle : 0.459 5.461 14015 Z= 0.247 Chirality : 0.037 0.177 1573 Planarity : 0.005 0.090 1761 Dihedral : 8.273 69.819 1448 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.64 % Allowed : 8.36 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.25), residues: 1221 helix: 2.10 (0.19), residues: 757 sheet: -0.18 (0.62), residues: 74 loop : 0.36 (0.35), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 749 TYR 0.022 0.001 TYR C 260 PHE 0.008 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10330) covalent geometry : angle 0.45465 / 0.25 (14009) hydrogen bonds : bond 0.03806 / 2.47 ( 572) hydrogen bonds : angle 4.33023 / 3.20 ( 1647) metal coordination : bond 0.00271 / 0.15 ( 4) metal coordination : angle 2.96490 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8802 (mmmm) cc_final: 0.8420 (tmmt) REVERT: F 760 GLU cc_start: 0.8989 (tt0) cc_final: 0.8069 (tm-30) REVERT: S 152 GLN cc_start: 0.9167 (tp40) cc_final: 0.8598 (tp-100) outliers start: 7 outliers final: 3 residues processed: 76 average time/residue: 1.5482 time to fit residues: 126.6508 Evaluate side-chains 74 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 0.4980 chunk 91 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.088945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064843 restraints weight = 61338.673| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.50 r_work: 0.2704 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10334 Z= 0.157 Angle : 0.469 5.718 14015 Z= 0.253 Chirality : 0.038 0.180 1573 Planarity : 0.006 0.129 1761 Dihedral : 8.246 70.078 1448 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.82 % Allowed : 8.36 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.25), residues: 1221 helix: 2.15 (0.19), residues: 751 sheet: -0.17 (0.62), residues: 74 loop : 0.44 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 724 TYR 0.023 0.001 TYR C 260 PHE 0.008 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (10330) covalent geometry : angle 0.46497 / 0.25 (14009) hydrogen bonds : bond 0.03839 / 2.49 ( 572) hydrogen bonds : angle 4.32687 / 3.20 ( 1647) metal coordination : bond 0.00408 / 0.23 ( 4) metal coordination : angle 3.08553 / 1.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 464 MET cc_start: 0.8218 (ptp) cc_final: 0.7809 (pmm) REVERT: F 724 ARG cc_start: 0.8889 (mmm160) cc_final: 0.8299 (tpm-80) REVERT: F 760 GLU cc_start: 0.8995 (tt0) cc_final: 0.8073 (tm-30) REVERT: S 152 GLN cc_start: 0.9164 (tp40) cc_final: 0.8594 (tp-100) outliers start: 9 outliers final: 3 residues processed: 79 average time/residue: 1.5041 time to fit residues: 128.1894 Evaluate side-chains 73 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 74 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 92 optimal weight: 0.4980 chunk 107 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.088138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.064114 restraints weight = 60136.498| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 2.50 r_work: 0.2701 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10334 Z= 0.150 Angle : 0.471 7.819 14015 Z= 0.253 Chirality : 0.038 0.187 1573 Planarity : 0.005 0.108 1761 Dihedral : 8.210 70.271 1448 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.27 % Allowed : 8.55 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.25), residues: 1221 helix: 2.15 (0.19), residues: 751 sheet: -0.20 (0.62), residues: 74 loop : 0.45 (0.35), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 749 TYR 0.025 0.001 TYR C 260 PHE 0.008 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (10330) covalent geometry : angle 0.46690 / 0.25 (14009) hydrogen bonds : bond 0.03807 / 2.47 ( 572) hydrogen bonds : angle 4.31388 / 3.19 ( 1647) metal coordination : bond 0.00401 / 0.23 ( 4) metal coordination : angle 2.93233 / 1.50 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8898 (tppt) cc_final: 0.8310 (tmmt) REVERT: F 760 GLU cc_start: 0.8994 (tt0) cc_final: 0.8070 (tm-30) REVERT: S 152 GLN cc_start: 0.9171 (tp40) cc_final: 0.8604 (tp-100) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 1.5002 time to fit residues: 120.9658 Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.088641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.064554 restraints weight = 60662.125| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.53 r_work: 0.2704 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10334 Z= 0.146 Angle : 0.474 6.831 14015 Z= 0.254 Chirality : 0.038 0.185 1573 Planarity : 0.005 0.113 1761 Dihedral : 8.171 70.397 1448 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.36 % Allowed : 8.73 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.25), residues: 1221 helix: 2.16 (0.19), residues: 751 sheet: -0.19 (0.62), residues: 74 loop : 0.33 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 749 TYR 0.024 0.001 TYR C 260 PHE 0.008 0.001 PHE F 747 TRP 0.008 0.001 TRP F 271 HIS 0.004 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10330) covalent geometry : angle 0.47067 / 0.25 (14009) hydrogen bonds : bond 0.03769 / 2.45 ( 572) hydrogen bonds : angle 4.30078 / 3.18 ( 1647) metal coordination : bond 0.00365 / 0.21 ( 4) metal coordination : angle 2.91469 / 1.51 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2442 Ramachandran restraints generated. 1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 453 LYS cc_start: 0.8897 (tppt) cc_final: 0.8298 (tmmt) REVERT: F 760 GLU cc_start: 0.8994 (tt0) cc_final: 0.8072 (tm-30) REVERT: S 152 GLN cc_start: 0.9163 (tp40) cc_final: 0.8594 (tp-100) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 1.6667 time to fit residues: 133.6622 Evaluate side-chains 72 residues out of total 1100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 219 PHE Chi-restraints excluded: chain F residue 345 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 105 optimal weight: 0.0970 chunk 10 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 109 optimal weight: 0.0170 chunk 17 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.088858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.064756 restraints weight = 60621.788| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 2.53 r_work: 0.2709 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10334 Z= 0.133 Angle : 0.478 7.439 14015 Z= 0.256 Chirality : 0.037 0.173 1573 Planarity : 0.005 0.112 1761 Dihedral : 8.148 70.450 1448 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.27 % Allowed : 9.00 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.12 (0.25), residues: 1221 helix: 2.18 (0.19), residues: 751 sheet: -0.22 (0.62), residues: 74 loop : 0.30 (0.34), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 749 TYR 0.025 0.001 TYR C 260 PHE 0.014 0.001 PHE F 692 TRP 0.008 0.001 TRP F 271 HIS 0.003 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10330) covalent geometry : angle 0.47474 / 0.26 (14009) hydrogen bonds : bond 0.03712 / 2.41 ( 572) hydrogen bonds : angle 4.27595 / 3.16 ( 1647) metal coordination : bond 0.00288 / 0.16 ( 4) metal coordination : angle 2.86424 / 1.49 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6401.08 seconds wall clock time: 109 minutes 31.48 seconds (6571.48 seconds total)