Starting phenix.real_space_refine on Fri Jul 25 07:00:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.map" model { file = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zqb_60381/07_2025/8zqb_60381.cif" } resolution = 3.65 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 38 5.49 5 S 24 5.16 5 C 4390 2.51 5 N 1333 2.21 5 O 1437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6412 Classifications: {'peptide': 787} Link IDs: {'PTRANS': 28, 'TRANS': 758} Chain breaks: 8 Chain: "B" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 810 Classifications: {'RNA': 38} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 2, 'rna3p_pur': 17, 'rna3p_pyr': 17} Link IDs: {'rna2p': 3, 'rna3p': 34} Time building chain proxies: 6.13, per 1000 atoms: 0.85 Number of scatterers: 7222 At special positions: 0 Unit cell: (95.04, 96.36, 100.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 38 15.00 O 1437 8.00 N 1333 7.00 C 4390 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 865.5 milliseconds 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 7 sheets defined 48.0% alpha, 17.8% beta 14 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.548A pdb=" N HIS A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 76 through 88 removed outlier: 3.584A pdb=" N LEU A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 211 through 252 Processing helix chain 'A' and resid 255 through 270 removed outlier: 3.525A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.373A pdb=" N LEU A 303 " --> pdb=" O GLY A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 330 removed outlier: 3.862A pdb=" N VAL A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TYR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.606A pdb=" N LYS A 451 " --> pdb=" O SER A 447 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLY A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 553 removed outlier: 4.069A pdb=" N ARG A 541 " --> pdb=" O PHE A 537 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG A 544 " --> pdb=" O ALA A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 566 removed outlier: 3.926A pdb=" N ALA A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 572 Processing helix chain 'A' and resid 579 through 606 Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 620 through 641 removed outlier: 4.252A pdb=" N PHE A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASN A 635 " --> pdb=" O LYS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 688 removed outlier: 3.730A pdb=" N GLU A 688 " --> pdb=" O ARG A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 720 removed outlier: 3.801A pdb=" N LEU A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 782 through 797 Processing helix chain 'A' and resid 820 through 831 removed outlier: 3.524A pdb=" N LEU A 827 " --> pdb=" O GLU A 823 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 885 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 899 through 903 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.583A pdb=" N LYS A 5 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 439 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 5 through 11 removed outlier: 3.583A pdb=" N LYS A 5 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR A 439 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 433 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU A 423 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASN A 440 " --> pdb=" O VAL A 421 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL A 421 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 415 " --> pdb=" O LYS A 409 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 419 " --> pdb=" O ILE A 405 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 360 through 365 Processing sheet with id=AA4, first strand: chain 'A' and resid 513 through 517 removed outlier: 4.048A pdb=" N SER A 513 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 517 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 486 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA A 488 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU A 697 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU A 479 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL A 743 " --> pdb=" O VAL A 694 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N MET A 696 " --> pdb=" O VAL A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503 removed outlier: 4.444A pdb=" N VAL A 503 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 760 through 761 removed outlier: 3.579A pdb=" N TYR A 760 " --> pdb=" O TYR A 770 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 845 through 848 removed outlier: 3.793A pdb=" N SER A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 814 " --> pdb=" O LEU A 838 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2162 1.33 - 1.45: 1280 1.45 - 1.57: 3880 1.57 - 1.69: 75 1.69 - 1.81: 37 Bond restraints: 7434 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.13e+00 bond pdb=" CG LEU A 670 " pdb=" CD2 LEU A 670 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CA THR A 837 " pdb=" C THR A 837 " ideal model delta sigma weight residual 1.522 1.507 0.016 1.23e-02 6.61e+03 1.60e+00 bond pdb=" C THR A 837 " pdb=" N LEU A 838 " ideal model delta sigma weight residual 1.334 1.319 0.015 1.29e-02 6.01e+03 1.43e+00 bond pdb=" C VAL A 743 " pdb=" O VAL A 743 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.01e-02 9.80e+03 9.46e-01 ... (remaining 7429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9819 1.40 - 2.81: 291 2.81 - 4.21: 66 4.21 - 5.62: 13 5.62 - 7.02: 2 Bond angle restraints: 10191 Sorted by residual: angle pdb=" N ASN A 482 " pdb=" CA ASN A 482 " pdb=" C ASN A 482 " ideal model delta sigma weight residual 112.35 107.68 4.67 1.34e+00 5.57e-01 1.22e+01 angle pdb=" N VAL A 743 " pdb=" CA VAL A 743 " pdb=" C VAL A 743 " ideal model delta sigma weight residual 108.45 113.57 -5.12 1.48e+00 4.57e-01 1.20e+01 angle pdb=" N SER A 6 " pdb=" CA SER A 6 " pdb=" C SER A 6 " ideal model delta sigma weight residual 108.55 113.87 -5.32 1.62e+00 3.81e-01 1.08e+01 angle pdb=" N ILE A 481 " pdb=" CA ILE A 481 " pdb=" C ILE A 481 " ideal model delta sigma weight residual 111.62 109.08 2.54 7.90e-01 1.60e+00 1.04e+01 angle pdb=" CB LYS A 94 " pdb=" CG LYS A 94 " pdb=" CD LYS A 94 " ideal model delta sigma weight residual 111.30 118.32 -7.02 2.30e+00 1.89e-01 9.32e+00 ... (remaining 10186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.87: 4359 35.87 - 71.74: 215 71.74 - 107.62: 18 107.62 - 143.49: 1 143.49 - 179.36: 1 Dihedral angle restraints: 4594 sinusoidal: 2303 harmonic: 2291 Sorted by residual: dihedral pdb=" O4' U B -32 " pdb=" C1' U B -32 " pdb=" N1 U B -32 " pdb=" C2 U B -32 " ideal model delta sinusoidal sigma weight residual 232.00 52.64 179.36 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' A B -21 " pdb=" C1' A B -21 " pdb=" N9 A B -21 " pdb=" C4 A B -21 " ideal model delta sinusoidal sigma weight residual -90.00 -18.62 -71.38 1 2.00e+01 2.50e-03 1.63e+01 dihedral pdb=" CA ARG A 873 " pdb=" C ARG A 873 " pdb=" N HIS A 874 " pdb=" CA HIS A 874 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 4591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 791 0.033 - 0.065: 249 0.065 - 0.098: 60 0.098 - 0.131: 31 0.131 - 0.164: 3 Chirality restraints: 1134 Sorted by residual: chirality pdb=" CA PRO A 310 " pdb=" N PRO A 310 " pdb=" C PRO A 310 " pdb=" CB PRO A 310 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA ILE A 780 " pdb=" N ILE A 780 " pdb=" C ILE A 780 " pdb=" CB ILE A 780 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CA VAL A 385 " pdb=" N VAL A 385 " pdb=" C VAL A 385 " pdb=" CB VAL A 385 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1131 not shown) Planarity restraints: 1181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 903 " -0.033 5.00e-02 4.00e+02 4.99e-02 3.98e+00 pdb=" N PRO A 904 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 904 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 904 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B -36 " -0.016 2.00e-02 2.50e+03 7.84e-03 1.84e+00 pdb=" N9 G B -36 " 0.019 2.00e-02 2.50e+03 pdb=" C8 G B -36 " 0.006 2.00e-02 2.50e+03 pdb=" N7 G B -36 " -0.004 2.00e-02 2.50e+03 pdb=" C5 G B -36 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B -36 " -0.000 2.00e-02 2.50e+03 pdb=" O6 G B -36 " -0.004 2.00e-02 2.50e+03 pdb=" N1 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B -36 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B -36 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B -36 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B -36 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 734 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C LYS A 734 " -0.023 2.00e-02 2.50e+03 pdb=" O LYS A 734 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 735 " 0.008 2.00e-02 2.50e+03 ... (remaining 1178 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1030 2.75 - 3.29: 7543 3.29 - 3.83: 12503 3.83 - 4.36: 14418 4.36 - 4.90: 23219 Nonbonded interactions: 58713 Sorted by model distance: nonbonded pdb=" O ARG A 40 " pdb=" NH1 ARG A 40 " model vdw 2.213 3.120 nonbonded pdb=" O PRO A 870 " pdb=" OG1 THR A 880 " model vdw 2.215 3.040 nonbonded pdb=" O ASN A 785 " pdb=" OD1 ASN A 789 " model vdw 2.217 3.040 nonbonded pdb=" N ASP A 341 " pdb=" OG SER A 345 " model vdw 2.223 3.120 nonbonded pdb=" OD1 ASP A 497 " pdb=" N GLY A 498 " model vdw 2.237 3.120 ... (remaining 58708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 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 0.046 7434 Z= 0.152 Angle : 0.608 7.021 10191 Z= 0.341 Chirality : 0.037 0.164 1134 Planarity : 0.004 0.050 1181 Dihedral : 19.010 179.362 3110 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.03 % Allowed : 19.41 % Favored : 79.56 % 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 (0.31), residues: 769 helix: 0.63 (0.30), residues: 309 sheet: -0.46 (0.54), residues: 109 loop : -2.03 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 229 HIS 0.010 0.002 HIS A 747 PHE 0.019 0.001 PHE A 771 TYR 0.013 0.001 TYR A 542 ARG 0.012 0.001 ARG A 613 Details of bonding type rmsd hydrogen bonds : bond 0.16657 ( 358) hydrogen bonds : angle 6.72235 ( 1008) covalent geometry : bond 0.00304 ( 7434) covalent geometry : angle 0.60776 (10191) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 185 time to evaluate : 0.799 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: A 477 ILE cc_start: 0.8688 (mm) cc_final: 0.8441 (mm) REVERT: A 623 TYR cc_start: 0.7488 (m-80) cc_final: 0.7283 (m-80) REVERT: A 793 ARG cc_start: 0.8562 (mtt180) cc_final: 0.8280 (mtt180) outliers start: 7 outliers final: 1 residues processed: 186 average time/residue: 0.2805 time to fit residues: 64.2685 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 41 optimal weight: 0.1980 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 24 optimal weight: 0.1980 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN A 773 GLN A 789 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.086792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.071074 restraints weight = 31256.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.073601 restraints weight = 16348.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.075236 restraints weight = 10178.755| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7434 Z= 0.158 Angle : 0.752 11.927 10191 Z= 0.382 Chirality : 0.043 0.187 1134 Planarity : 0.006 0.070 1181 Dihedral : 17.298 176.960 1501 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.53 % Allowed : 20.44 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.31), residues: 769 helix: 1.02 (0.29), residues: 326 sheet: -0.15 (0.49), residues: 113 loop : -1.92 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 640 HIS 0.010 0.002 HIS A 747 PHE 0.027 0.002 PHE A 571 TYR 0.034 0.002 TYR A 308 ARG 0.012 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 358) hydrogen bonds : angle 4.94029 ( 1008) covalent geometry : bond 0.00347 ( 7434) covalent geometry : angle 0.75162 (10191) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.787 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: A 242 GLU cc_start: 0.9326 (tm-30) cc_final: 0.9102 (pp20) REVERT: A 343 ASP cc_start: 0.8825 (m-30) cc_final: 0.8269 (p0) REVERT: A 391 TRP cc_start: 0.8438 (t-100) cc_final: 0.8215 (t-100) REVERT: A 438 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8574 (p0) REVERT: A 548 LYS cc_start: 0.8882 (tttt) cc_final: 0.8539 (tttm) REVERT: A 607 ARG cc_start: 0.8819 (ptt-90) cc_final: 0.8397 (ptt-90) REVERT: A 735 ASN cc_start: 0.8888 (p0) cc_final: 0.8642 (p0) REVERT: A 799 ARG cc_start: 0.8737 (tpt90) cc_final: 0.8510 (mmm160) REVERT: A 869 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8712 (tp30) outliers start: 24 outliers final: 10 residues processed: 137 average time/residue: 0.2458 time to fit residues: 42.9886 Evaluate side-chains 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 22 optimal weight: 0.0050 chunk 54 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 689 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.085074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.070040 restraints weight = 31894.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.072473 restraints weight = 16653.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.074201 restraints weight = 10447.473| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7434 Z= 0.149 Angle : 0.682 7.932 10191 Z= 0.350 Chirality : 0.042 0.184 1134 Planarity : 0.005 0.042 1181 Dihedral : 17.185 176.524 1497 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 4.71 % Allowed : 19.41 % Favored : 75.88 % 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: -0.30 (0.31), residues: 769 helix: 1.13 (0.29), residues: 331 sheet: -0.26 (0.46), residues: 123 loop : -1.64 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 640 HIS 0.008 0.001 HIS A 747 PHE 0.021 0.002 PHE A 571 TYR 0.026 0.002 TYR A 308 ARG 0.008 0.000 ARG A 49 Details of bonding type rmsd hydrogen bonds : bond 0.04092 ( 358) hydrogen bonds : angle 4.54071 ( 1008) covalent geometry : bond 0.00334 ( 7434) covalent geometry : angle 0.68236 (10191) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 0.810 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: A 34 ARG cc_start: 0.7839 (mmm-85) cc_final: 0.7572 (mmt90) REVERT: A 64 PHE cc_start: 0.8302 (m-80) cc_final: 0.7594 (m-80) REVERT: A 229 TRP cc_start: 0.8616 (t60) cc_final: 0.8399 (t60) REVERT: A 328 TRP cc_start: 0.9140 (t60) cc_final: 0.8856 (t60) REVERT: A 343 ASP cc_start: 0.8816 (m-30) cc_final: 0.8325 (p0) REVERT: A 345 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8510 (p) REVERT: A 391 TRP cc_start: 0.8498 (t-100) cc_final: 0.8293 (t-100) REVERT: A 405 ILE cc_start: 0.9201 (pt) cc_final: 0.8977 (mp) REVERT: A 426 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8803 (tt) REVERT: A 548 LYS cc_start: 0.8890 (tttt) cc_final: 0.8465 (tttm) REVERT: A 607 ARG cc_start: 0.8862 (ptt-90) cc_final: 0.8646 (ptt-90) REVERT: A 608 TYR cc_start: 0.8391 (m-80) cc_final: 0.8167 (m-80) REVERT: A 658 ASP cc_start: 0.6829 (m-30) cc_final: 0.6169 (t0) REVERT: A 661 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7998 (pttm) REVERT: A 696 MET cc_start: 0.9223 (ptp) cc_final: 0.8791 (ptp) REVERT: A 730 GLU cc_start: 0.9076 (tt0) cc_final: 0.8592 (pp20) REVERT: A 735 ASN cc_start: 0.8819 (p0) cc_final: 0.8540 (p0) outliers start: 32 outliers final: 15 residues processed: 137 average time/residue: 0.2774 time to fit residues: 48.2217 Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.0670 chunk 12 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 641 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.083894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.068515 restraints weight = 32548.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.070926 restraints weight = 17200.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.072535 restraints weight = 10810.967| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7434 Z= 0.144 Angle : 0.650 10.595 10191 Z= 0.331 Chirality : 0.041 0.259 1134 Planarity : 0.004 0.037 1181 Dihedral : 17.093 176.976 1497 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 4.56 % Allowed : 19.56 % Favored : 75.88 % 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: -0.12 (0.31), residues: 769 helix: 1.34 (0.29), residues: 331 sheet: -0.28 (0.45), residues: 127 loop : -1.57 (0.35), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 229 HIS 0.006 0.001 HIS A 747 PHE 0.014 0.002 PHE A 571 TYR 0.024 0.002 TYR A 308 ARG 0.003 0.000 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 358) hydrogen bonds : angle 4.34622 ( 1008) covalent geometry : bond 0.00314 ( 7434) covalent geometry : angle 0.65008 (10191) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.708 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: A 34 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7606 (mmt90) REVERT: A 64 PHE cc_start: 0.8400 (m-80) cc_final: 0.7724 (m-80) REVERT: A 242 GLU cc_start: 0.9354 (tm-30) cc_final: 0.9139 (pp20) REVERT: A 328 TRP cc_start: 0.9181 (t60) cc_final: 0.8901 (t60) REVERT: A 345 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8462 (p) REVERT: A 391 TRP cc_start: 0.8554 (t-100) cc_final: 0.8344 (t-100) REVERT: A 426 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8831 (tt) REVERT: A 548 LYS cc_start: 0.8855 (tttt) cc_final: 0.8440 (tttm) REVERT: A 608 TYR cc_start: 0.8561 (m-80) cc_final: 0.8358 (m-80) REVERT: A 658 ASP cc_start: 0.6957 (m-30) cc_final: 0.6211 (t0) REVERT: A 661 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.7980 (pttm) REVERT: A 672 MET cc_start: 0.7522 (tpp) cc_final: 0.7255 (tpp) REVERT: A 696 MET cc_start: 0.9262 (ptp) cc_final: 0.8896 (ptp) REVERT: A 730 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8542 (pp20) REVERT: A 735 ASN cc_start: 0.8802 (p0) cc_final: 0.8570 (p0) outliers start: 31 outliers final: 23 residues processed: 124 average time/residue: 0.2686 time to fit residues: 41.6129 Evaluate side-chains 128 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 0.0370 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.078174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.062994 restraints weight = 34159.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.065205 restraints weight = 18316.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.066695 restraints weight = 11712.494| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7434 Z= 0.268 Angle : 0.760 9.861 10191 Z= 0.390 Chirality : 0.044 0.210 1134 Planarity : 0.005 0.036 1181 Dihedral : 17.301 176.488 1497 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 6.32 % Allowed : 18.68 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.30), residues: 769 helix: 1.00 (0.28), residues: 331 sheet: -0.48 (0.44), residues: 132 loop : -1.82 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 741 HIS 0.009 0.002 HIS A 26 PHE 0.018 0.002 PHE A 571 TYR 0.029 0.003 TYR A 542 ARG 0.006 0.001 ARG A 607 Details of bonding type rmsd hydrogen bonds : bond 0.04876 ( 358) hydrogen bonds : angle 4.72610 ( 1008) covalent geometry : bond 0.00573 ( 7434) covalent geometry : angle 0.75981 (10191) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 92 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8034 (mmm-85) cc_final: 0.7673 (mmt90) REVERT: A 216 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8385 (mtpt) REVERT: A 345 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.7991 (p) REVERT: A 391 TRP cc_start: 0.8747 (t-100) cc_final: 0.8426 (t-100) REVERT: A 529 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6907 (ptp) REVERT: A 658 ASP cc_start: 0.7355 (m-30) cc_final: 0.6498 (t0) REVERT: A 661 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8198 (pttm) REVERT: A 672 MET cc_start: 0.7908 (tpp) cc_final: 0.7675 (tpp) REVERT: A 730 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8590 (pp20) REVERT: A 735 ASN cc_start: 0.8823 (p0) cc_final: 0.8576 (p0) outliers start: 43 outliers final: 26 residues processed: 118 average time/residue: 0.2482 time to fit residues: 37.3413 Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 85 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 345 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 783 ASP Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 26 HIS ** 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 = 0.3747 r_free = 0.3747 target = 0.079401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.064174 restraints weight = 33337.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.066505 restraints weight = 17481.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.068038 restraints weight = 11039.745| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7434 Z= 0.193 Angle : 0.700 10.688 10191 Z= 0.355 Chirality : 0.042 0.233 1134 Planarity : 0.005 0.046 1181 Dihedral : 17.319 178.738 1497 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 5.15 % Allowed : 21.18 % Favored : 73.68 % 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: -0.34 (0.30), residues: 769 helix: 1.03 (0.28), residues: 336 sheet: -0.14 (0.46), residues: 125 loop : -1.68 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 741 HIS 0.010 0.002 HIS A 26 PHE 0.018 0.002 PHE A 571 TYR 0.023 0.002 TYR A 542 ARG 0.004 0.000 ARG A 197 Details of bonding type rmsd hydrogen bonds : bond 0.04163 ( 358) hydrogen bonds : angle 4.59006 ( 1008) covalent geometry : bond 0.00418 ( 7434) covalent geometry : angle 0.70031 (10191) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8235 (tpp) cc_final: 0.8006 (tpp) REVERT: A 391 TRP cc_start: 0.8730 (t-100) cc_final: 0.8522 (t-100) REVERT: A 475 MET cc_start: 0.8295 (tmm) cc_final: 0.8075 (tmm) REVERT: A 641 ASN cc_start: 0.8932 (t0) cc_final: 0.8522 (t0) REVERT: A 672 MET cc_start: 0.7838 (tpp) cc_final: 0.7571 (tpp) REVERT: A 694 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8674 (p) REVERT: A 696 MET cc_start: 0.9372 (ptp) cc_final: 0.8609 (pmm) REVERT: A 730 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8427 (pp20) REVERT: A 735 ASN cc_start: 0.8763 (p0) cc_final: 0.8545 (p0) outliers start: 35 outliers final: 25 residues processed: 117 average time/residue: 0.2366 time to fit residues: 35.9033 Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 829 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 0.4980 chunk 75 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 33 optimal weight: 4.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.080820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.065811 restraints weight = 33088.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.068118 restraints weight = 17424.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069660 restraints weight = 10946.611| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.5787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7434 Z= 0.138 Angle : 0.676 7.801 10191 Z= 0.340 Chirality : 0.042 0.251 1134 Planarity : 0.004 0.036 1181 Dihedral : 17.209 178.163 1497 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.97 % Allowed : 22.65 % Favored : 73.38 % 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: -0.11 (0.31), residues: 769 helix: 1.27 (0.28), residues: 329 sheet: 0.04 (0.48), residues: 119 loop : -1.57 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 720 HIS 0.010 0.001 HIS A 747 PHE 0.020 0.002 PHE A 360 TYR 0.017 0.001 TYR A 308 ARG 0.004 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 358) hydrogen bonds : angle 4.49395 ( 1008) covalent geometry : bond 0.00306 ( 7434) covalent geometry : angle 0.67621 (10191) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 101 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8343 (tpp) cc_final: 0.8129 (tpp) REVERT: A 34 ARG cc_start: 0.7860 (mmm-85) cc_final: 0.7521 (mmt90) REVERT: A 328 TRP cc_start: 0.9212 (t60) cc_final: 0.8914 (t60) REVERT: A 343 ASP cc_start: 0.8865 (m-30) cc_final: 0.8353 (p0) REVERT: A 506 MET cc_start: 0.8928 (mmt) cc_final: 0.8521 (mmp) REVERT: A 641 ASN cc_start: 0.8856 (t0) cc_final: 0.8439 (t0) REVERT: A 672 MET cc_start: 0.7788 (tpp) cc_final: 0.7496 (tpp) REVERT: A 694 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8678 (p) REVERT: A 696 MET cc_start: 0.9262 (ptp) cc_final: 0.8848 (pmm) REVERT: A 730 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8319 (pp20) REVERT: A 735 ASN cc_start: 0.8580 (p0) cc_final: 0.8348 (p0) outliers start: 27 outliers final: 23 residues processed: 114 average time/residue: 0.2385 time to fit residues: 35.2450 Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 91 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 22 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 64 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 10 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 789 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.081899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.066860 restraints weight = 32790.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069182 restraints weight = 17167.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.070836 restraints weight = 10786.251| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7434 Z= 0.131 Angle : 0.679 8.363 10191 Z= 0.336 Chirality : 0.041 0.216 1134 Planarity : 0.004 0.041 1181 Dihedral : 17.074 178.082 1497 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.68 % Allowed : 24.41 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 769 helix: 1.38 (0.29), residues: 330 sheet: -0.22 (0.46), residues: 127 loop : -1.51 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 720 HIS 0.010 0.001 HIS A 747 PHE 0.020 0.002 PHE A 202 TYR 0.017 0.001 TYR A 308 ARG 0.006 0.000 ARG A 199 Details of bonding type rmsd hydrogen bonds : bond 0.03633 ( 358) hydrogen bonds : angle 4.36690 ( 1008) covalent geometry : bond 0.00289 ( 7434) covalent geometry : angle 0.67933 (10191) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.8413 (tpp) cc_final: 0.8194 (tpp) REVERT: A 7 SER cc_start: 0.8496 (t) cc_final: 0.8150 (p) REVERT: A 34 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7517 (mmt90) REVERT: A 328 TRP cc_start: 0.9215 (t60) cc_final: 0.8918 (t60) REVERT: A 343 ASP cc_start: 0.8852 (m-30) cc_final: 0.8378 (p0) REVERT: A 497 ASP cc_start: 0.8052 (t0) cc_final: 0.7605 (p0) REVERT: A 506 MET cc_start: 0.8879 (mmt) cc_final: 0.8559 (mmt) REVERT: A 548 LYS cc_start: 0.8863 (tttt) cc_final: 0.8442 (tttm) REVERT: A 641 ASN cc_start: 0.8833 (t0) cc_final: 0.8398 (t0) REVERT: A 672 MET cc_start: 0.7776 (tpp) cc_final: 0.7471 (tpp) REVERT: A 696 MET cc_start: 0.9225 (ptp) cc_final: 0.8810 (pmm) REVERT: A 730 GLU cc_start: 0.8976 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: A 735 ASN cc_start: 0.8498 (p0) cc_final: 0.8279 (p0) REVERT: A 793 ARG cc_start: 0.9109 (mtt180) cc_final: 0.8897 (mtp180) outliers start: 25 outliers final: 24 residues processed: 113 average time/residue: 0.2552 time to fit residues: 36.6942 Evaluate side-chains 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 481 ILE Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 74 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 48 optimal weight: 0.0060 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 55 optimal weight: 7.9990 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.083279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.067979 restraints weight = 32865.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070386 restraints weight = 17342.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071996 restraints weight = 10908.640| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7434 Z= 0.121 Angle : 0.671 9.363 10191 Z= 0.332 Chirality : 0.040 0.195 1134 Planarity : 0.004 0.043 1181 Dihedral : 16.942 178.050 1497 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.24 % Allowed : 23.97 % Favored : 72.79 % 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: 0.14 (0.31), residues: 769 helix: 1.50 (0.28), residues: 332 sheet: -0.11 (0.46), residues: 128 loop : -1.41 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 720 HIS 0.013 0.001 HIS A 747 PHE 0.014 0.001 PHE A 360 TYR 0.015 0.001 TYR A 308 ARG 0.008 0.000 ARG A 868 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 358) hydrogen bonds : angle 4.26837 ( 1008) covalent geometry : bond 0.00266 ( 7434) covalent geometry : angle 0.67149 (10191) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.771 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: A 1 MET cc_start: 0.8451 (tpp) cc_final: 0.8243 (tpp) REVERT: A 242 GLU cc_start: 0.9146 (pp20) cc_final: 0.8903 (mm-30) REVERT: A 328 TRP cc_start: 0.9223 (t60) cc_final: 0.8930 (t60) REVERT: A 343 ASP cc_start: 0.8784 (m-30) cc_final: 0.8258 (p0) REVERT: A 368 ARG cc_start: 0.8213 (mtm110) cc_final: 0.7996 (ttp80) REVERT: A 497 ASP cc_start: 0.8048 (t0) cc_final: 0.7616 (p0) REVERT: A 548 LYS cc_start: 0.8842 (tttt) cc_final: 0.8419 (tttm) REVERT: A 641 ASN cc_start: 0.8791 (t0) cc_final: 0.8355 (t0) REVERT: A 672 MET cc_start: 0.7777 (tpp) cc_final: 0.7472 (tpp) REVERT: A 696 MET cc_start: 0.9148 (ptp) cc_final: 0.8756 (pmm) REVERT: A 730 GLU cc_start: 0.8982 (tt0) cc_final: 0.8286 (pp20) REVERT: A 735 ASN cc_start: 0.8356 (p0) cc_final: 0.8149 (p0) outliers start: 22 outliers final: 20 residues processed: 112 average time/residue: 0.2975 time to fit residues: 42.7171 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 781 ASP Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 71 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.082010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.066480 restraints weight = 33479.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068896 restraints weight = 17883.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.070515 restraints weight = 11226.393| |-----------------------------------------------------------------------------| r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7434 Z= 0.141 Angle : 0.682 8.191 10191 Z= 0.338 Chirality : 0.040 0.194 1134 Planarity : 0.004 0.054 1181 Dihedral : 16.932 177.997 1497 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.79 % Allowed : 24.85 % Favored : 72.35 % 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: 0.12 (0.31), residues: 769 helix: 1.44 (0.28), residues: 331 sheet: 0.04 (0.47), residues: 119 loop : -1.38 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 720 HIS 0.010 0.001 HIS A 747 PHE 0.016 0.002 PHE A 604 TYR 0.016 0.002 TYR A 417 ARG 0.009 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 358) hydrogen bonds : angle 4.37280 ( 1008) covalent geometry : bond 0.00319 ( 7434) covalent geometry : angle 0.68233 (10191) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1538 Ramachandran restraints generated. 769 Oldfield, 0 Emsley, 769 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.902 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: A 1 MET cc_start: 0.8450 (tpp) cc_final: 0.8209 (tpp) REVERT: A 242 GLU cc_start: 0.9171 (pp20) cc_final: 0.8858 (mm-30) REVERT: A 328 TRP cc_start: 0.9230 (t60) cc_final: 0.8938 (t60) REVERT: A 343 ASP cc_start: 0.8819 (m-30) cc_final: 0.8301 (p0) REVERT: A 368 ARG cc_start: 0.8256 (mtm110) cc_final: 0.8038 (ttp80) REVERT: A 426 LEU cc_start: 0.9083 (tt) cc_final: 0.8675 (pp) REVERT: A 497 ASP cc_start: 0.8012 (t0) cc_final: 0.7591 (p0) REVERT: A 548 LYS cc_start: 0.8835 (tttt) cc_final: 0.8501 (tttt) REVERT: A 641 ASN cc_start: 0.8844 (t0) cc_final: 0.8464 (t0) REVERT: A 672 MET cc_start: 0.7843 (tpp) cc_final: 0.7570 (tpp) REVERT: A 730 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8295 (pp20) REVERT: A 735 ASN cc_start: 0.8352 (p0) cc_final: 0.8127 (p0) outliers start: 19 outliers final: 17 residues processed: 104 average time/residue: 0.3645 time to fit residues: 50.4502 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 83 PHE Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 216 LYS Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 730 GLU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 77 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.080567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.065158 restraints weight = 33550.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.067443 restraints weight = 17761.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.069052 restraints weight = 11360.135| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 7434 Z= 0.160 Angle : 0.701 9.455 10191 Z= 0.349 Chirality : 0.041 0.190 1134 Planarity : 0.004 0.048 1181 Dihedral : 16.996 178.390 1497 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.09 % Allowed : 24.85 % Favored : 72.06 % 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: 0.06 (0.31), residues: 769 helix: 1.30 (0.28), residues: 340 sheet: 0.00 (0.44), residues: 132 loop : -1.43 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 720 HIS 0.012 0.001 HIS A 747 PHE 0.016 0.002 PHE A 360 TYR 0.034 0.002 TYR A 760 ARG 0.008 0.000 ARG A 793 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 358) hydrogen bonds : angle 4.41344 ( 1008) covalent geometry : bond 0.00356 ( 7434) covalent geometry : angle 0.70055 (10191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3357.11 seconds wall clock time: 60 minutes 32.33 seconds (3632.33 seconds total)