Starting phenix.real_space_refine on Sat Aug 23 05:19:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.map" model { file = "/net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f19_28788/08_2025/8f19_28788.cif" } resolution = 3.49 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= 0.005 sd= 0.054 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1516 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 37 5.16 5 C 5590 2.51 5 N 1416 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8717 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 916, 7291 Classifications: {'peptide': 916} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 891} Chain breaks: 3 Chain: "B" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1393 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.87, per 1000 atoms: 0.21 Number of scatterers: 8717 At special positions: 0 Unit cell: (92.133, 102.723, 119.667, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 37 16.00 P 3 15.00 Mg 1 11.99 O 1670 8.00 N 1416 7.00 C 5590 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: 0.79 Conformation dependent library (CDL) restraints added in 263.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 3 sheets defined 77.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 32 Processing helix chain 'A' and resid 32 through 46 removed outlier: 3.654A pdb=" N VAL A 36 " --> pdb=" O ASP A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.514A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.519A pdb=" N PHE A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 4.291A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 142 removed outlier: 4.174A pdb=" N LEU A 131 " --> pdb=" O TRP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 157 Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 186 through 207 removed outlier: 4.234A pdb=" N HIS A 207 " --> pdb=" O GLN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 236 removed outlier: 4.127A pdb=" N PHE A 218 " --> pdb=" O SER A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 264 Processing helix chain 'A' and resid 265 through 269 Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 302 through 322 Processing helix chain 'A' and resid 327 through 343 removed outlier: 3.775A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.982A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 removed outlier: 3.548A pdb=" N GLN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 402 removed outlier: 3.722A pdb=" N LYS A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.562A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 448 removed outlier: 3.743A pdb=" N SER A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 497 through 513 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 522 through 542 removed outlier: 3.980A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 561 removed outlier: 3.918A pdb=" N ALA A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 587 removed outlier: 3.656A pdb=" N SER A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 610 through 632 removed outlier: 4.081A pdb=" N LYS A 615 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASN A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 619 " --> pdb=" O LYS A 615 " (cutoff:3.500A) Proline residue: A 623 - end of helix removed outlier: 3.565A pdb=" N VAL A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 664 through 682 removed outlier: 3.729A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 702 removed outlier: 3.505A pdb=" N TYR A 697 " --> pdb=" O GLU A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 Processing helix chain 'A' and resid 727 through 732 Processing helix chain 'A' and resid 733 through 745 removed outlier: 4.153A pdb=" N LEU A 737 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 767 removed outlier: 4.731A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N GLY A 754 " --> pdb=" O GLN A 750 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG A 755 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 787 Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 820 Processing helix chain 'A' and resid 822 through 838 removed outlier: 3.970A pdb=" N GLU A 828 " --> pdb=" O LYS A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.899A pdb=" N GLN A 845 " --> pdb=" O ASP A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 896 removed outlier: 3.858A pdb=" N LYS A 896 " --> pdb=" O SER A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 978 removed outlier: 3.544A pdb=" N LEU A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 4.020A pdb=" N CYS A 986 " --> pdb=" O SER A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1003 Processing helix chain 'B' and resid 24 through 35 Processing helix chain 'B' and resid 77 through 82 Processing helix chain 'B' and resid 96 through 114 removed outlier: 3.703A pdb=" N TYR B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 3.525A pdb=" N VAL B 113 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 135 No H-bonds generated for 'chain 'B' and resid 133 through 135' Processing helix chain 'B' and resid 136 through 145 removed outlier: 4.238A pdb=" N PHE B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS B 143 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B 144 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 172 Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 849 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 56 removed outlier: 3.570A pdb=" N GLY B 59 " --> pdb=" O THR B 56 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N PHE B 13 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N TRP B 66 " --> pdb=" O PHE B 13 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 15 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR B 68 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 17 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N CYS B 87 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LYS B 14 " --> pdb=" O CYS B 87 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE B 89 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 16 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N MET B 91 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL B 18 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ASP B 93 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ILE B 119 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N TYR B 149 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 121 " --> pdb=" O TYR B 149 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1728 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: 0.99 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2807 1.34 - 1.46: 1789 1.46 - 1.58: 4212 1.58 - 1.69: 5 1.69 - 1.81: 54 Bond restraints: 8867 Sorted by residual: bond pdb=" C2 GTP B 201 " pdb=" N3 GTP B 201 " ideal model delta sigma weight residual 1.380 1.333 0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" N LYS B 125 " pdb=" CA LYS B 125 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.45e-02 4.76e+03 4.98e+00 bond pdb=" N ASP A 665 " pdb=" CA ASP A 665 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.28e-02 6.10e+03 4.73e+00 bond pdb=" C8 GTP B 201 " pdb=" N7 GTP B 201 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C4' GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sigma weight residual 1.410 1.450 -0.040 2.00e-02 2.50e+03 3.96e+00 ... (remaining 8862 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 11843 2.14 - 4.27: 132 4.27 - 6.41: 31 6.41 - 8.54: 8 8.54 - 10.68: 5 Bond angle restraints: 12019 Sorted by residual: angle pdb=" CA TYR A 513 " pdb=" C TYR A 513 " pdb=" N PHE A 514 " ideal model delta sigma weight residual 118.59 124.93 -6.34 1.63e+00 3.76e-01 1.51e+01 angle pdb=" CA LYS B 125 " pdb=" C LYS B 125 " pdb=" O LYS B 125 " ideal model delta sigma weight residual 122.14 117.37 4.77 1.24e+00 6.50e-01 1.48e+01 angle pdb=" N VAL B 94 " pdb=" CA VAL B 94 " pdb=" C VAL B 94 " ideal model delta sigma weight residual 113.00 108.32 4.68 1.30e+00 5.92e-01 1.29e+01 angle pdb=" C2' GTP B 201 " pdb=" C3' GTP B 201 " pdb=" C4' GTP B 201 " ideal model delta sigma weight residual 111.00 100.32 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" O1B GTP B 201 " pdb=" PB GTP B 201 " pdb=" O2B GTP B 201 " ideal model delta sigma weight residual 109.50 119.93 -10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 12014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5303 35.90 - 71.81: 75 71.81 - 107.71: 12 107.71 - 143.61: 1 143.61 - 179.51: 1 Dihedral angle restraints: 5392 sinusoidal: 2169 harmonic: 3223 Sorted by residual: dihedral pdb=" C8 GTP B 201 " pdb=" C1' GTP B 201 " pdb=" N9 GTP B 201 " pdb=" O4' GTP B 201 " ideal model delta sinusoidal sigma weight residual 104.59 -75.89 -179.51 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O3B GTP B 201 " pdb=" O3A GTP B 201 " pdb=" PB GTP B 201 " pdb=" PA GTP B 201 " ideal model delta sinusoidal sigma weight residual -68.92 64.23 -133.15 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O3A GTP B 201 " pdb=" O3B GTP B 201 " pdb=" PB GTP B 201 " pdb=" PG GTP B 201 " ideal model delta sinusoidal sigma weight residual -56.21 -160.47 104.26 1 2.00e+01 2.50e-03 2.99e+01 ... (remaining 5389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1101 0.045 - 0.089: 265 0.089 - 0.134: 55 0.134 - 0.179: 6 0.179 - 0.223: 1 Chirality restraints: 1428 Sorted by residual: chirality pdb=" C3' GTP B 201 " pdb=" C2' GTP B 201 " pdb=" C4' GTP B 201 " pdb=" O3' GTP B 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.70 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 235 " pdb=" CA THR A 235 " pdb=" OG1 THR A 235 " pdb=" CG2 THR A 235 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA TYR A 254 " pdb=" N TYR A 254 " pdb=" C TYR A 254 " pdb=" CB TYR A 254 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1425 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 123 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO A 124 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 563 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO A 564 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 564 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 564 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 817 " 0.007 2.00e-02 2.50e+03 1.09e-02 2.06e+00 pdb=" CG PHE A 817 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 817 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 817 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 817 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 817 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 817 " -0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 37 2.50 - 3.10: 6692 3.10 - 3.70: 13163 3.70 - 4.30: 19193 4.30 - 4.90: 31566 Nonbonded interactions: 70651 Sorted by model distance: nonbonded pdb=" O3B GTP B 201 " pdb="MG MG B 202 " model vdw 1.897 2.170 nonbonded pdb=" PG GTP B 201 " pdb="MG MG B 202 " model vdw 1.990 2.530 nonbonded pdb=" O2G GTP B 201 " pdb="MG MG B 202 " model vdw 2.015 2.170 nonbonded pdb=" O3G GTP B 201 " pdb="MG MG B 202 " model vdw 2.190 2.170 nonbonded pdb=" OH TYR A 154 " pdb=" OG1 THR A 172 " model vdw 2.225 3.040 ... (remaining 70646 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 0.047 8867 Z= 0.146 Angle : 0.667 10.680 12019 Z= 0.339 Chirality : 0.040 0.223 1428 Planarity : 0.004 0.047 1513 Dihedral : 14.178 179.514 3282 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 1.08 (0.26), residues: 1077 helix: 1.02 (0.19), residues: 768 sheet: -0.83 (0.72), residues: 50 loop : 0.49 (0.42), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 108 TYR 0.019 0.001 TYR A 511 PHE 0.025 0.002 PHE A 817 TRP 0.011 0.001 TRP A 127 HIS 0.007 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8867) covalent geometry : angle 0.66720 (12019) hydrogen bonds : bond 0.13951 ( 584) hydrogen bonds : angle 5.37939 ( 1728) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.7807 (m-80) cc_final: 0.7531 (m-10) REVERT: A 263 ASP cc_start: 0.7757 (m-30) cc_final: 0.7479 (m-30) REVERT: A 280 MET cc_start: 0.8411 (mmm) cc_final: 0.8199 (mmp) REVERT: A 427 THR cc_start: 0.8201 (p) cc_final: 0.7928 (t) REVERT: A 431 ILE cc_start: 0.7552 (mt) cc_final: 0.7179 (tt) REVERT: A 478 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7740 (ttmm) REVERT: A 578 PHE cc_start: 0.7980 (t80) cc_final: 0.7740 (t80) REVERT: A 611 MET cc_start: 0.7673 (mtp) cc_final: 0.7440 (mtp) REVERT: A 615 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7458 (ttpp) REVERT: A 786 ASN cc_start: 0.8488 (t0) cc_final: 0.8061 (t0) REVERT: A 887 PHE cc_start: 0.8898 (m-10) cc_final: 0.8457 (m-80) REVERT: A 959 MET cc_start: 0.6477 (mmm) cc_final: 0.6275 (mmm) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.0893 time to fit residues: 18.6421 Evaluate side-chains 90 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 117 GLN A 140 HIS ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 GLN B 147 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110303 restraints weight = 11543.549| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 2.55 r_work: 0.3114 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8867 Z= 0.189 Angle : 0.614 8.206 12019 Z= 0.320 Chirality : 0.043 0.302 1428 Planarity : 0.004 0.043 1513 Dihedral : 9.101 164.708 1161 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 5.33 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 1.53 (0.26), residues: 1077 helix: 1.45 (0.19), residues: 770 sheet: -1.16 (0.69), residues: 53 loop : 0.40 (0.44), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 131 TYR 0.017 0.002 TYR B 81 PHE 0.023 0.002 PHE B 28 TRP 0.010 0.001 TRP B 66 HIS 0.005 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8867) covalent geometry : angle 0.61441 (12019) hydrogen bonds : bond 0.04219 ( 584) hydrogen bonds : angle 4.37787 ( 1728) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8653 (t60) cc_final: 0.8372 (t60) REVERT: A 68 TYR cc_start: 0.8207 (m-80) cc_final: 0.7904 (m-10) REVERT: A 478 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7738 (ttmm) REVERT: A 570 ARG cc_start: 0.8086 (mmm160) cc_final: 0.7877 (mmm160) REVERT: A 611 MET cc_start: 0.7832 (mtp) cc_final: 0.7593 (mtp) REVERT: A 615 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7206 (ttpp) REVERT: A 887 PHE cc_start: 0.9126 (m-10) cc_final: 0.8726 (m-80) REVERT: B 173 ASN cc_start: 0.8622 (t0) cc_final: 0.8013 (p0) outliers start: 11 outliers final: 5 residues processed: 110 average time/residue: 0.0873 time to fit residues: 13.4053 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 19 optimal weight: 0.7980 chunk 1 optimal weight: 0.0020 chunk 77 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 103 optimal weight: 0.0070 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114487 restraints weight = 11436.501| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.55 r_work: 0.3170 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8867 Z= 0.112 Angle : 0.531 13.608 12019 Z= 0.268 Chirality : 0.039 0.268 1428 Planarity : 0.004 0.044 1513 Dihedral : 8.697 159.486 1161 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.60 % Allowed : 8.15 % Favored : 91.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 1.83 (0.26), residues: 1077 helix: 1.72 (0.19), residues: 771 sheet: -0.75 (0.70), residues: 52 loop : 0.23 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 705 TYR 0.012 0.001 TYR A 511 PHE 0.018 0.002 PHE B 28 TRP 0.005 0.001 TRP A 127 HIS 0.004 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8867) covalent geometry : angle 0.53143 (12019) hydrogen bonds : bond 0.03574 ( 584) hydrogen bonds : angle 4.15266 ( 1728) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 98 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8664 (t60) cc_final: 0.8303 (t60) REVERT: A 68 TYR cc_start: 0.8128 (m-80) cc_final: 0.7905 (m-10) REVERT: A 284 ASP cc_start: 0.7860 (m-30) cc_final: 0.7319 (m-30) REVERT: A 478 LYS cc_start: 0.8059 (ttpt) cc_final: 0.7658 (ttmm) REVERT: A 570 ARG cc_start: 0.8031 (mmm160) cc_final: 0.7785 (mmm160) REVERT: A 806 LEU cc_start: 0.8718 (mt) cc_final: 0.8501 (mt) REVERT: B 38 GLU cc_start: 0.7854 (tp30) cc_final: 0.7586 (tm-30) REVERT: B 173 ASN cc_start: 0.8539 (t0) cc_final: 0.7875 (p0) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.0864 time to fit residues: 12.2178 Evaluate side-chains 86 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 65 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.161741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.112962 restraints weight = 11540.636| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.50 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8867 Z= 0.122 Angle : 0.502 6.165 12019 Z= 0.259 Chirality : 0.038 0.155 1428 Planarity : 0.004 0.045 1513 Dihedral : 8.448 157.399 1161 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.31 % Allowed : 8.85 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 1.92 (0.26), residues: 1077 helix: 1.84 (0.19), residues: 769 sheet: -0.63 (0.72), residues: 52 loop : 0.08 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 705 TYR 0.010 0.001 TYR A 511 PHE 0.017 0.001 PHE B 28 TRP 0.004 0.001 TRP B 66 HIS 0.003 0.001 HIS B 32 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8867) covalent geometry : angle 0.50204 (12019) hydrogen bonds : bond 0.03392 ( 584) hydrogen bonds : angle 4.06692 ( 1728) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8669 (t60) cc_final: 0.8253 (t60) REVERT: A 68 TYR cc_start: 0.8101 (m-80) cc_final: 0.7899 (m-10) REVERT: A 165 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: A 478 LYS cc_start: 0.8084 (ttpt) cc_final: 0.7671 (ttmm) REVERT: A 574 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8030 (tt) outliers start: 13 outliers final: 8 residues processed: 100 average time/residue: 0.0743 time to fit residues: 10.5621 Evaluate side-chains 93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 36 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3907 r_free = 0.3907 target = 0.161630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112743 restraints weight = 11588.659| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.51 r_work: 0.3153 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8867 Z= 0.118 Angle : 0.497 8.476 12019 Z= 0.254 Chirality : 0.039 0.187 1428 Planarity : 0.003 0.045 1513 Dihedral : 8.269 154.398 1161 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.21 % Allowed : 10.46 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.06 (0.26), residues: 1077 helix: 1.93 (0.18), residues: 772 sheet: 0.33 (0.87), residues: 39 loop : -0.04 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 705 TYR 0.010 0.001 TYR A 511 PHE 0.018 0.001 PHE B 28 TRP 0.005 0.001 TRP A 813 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8867) covalent geometry : angle 0.49726 (12019) hydrogen bonds : bond 0.03307 ( 584) hydrogen bonds : angle 4.01502 ( 1728) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8672 (t60) cc_final: 0.8233 (t60) REVERT: A 68 TYR cc_start: 0.8090 (m-80) cc_final: 0.7869 (m-10) REVERT: A 160 GLU cc_start: 0.7806 (mp0) cc_final: 0.7506 (pm20) REVERT: A 165 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6776 (mp0) REVERT: A 284 ASP cc_start: 0.7832 (m-30) cc_final: 0.7291 (m-30) REVERT: A 574 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8034 (tt) REVERT: A 617 TYR cc_start: 0.7584 (m-80) cc_final: 0.7349 (m-10) REVERT: A 707 MET cc_start: 0.7978 (tpp) cc_final: 0.7519 (tpp) REVERT: B 173 ASN cc_start: 0.8526 (t0) cc_final: 0.7966 (p0) outliers start: 12 outliers final: 7 residues processed: 101 average time/residue: 0.0817 time to fit residues: 11.7379 Evaluate side-chains 92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 107 optimal weight: 0.2980 chunk 57 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 876 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.161686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112789 restraints weight = 11558.333| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.51 r_work: 0.3152 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8867 Z= 0.114 Angle : 0.489 6.821 12019 Z= 0.253 Chirality : 0.038 0.172 1428 Planarity : 0.004 0.044 1513 Dihedral : 8.119 152.583 1161 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.01 % Allowed : 11.77 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.12 (0.26), residues: 1077 helix: 2.01 (0.19), residues: 771 sheet: -0.31 (0.74), residues: 52 loop : 0.01 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 710 TYR 0.010 0.001 TYR B 100 PHE 0.022 0.002 PHE A 745 TRP 0.004 0.001 TRP B 66 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8867) covalent geometry : angle 0.48917 (12019) hydrogen bonds : bond 0.03231 ( 584) hydrogen bonds : angle 3.98271 ( 1728) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8653 (t60) cc_final: 0.8182 (t60) REVERT: A 165 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: A 574 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8001 (tt) REVERT: A 707 MET cc_start: 0.8064 (tpp) cc_final: 0.7757 (tpp) REVERT: B 173 ASN cc_start: 0.8474 (t0) cc_final: 0.7939 (p0) outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.0749 time to fit residues: 10.2952 Evaluate side-chains 91 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3896 r_free = 0.3896 target = 0.160599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.110972 restraints weight = 11644.309| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.58 r_work: 0.3123 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8867 Z= 0.129 Angle : 0.517 10.681 12019 Z= 0.263 Chirality : 0.039 0.155 1428 Planarity : 0.003 0.042 1513 Dihedral : 7.976 150.974 1161 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.61 % Allowed : 11.97 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.14 (0.26), residues: 1077 helix: 2.00 (0.19), residues: 771 sheet: 0.64 (0.91), residues: 39 loop : -0.10 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.011 0.001 TYR B 100 PHE 0.020 0.002 PHE B 28 TRP 0.005 0.001 TRP A 813 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8867) covalent geometry : angle 0.51747 (12019) hydrogen bonds : bond 0.03333 ( 584) hydrogen bonds : angle 3.99082 ( 1728) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8678 (t60) cc_final: 0.8291 (t60) REVERT: A 160 GLU cc_start: 0.7927 (mp0) cc_final: 0.6970 (pm20) REVERT: A 165 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: A 284 ASP cc_start: 0.7616 (m-30) cc_final: 0.7159 (m-30) REVERT: A 574 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7982 (tt) REVERT: A 707 MET cc_start: 0.8194 (tpp) cc_final: 0.7756 (tpp) REVERT: B 136 LYS cc_start: 0.6926 (ptmt) cc_final: 0.6657 (pttt) REVERT: B 173 ASN cc_start: 0.8494 (t0) cc_final: 0.7934 (p0) outliers start: 16 outliers final: 9 residues processed: 105 average time/residue: 0.0856 time to fit residues: 12.6839 Evaluate side-chains 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 81 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.159628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.110412 restraints weight = 11513.016| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.56 r_work: 0.3122 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8867 Z= 0.137 Angle : 0.534 11.595 12019 Z= 0.268 Chirality : 0.040 0.271 1428 Planarity : 0.004 0.041 1513 Dihedral : 7.900 149.990 1161 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.41 % Allowed : 11.97 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.11 (0.26), residues: 1077 helix: 2.00 (0.19), residues: 771 sheet: 0.67 (0.91), residues: 39 loop : -0.20 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 705 TYR 0.011 0.001 TYR B 100 PHE 0.020 0.002 PHE A 745 TRP 0.005 0.001 TRP A 127 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8867) covalent geometry : angle 0.53398 (12019) hydrogen bonds : bond 0.03368 ( 584) hydrogen bonds : angle 4.00978 ( 1728) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8679 (t60) cc_final: 0.8280 (t60) REVERT: A 165 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6401 (mp0) REVERT: A 284 ASP cc_start: 0.7737 (m-30) cc_final: 0.7247 (m-30) REVERT: A 478 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7638 (ttmm) REVERT: A 574 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7973 (tt) REVERT: A 707 MET cc_start: 0.8183 (tpp) cc_final: 0.7812 (tpp) REVERT: A 806 LEU cc_start: 0.8730 (mt) cc_final: 0.8525 (mt) REVERT: B 136 LYS cc_start: 0.7039 (ptmt) cc_final: 0.6759 (pttt) REVERT: B 173 ASN cc_start: 0.8499 (t0) cc_final: 0.7909 (p0) outliers start: 14 outliers final: 11 residues processed: 101 average time/residue: 0.0744 time to fit residues: 10.6238 Evaluate side-chains 99 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 165 GLU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 265 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 35 optimal weight: 0.2980 chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 41 optimal weight: 0.0010 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3910 r_free = 0.3910 target = 0.161825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114300 restraints weight = 11590.859| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 3.04 r_work: 0.3132 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8867 Z= 0.107 Angle : 0.518 11.619 12019 Z= 0.257 Chirality : 0.039 0.311 1428 Planarity : 0.003 0.041 1513 Dihedral : 7.667 146.987 1161 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.91 % Allowed : 12.68 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.26 (0.26), residues: 1077 helix: 2.15 (0.19), residues: 765 sheet: -0.02 (0.76), residues: 52 loop : -0.11 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.010 0.001 TYR A 511 PHE 0.019 0.001 PHE A 745 TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8867) covalent geometry : angle 0.51805 (12019) hydrogen bonds : bond 0.03131 ( 584) hydrogen bonds : angle 3.94131 ( 1728) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8666 (t60) cc_final: 0.8272 (t60) REVERT: A 284 ASP cc_start: 0.7542 (m-30) cc_final: 0.6970 (m-30) REVERT: A 574 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7961 (tt) REVERT: A 707 MET cc_start: 0.8170 (tpp) cc_final: 0.7808 (tpp) REVERT: B 173 ASN cc_start: 0.8472 (t0) cc_final: 0.7955 (p0) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.0727 time to fit residues: 9.5644 Evaluate side-chains 89 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.0970 chunk 77 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3914 r_free = 0.3914 target = 0.162183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114622 restraints weight = 11524.997| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.11 r_work: 0.3122 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8867 Z= 0.106 Angle : 0.533 12.151 12019 Z= 0.262 Chirality : 0.039 0.245 1428 Planarity : 0.003 0.040 1513 Dihedral : 7.473 145.304 1161 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.70 % Allowed : 12.58 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.29 (0.26), residues: 1077 helix: 2.20 (0.18), residues: 767 sheet: 0.01 (0.76), residues: 52 loop : -0.20 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.009 0.001 TYR A 511 PHE 0.019 0.001 PHE A 745 TRP 0.005 0.001 TRP A 69 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8867) covalent geometry : angle 0.53275 (12019) hydrogen bonds : bond 0.03063 ( 584) hydrogen bonds : angle 3.89493 ( 1728) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2154 Ramachandran restraints generated. 1077 Oldfield, 0 Emsley, 1077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.8644 (t60) cc_final: 0.8256 (t60) REVERT: A 574 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7929 (tt) REVERT: A 707 MET cc_start: 0.8170 (tpp) cc_final: 0.7696 (tpp) REVERT: B 173 ASN cc_start: 0.8438 (t0) cc_final: 0.7965 (p0) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.0648 time to fit residues: 9.0830 Evaluate side-chains 88 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.161473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114153 restraints weight = 11539.335| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.96 r_work: 0.3133 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8867 Z= 0.114 Angle : 0.535 11.893 12019 Z= 0.264 Chirality : 0.039 0.231 1428 Planarity : 0.003 0.039 1513 Dihedral : 7.401 144.858 1161 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.80 % Allowed : 12.58 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 aren not related in a simple way. whole: 2.29 (0.26), residues: 1077 helix: 2.20 (0.18), residues: 767 sheet: 0.03 (0.77), residues: 52 loop : -0.22 (0.41), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 705 TYR 0.009 0.001 TYR A 511 PHE 0.020 0.001 PHE A 745 TRP 0.005 0.001 TRP A 69 HIS 0.003 0.001 HIS B 141 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 8867) covalent geometry : angle 0.53510 (12019) hydrogen bonds : bond 0.03103 ( 584) hydrogen bonds : angle 3.89732 ( 1728) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1635.45 seconds wall clock time: 28 minutes 42.79 seconds (1722.79 seconds total)