Starting phenix.real_space_refine on Wed Apr 30 22:22:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f19_28788/04_2025/8f19_28788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f19_28788/04_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_28788/04_2025/8f19_28788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f19_28788/04_2025/8f19_28788.map" model { file = "/net/cci-nas-00/data/ceres_data/8f19_28788/04_2025/8f19_28788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f19_28788/04_2025/8f19_28788.cif" } resolution = 3.49 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= 0.005 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.22, per 1000 atoms: 0.60 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: 2.35 Conformation dependent library (CDL) restraints added in 972.2 milliseconds 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: 0.84 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: 2.55 Time building geometry restraints manager: 2.74 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.540 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.790 ------------------------------------------------------------------------------- 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 (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: 1.08 (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 TRP 0.011 0.001 TRP A 127 HIS 0.007 0.001 HIS B 32 PHE 0.025 0.002 PHE A 817 TYR 0.019 0.001 TYR A 511 ARG 0.005 0.000 ARG B 108 Details of bonding type rmsd hydrogen bonds : bond 0.13951 ( 584) hydrogen bonds : angle 5.37939 ( 1728) covalent geometry : bond 0.00292 ( 8867) covalent geometry : angle 0.66720 (12019) *********************** 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 : 0.993 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: 0.6276 (mmm) outliers start: 2 outliers final: 0 residues processed: 154 average time/residue: 0.2238 time to fit residues: 46.7999 Evaluate side-chains 89 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.164542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115540 restraints weight = 11444.444| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.53 r_work: 0.3186 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8867 Z= 0.137 Angle : 0.565 8.577 12019 Z= 0.294 Chirality : 0.041 0.304 1428 Planarity : 0.004 0.045 1513 Dihedral : 9.019 166.212 1161 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.50 % Allowed : 5.73 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.73 (0.26), residues: 1077 helix: 1.60 (0.19), residues: 769 sheet: -1.15 (0.77), residues: 45 loop : 0.42 (0.42), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 66 HIS 0.005 0.001 HIS B 32 PHE 0.020 0.002 PHE A 893 TYR 0.016 0.001 TYR B 81 ARG 0.005 0.001 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 584) hydrogen bonds : angle 4.31323 ( 1728) covalent geometry : bond 0.00311 ( 8867) covalent geometry : angle 0.56499 (12019) *********************** 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: 5 poor density : 110 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8090 (m-80) cc_final: 0.7883 (m-10) REVERT: A 478 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7708 (ttmm) REVERT: A 611 MET cc_start: 0.7771 (mtp) cc_final: 0.7505 (mtp) REVERT: A 615 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7221 (ttpp) REVERT: A 887 PHE cc_start: 0.9128 (m-10) cc_final: 0.8719 (m-80) REVERT: B 173 ASN cc_start: 0.8554 (t0) cc_final: 0.7997 (p0) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.3048 time to fit residues: 48.0701 Evaluate side-chains 92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 757 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 67 optimal weight: 0.2980 chunk 47 optimal weight: 0.0570 chunk 77 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 117 GLN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118917 restraints weight = 11690.338| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.06 r_work: 0.3161 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8867 Z= 0.113 Angle : 0.531 13.957 12019 Z= 0.268 Chirality : 0.039 0.294 1428 Planarity : 0.004 0.044 1513 Dihedral : 8.680 161.584 1161 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.01 % Allowed : 7.95 % Favored : 91.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.92 (0.26), residues: 1077 helix: 1.78 (0.19), residues: 771 sheet: -0.77 (0.69), residues: 52 loop : 0.32 (0.43), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 66 HIS 0.003 0.001 HIS B 32 PHE 0.018 0.002 PHE B 28 TYR 0.012 0.001 TYR A 511 ARG 0.004 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 584) hydrogen bonds : angle 4.11761 ( 1728) covalent geometry : bond 0.00247 ( 8867) covalent geometry : angle 0.53099 (12019) *********************** 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 108 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 TYR cc_start: 0.8104 (m-80) cc_final: 0.7904 (m-10) REVERT: A 284 ASP cc_start: 0.7574 (m-30) cc_final: 0.7086 (m-30) REVERT: A 478 LYS cc_start: 0.7960 (ttpt) cc_final: 0.7561 (ttmm) REVERT: B 173 ASN cc_start: 0.8465 (t0) cc_final: 0.7830 (p0) outliers start: 10 outliers final: 6 residues processed: 104 average time/residue: 0.2352 time to fit residues: 34.3080 Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 214 SER Chi-restraints excluded: chain A residue 291 ILE 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 62 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.161458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112512 restraints weight = 11493.882| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.49 r_work: 0.3169 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8867 Z= 0.139 Angle : 0.516 5.623 12019 Z= 0.266 Chirality : 0.039 0.157 1428 Planarity : 0.004 0.045 1513 Dihedral : 8.408 155.814 1161 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.31 % Allowed : 8.75 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.97 (0.26), residues: 1077 helix: 1.85 (0.19), residues: 769 sheet: 0.09 (0.84), residues: 39 loop : 0.01 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 66 HIS 0.004 0.001 HIS B 32 PHE 0.022 0.002 PHE B 28 TYR 0.011 0.001 TYR B 100 ARG 0.007 0.001 ARG A 825 Details of bonding type rmsd hydrogen bonds : bond 0.03492 ( 584) hydrogen bonds : angle 4.10147 ( 1728) covalent geometry : bond 0.00331 ( 8867) covalent geometry : angle 0.51551 (12019) *********************** 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 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6887 (mp0) REVERT: A 478 LYS cc_start: 0.8121 (ttpt) cc_final: 0.7711 (ttmm) REVERT: A 570 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7905 (mmm160) REVERT: A 574 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8081 (tt) REVERT: B 38 GLU cc_start: 0.7830 (tp30) cc_final: 0.7529 (tm-30) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.2120 time to fit residues: 29.9784 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 147 MET 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 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU 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 59 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 0.0470 chunk 41 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.163109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114108 restraints weight = 11337.316| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.52 r_work: 0.3176 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8867 Z= 0.110 Angle : 0.496 8.354 12019 Z= 0.252 Chirality : 0.038 0.204 1428 Planarity : 0.003 0.043 1513 Dihedral : 8.107 151.532 1161 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.31 % Allowed : 9.86 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.11 (0.26), residues: 1077 helix: 2.00 (0.18), residues: 770 sheet: -0.41 (0.73), residues: 52 loop : 0.04 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.004 0.001 HIS B 32 PHE 0.020 0.001 PHE A 745 TYR 0.010 0.001 TYR A 511 ARG 0.005 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03211 ( 584) hydrogen bonds : angle 4.01534 ( 1728) covalent geometry : bond 0.00243 ( 8867) covalent geometry : angle 0.49633 (12019) *********************** 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 102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7688 (m-30) cc_final: 0.7123 (m-30) REVERT: A 574 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8027 (tt) REVERT: A 707 MET cc_start: 0.7962 (tpp) cc_final: 0.7742 (tpp) REVERT: B 173 ASN cc_start: 0.8539 (t0) cc_final: 0.8014 (p0) outliers start: 13 outliers final: 9 residues processed: 98 average time/residue: 0.1999 time to fit residues: 28.4523 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.973 ------------------------------------------------------------------------------- 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 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 711 LEU 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 73 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 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 = 0.3913 r_free = 0.3913 target = 0.162244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113281 restraints weight = 11433.358| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.55 r_work: 0.3167 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8867 Z= 0.117 Angle : 0.493 7.586 12019 Z= 0.254 Chirality : 0.038 0.154 1428 Planarity : 0.003 0.043 1513 Dihedral : 7.921 149.444 1161 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.31 % Allowed : 10.76 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.21 (0.26), residues: 1077 helix: 2.03 (0.19), residues: 771 sheet: 0.53 (0.91), residues: 39 loop : 0.04 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 106 HIS 0.004 0.001 HIS B 32 PHE 0.018 0.001 PHE B 28 TYR 0.011 0.001 TYR B 100 ARG 0.006 0.001 ARG A 763 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 584) hydrogen bonds : angle 3.97707 ( 1728) covalent geometry : bond 0.00269 ( 8867) covalent geometry : angle 0.49286 (12019) *********************** 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 99 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7717 (mp0) cc_final: 0.7515 (pm20) REVERT: A 165 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6750 (mp0) REVERT: A 574 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8005 (tt) REVERT: A 707 MET cc_start: 0.8175 (tpp) cc_final: 0.7737 (tpp) REVERT: B 173 ASN cc_start: 0.8478 (t0) cc_final: 0.7935 (p0) outliers start: 13 outliers final: 9 residues processed: 94 average time/residue: 0.2043 time to fit residues: 27.8758 Evaluate side-chains 93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 MET 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 0.8980 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 1 optimal weight: 0.0000 chunk 55 optimal weight: 0.9980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.163147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.115884 restraints weight = 11505.456| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.02 r_work: 0.3153 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8867 Z= 0.105 Angle : 0.493 9.963 12019 Z= 0.251 Chirality : 0.038 0.172 1428 Planarity : 0.003 0.043 1513 Dihedral : 7.652 145.494 1161 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.31 % Allowed : 11.57 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.27 (0.26), residues: 1077 helix: 2.11 (0.18), residues: 772 sheet: 0.66 (0.92), residues: 39 loop : -0.10 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.004 0.001 HIS B 32 PHE 0.016 0.001 PHE A 123 TYR 0.010 0.001 TYR A 511 ARG 0.005 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03101 ( 584) hydrogen bonds : angle 3.92208 ( 1728) covalent geometry : bond 0.00234 ( 8867) covalent geometry : angle 0.49346 (12019) *********************** 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 102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7656 (mp0) cc_final: 0.7412 (pm20) REVERT: A 165 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: A 284 ASP cc_start: 0.7300 (m-30) cc_final: 0.6828 (m-30) REVERT: A 574 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7955 (tt) REVERT: A 707 MET cc_start: 0.8200 (tpp) cc_final: 0.7746 (tpp) REVERT: B 136 LYS cc_start: 0.6682 (ptmt) cc_final: 0.6415 (pttt) REVERT: B 173 ASN cc_start: 0.8444 (t0) cc_final: 0.7948 (p0) outliers start: 13 outliers final: 6 residues processed: 97 average time/residue: 0.2208 time to fit residues: 31.5514 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.958 ------------------------------------------------------------------------------- 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 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 713 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.161873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112730 restraints weight = 11622.954| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.57 r_work: 0.3159 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2722 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= 0.121 Angle : 0.519 10.532 12019 Z= 0.260 Chirality : 0.039 0.176 1428 Planarity : 0.003 0.041 1513 Dihedral : 7.504 144.056 1161 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.91 % Allowed : 12.07 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.29 (0.26), residues: 1077 helix: 2.12 (0.19), residues: 772 sheet: 0.78 (0.93), residues: 39 loop : -0.13 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 127 HIS 0.003 0.001 HIS B 32 PHE 0.018 0.001 PHE B 28 TYR 0.010 0.001 TYR B 100 ARG 0.005 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 584) hydrogen bonds : angle 3.91916 ( 1728) covalent geometry : bond 0.00284 ( 8867) covalent geometry : angle 0.51937 (12019) *********************** 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 98 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7712 (mp0) cc_final: 0.7474 (pm20) REVERT: A 165 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: A 284 ASP cc_start: 0.7484 (m-30) cc_final: 0.6974 (m-30) REVERT: A 574 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7998 (tt) REVERT: A 707 MET cc_start: 0.8173 (tpp) cc_final: 0.7776 (tpp) REVERT: B 136 LYS cc_start: 0.6769 (ptmt) cc_final: 0.6567 (pttt) REVERT: B 173 ASN cc_start: 0.8471 (t0) cc_final: 0.7955 (p0) outliers start: 9 outliers final: 7 residues processed: 95 average time/residue: 0.2025 time to fit residues: 28.1210 Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 0 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 9 optimal weight: 0.0470 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 10.0000 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.162558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113174 restraints weight = 11657.656| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.59 r_work: 0.3165 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8867 Z= 0.107 Angle : 0.504 11.191 12019 Z= 0.253 Chirality : 0.038 0.154 1428 Planarity : 0.003 0.040 1513 Dihedral : 7.273 141.144 1161 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.11 % Allowed : 12.27 % 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 (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: 2.32 (0.26), residues: 1077 helix: 2.18 (0.18), residues: 772 sheet: -0.05 (0.77), residues: 52 loop : -0.08 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.003 0.001 HIS B 32 PHE 0.016 0.001 PHE A 123 TYR 0.009 0.001 TYR A 511 ARG 0.005 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 584) hydrogen bonds : angle 3.87822 ( 1728) covalent geometry : bond 0.00242 ( 8867) covalent geometry : angle 0.50426 (12019) *********************** 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 99 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7713 (mp0) cc_final: 0.7499 (pm20) REVERT: A 284 ASP cc_start: 0.7486 (m-30) cc_final: 0.6917 (m-30) REVERT: A 574 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7984 (tt) REVERT: A 707 MET cc_start: 0.8157 (tpp) cc_final: 0.7728 (tpp) REVERT: B 128 VAL cc_start: 0.7805 (t) cc_final: 0.7535 (m) REVERT: B 173 ASN cc_start: 0.8443 (t0) cc_final: 0.7954 (p0) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.1915 time to fit residues: 27.2361 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 : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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 713 ASP Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 65 optimal weight: 9.9990 chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.162005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112624 restraints weight = 11561.028| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.59 r_work: 0.3153 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8867 Z= 0.115 Angle : 0.526 11.565 12019 Z= 0.261 Chirality : 0.039 0.377 1428 Planarity : 0.003 0.037 1513 Dihedral : 7.149 140.444 1161 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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 (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: 2.35 (0.26), residues: 1077 helix: 2.19 (0.18), residues: 772 sheet: 0.83 (0.95), residues: 39 loop : -0.19 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 28 HIS 0.003 0.001 HIS B 141 PHE 0.017 0.001 PHE B 28 TYR 0.009 0.001 TYR B 100 ARG 0.008 0.000 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03110 ( 584) hydrogen bonds : angle 3.89029 ( 1728) covalent geometry : bond 0.00267 ( 8867) covalent geometry : angle 0.52620 (12019) ********************** 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 97 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 GLU cc_start: 0.7622 (mp0) cc_final: 0.7365 (pm20) REVERT: A 284 ASP cc_start: 0.7527 (m-30) cc_final: 0.6945 (m-30) REVERT: A 574 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 707 MET cc_start: 0.8156 (tpp) cc_final: 0.7755 (tpp) REVERT: B 128 VAL cc_start: 0.7831 (t) cc_final: 0.7577 (m) REVERT: B 173 ASN cc_start: 0.8435 (t0) cc_final: 0.7936 (p0) outliers start: 9 outliers final: 7 residues processed: 94 average time/residue: 0.1863 time to fit residues: 25.9134 Evaluate side-chains 93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER 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 Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 18 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 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 = 0.3910 r_free = 0.3910 target = 0.162012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.114902 restraints weight = 11483.208| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.19 r_work: 0.3137 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8867 Z= 0.116 Angle : 0.525 11.899 12019 Z= 0.262 Chirality : 0.039 0.300 1428 Planarity : 0.004 0.036 1513 Dihedral : 6.973 138.869 1161 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.91 % Allowed : 13.28 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.38 (0.26), residues: 1077 helix: 2.22 (0.18), residues: 773 sheet: 0.78 (0.94), residues: 39 loop : -0.21 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 813 HIS 0.003 0.001 HIS B 141 PHE 0.017 0.001 PHE B 28 TYR 0.009 0.001 TYR A 511 ARG 0.008 0.001 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03116 ( 584) hydrogen bonds : angle 3.89011 ( 1728) covalent geometry : bond 0.00269 ( 8867) covalent geometry : angle 0.52543 (12019) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4011.64 seconds wall clock time: 71 minutes 24.09 seconds (4284.09 seconds total)