Starting phenix.real_space_refine on Sat Nov 16 00:14:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_28788.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_28788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_28788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_28788.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f19_28788/11_2024/8f19_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.77, per 1000 atoms: 0.66 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: 2.77 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.97 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: 2.57 Time building geometry restraints manager: 3.10 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: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.190 ------------------------------------------------------------------------------- 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= 0.193 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 *********************** 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 : 1.049 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: 0.2452 time to fit residues: 50.6890 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 : 1.022 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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= 0.203 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 *********************** 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 : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 478 LYS cc_start: 0.8094 (ttpt) cc_final: 0.7755 (ttmm) REVERT: A 611 MET cc_start: 0.7696 (mtp) cc_final: 0.7437 (mtp) REVERT: A 615 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7238 (ttpp) REVERT: A 810 MET cc_start: 0.5794 (mmm) cc_final: 0.5497 (mmm) REVERT: A 887 PHE cc_start: 0.8817 (m-10) cc_final: 0.8510 (m-80) REVERT: B 173 ASN cc_start: 0.7458 (t0) cc_final: 0.7194 (p0) outliers start: 5 outliers final: 3 residues processed: 111 average time/residue: 0.2381 time to fit residues: 36.3608 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 : 1.046 ------------------------------------------------------------------------------- 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 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8867 Z= 0.184 Angle : 0.535 13.954 12019 Z= 0.271 Chirality : 0.040 0.293 1428 Planarity : 0.004 0.043 1513 Dihedral : 8.694 161.558 1161 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.01 % Allowed : 8.15 % Favored : 90.85 % 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: 1.88 (0.26), residues: 1077 helix: 1.76 (0.19), residues: 770 sheet: -0.79 (0.69), residues: 52 loop : 0.27 (0.43), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 66 HIS 0.004 0.001 HIS B 32 PHE 0.020 0.002 PHE B 28 TYR 0.020 0.001 TYR A 68 ARG 0.004 0.000 ARG B 131 *********************** 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 106 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 284 ASP cc_start: 0.7502 (m-30) cc_final: 0.7104 (m-30) REVERT: A 478 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7710 (ttmm) REVERT: B 173 ASN cc_start: 0.7436 (t0) cc_final: 0.7153 (p0) outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 0.2169 time to fit residues: 30.8021 Evaluate side-chains 93 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 97 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.1980 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8867 Z= 0.167 Angle : 0.511 11.106 12019 Z= 0.258 Chirality : 0.038 0.152 1428 Planarity : 0.004 0.046 1513 Dihedral : 8.398 156.183 1161 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.11 % Allowed : 9.26 % Favored : 89.64 % 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: 2.01 (0.26), residues: 1077 helix: 1.91 (0.19), residues: 769 sheet: -0.61 (0.70), residues: 52 loop : 0.11 (0.42), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 66 HIS 0.003 0.001 HIS B 32 PHE 0.019 0.001 PHE B 28 TYR 0.010 0.001 TYR A 511 ARG 0.004 0.001 ARG A 705 *********************** 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: 11 poor density : 91 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6904 (mp0) REVERT: A 574 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8059 (tt) REVERT: B 38 GLU cc_start: 0.7556 (tp30) cc_final: 0.7345 (tm-30) outliers start: 11 outliers final: 7 residues processed: 99 average time/residue: 0.2010 time to fit residues: 28.8028 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 : 1.020 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 40.0000 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.1980 chunk 93 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 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** A 876 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8867 Z= 0.166 Angle : 0.496 8.179 12019 Z= 0.253 Chirality : 0.038 0.187 1428 Planarity : 0.004 0.045 1513 Dihedral : 8.122 152.269 1161 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.21 % Allowed : 9.66 % Favored : 89.13 % 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: 2.14 (0.26), residues: 1077 helix: 2.02 (0.18), residues: 770 sheet: -0.48 (0.73), residues: 52 loop : 0.07 (0.42), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 813 HIS 0.003 0.001 HIS B 32 PHE 0.018 0.002 PHE B 28 TYR 0.010 0.001 TYR A 511 ARG 0.004 0.000 ARG A 825 *********************** 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 103 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: A 574 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8116 (tt) outliers start: 12 outliers final: 8 residues processed: 99 average time/residue: 0.2088 time to fit residues: 29.3448 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 : 1.031 ------------------------------------------------------------------------------- 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 291 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 574 LEU 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 35 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** B 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2518 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= 0.188 Angle : 0.507 8.358 12019 Z= 0.260 Chirality : 0.039 0.150 1428 Planarity : 0.004 0.043 1513 Dihedral : 7.967 149.944 1161 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.21 % Allowed : 11.17 % Favored : 87.63 % 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: 2.19 (0.26), residues: 1077 helix: 2.01 (0.19), residues: 771 sheet: 0.52 (0.90), residues: 39 loop : 0.03 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 28 HIS 0.004 0.001 HIS B 32 PHE 0.019 0.002 PHE B 28 TYR 0.012 0.001 TYR B 100 ARG 0.004 0.000 ARG A 705 *********************** 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: 12 poor density : 87 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: A 574 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8131 (tt) REVERT: A 745 PHE cc_start: 0.8153 (m-10) cc_final: 0.7891 (m-10) outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 0.2243 time to fit residues: 29.6047 Evaluate side-chains 92 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 100 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 0.4980 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8867 Z= 0.167 Angle : 0.503 9.514 12019 Z= 0.257 Chirality : 0.038 0.223 1428 Planarity : 0.004 0.042 1513 Dihedral : 7.755 146.774 1161 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.51 % Allowed : 11.27 % 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 (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: 2.23 (0.26), residues: 1077 helix: 2.07 (0.19), residues: 771 sheet: 0.66 (0.91), residues: 39 loop : -0.09 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 813 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE B 28 TYR 0.010 0.001 TYR A 697 ARG 0.007 0.000 ARG A 705 *********************** 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 104 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6665 (mp0) REVERT: A 284 ASP cc_start: 0.7378 (m-30) cc_final: 0.6988 (m-30) REVERT: A 574 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8119 (tt) REVERT: A 707 MET cc_start: 0.7781 (tpp) cc_final: 0.7333 (mpp) REVERT: A 745 PHE cc_start: 0.8097 (m-10) cc_final: 0.7823 (m-10) outliers start: 15 outliers final: 9 residues processed: 100 average time/residue: 0.2078 time to fit residues: 29.6739 Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 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 B residue 137 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 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 : 0.004 0.052 8867 Z= 0.260 Angle : 0.560 10.911 12019 Z= 0.282 Chirality : 0.040 0.172 1428 Planarity : 0.004 0.045 1513 Dihedral : 7.713 146.950 1161 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.41 % Allowed : 11.87 % 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 (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: 2.07 (0.26), residues: 1077 helix: 1.96 (0.19), residues: 771 sheet: 0.53 (0.93), residues: 39 loop : -0.18 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.004 0.001 HIS B 141 PHE 0.021 0.002 PHE B 28 TYR 0.014 0.001 TYR B 100 ARG 0.008 0.001 ARG A 705 *********************** 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 102 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6648 (mp0) REVERT: A 478 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7672 (ttmm) REVERT: A 570 ARG cc_start: 0.8070 (mmm160) cc_final: 0.7862 (mmm160) REVERT: A 574 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8127 (tt) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.2303 time to fit residues: 31.4896 Evaluate side-chains 96 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8867 Z= 0.162 Angle : 0.522 11.027 12019 Z= 0.263 Chirality : 0.038 0.156 1428 Planarity : 0.004 0.048 1513 Dihedral : 7.518 143.933 1161 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.21 % Allowed : 12.37 % 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: 2.18 (0.26), residues: 1077 helix: 2.07 (0.18), residues: 772 sheet: 0.65 (0.92), residues: 39 loop : -0.26 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.003 0.001 HIS B 32 PHE 0.017 0.001 PHE B 28 TYR 0.010 0.001 TYR A 697 ARG 0.010 0.001 ARG A 705 *********************** 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 96 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.6612 (mp0) REVERT: A 284 ASP cc_start: 0.7027 (m-30) cc_final: 0.6685 (m-30) REVERT: A 574 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8086 (tt) REVERT: A 745 PHE cc_start: 0.7950 (m-10) cc_final: 0.7608 (m-80) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1915 time to fit residues: 25.7564 Evaluate side-chains 94 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 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 102 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8867 Z= 0.178 Angle : 0.526 11.932 12019 Z= 0.264 Chirality : 0.039 0.157 1428 Planarity : 0.004 0.049 1513 Dihedral : 7.371 142.696 1161 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.11 % Allowed : 12.47 % 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: 2.20 (0.26), residues: 1077 helix: 2.08 (0.18), residues: 772 sheet: 0.81 (0.94), residues: 39 loop : -0.27 (0.40), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 28 HIS 0.003 0.001 HIS B 141 PHE 0.018 0.001 PHE B 28 TYR 0.010 0.001 TYR A 697 ARG 0.009 0.001 ARG A 705 ********************** 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: 11 poor density : 84 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6564 (mp0) REVERT: A 284 ASP cc_start: 0.7025 (m-30) cc_final: 0.6652 (m-30) REVERT: A 574 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 745 PHE cc_start: 0.7952 (m-10) cc_final: 0.7472 (m-80) REVERT: B 128 VAL cc_start: 0.7770 (t) cc_final: 0.7472 (m) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.1973 time to fit residues: 26.1799 Evaluate side-chains 95 residues out of total 994 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- 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 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 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 91 optimal weight: 0.3980 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.162501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114940 restraints weight = 11379.386| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.97 r_work: 0.3143 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8867 Z= 0.154 Angle : 0.509 11.822 12019 Z= 0.256 Chirality : 0.038 0.155 1428 Planarity : 0.004 0.050 1513 Dihedral : 7.104 139.501 1161 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.01 % Allowed : 12.68 % Favored : 86.32 % 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: 2.28 (0.26), residues: 1077 helix: 2.18 (0.18), residues: 772 sheet: -0.08 (0.76), residues: 52 loop : -0.21 (0.42), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 813 HIS 0.003 0.001 HIS B 32 PHE 0.015 0.001 PHE B 28 TYR 0.011 0.001 TYR A 697 ARG 0.009 0.001 ARG A 705 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1883.07 seconds wall clock time: 35 minutes 8.03 seconds (2108.03 seconds total)