Starting phenix.real_space_refine on Wed Aug 5 09:15:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8q_63718/08_2026/9m8q_63718.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 79 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 5417 2.51 5 N 1541 2.21 5 O 1934 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9000 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 904, 7303 Classifications: {'peptide': 904} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 887} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 1165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1165 Classifications: {'RNA': 55} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 25, 'rna3p_pyr': 22} Link IDs: {'rna2p': 8, 'rna3p': 46} Chain: "C" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 531 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 14} Link IDs: {'rna3p': 24} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.55, per 1000 atoms: 0.17 Number of scatterers: 9000 At special positions: 0 Unit cell: (119.7, 94.05, 104.31, 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 28 16.00 P 79 15.00 Mg 1 11.99 O 1934 8.00 N 1541 7.00 C 5417 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 251.1 milliseconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1722 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 3 sheets defined 67.3% alpha, 2.9% beta 12 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.751A pdb=" N GLY A 11 " --> pdb=" O SER A 7 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 99 through 109 removed outlier: 3.525A pdb=" N LEU A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 147 removed outlier: 3.634A pdb=" N HIS A 124 " --> pdb=" O ILE A 120 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU A 133 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLU A 135 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 removed outlier: 3.708A pdb=" N ASP A 171 " --> pdb=" O ASP A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.913A pdb=" N ASN A 180 " --> pdb=" O ALA A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 201 removed outlier: 3.710A pdb=" N ASN A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 208 removed outlier: 3.664A pdb=" N TYR A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 243 removed outlier: 3.714A pdb=" N CYS A 228 " --> pdb=" O TYR A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 290 Processing helix chain 'A' and resid 291 through 300 removed outlier: 3.584A pdb=" N VAL A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 318 Processing helix chain 'A' and resid 328 through 338 removed outlier: 3.594A pdb=" N LEU A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.670A pdb=" N SER A 354 " --> pdb=" O VAL A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 355 through 385 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.946A pdb=" N ASP A 396 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 removed outlier: 4.497A pdb=" N ASP A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU A 418 " --> pdb=" O LEU A 414 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 419 " --> pdb=" O TYR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 436 removed outlier: 3.635A pdb=" N MET A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.537A pdb=" N LYS A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 505 removed outlier: 3.621A pdb=" N ASN A 482 " --> pdb=" O GLY A 478 " (cutoff:3.500A) Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 516 through 519 removed outlier: 3.572A pdb=" N LYS A 519 " --> pdb=" O ALA A 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 516 through 519' Processing helix chain 'A' and resid 520 through 535 Processing helix chain 'A' and resid 544 through 556 removed outlier: 3.637A pdb=" N ILE A 550 " --> pdb=" O ARG A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 4.193A pdb=" N SER A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 597 Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.794A pdb=" N LEU A 605 " --> pdb=" O ARG A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.538A pdb=" N VAL A 627 " --> pdb=" O VAL A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 655 removed outlier: 3.687A pdb=" N TYR A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 674 removed outlier: 3.735A pdb=" N THR A 670 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS A 671 " --> pdb=" O ASP A 667 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 704 removed outlier: 3.701A pdb=" N LYS A 700 " --> pdb=" O ALA A 696 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N PHE A 701 " --> pdb=" O GLU A 697 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LYS A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 744 removed outlier: 3.712A pdb=" N TYR A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU A 709 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N THR A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 744 " --> pdb=" O TYR A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 753 removed outlier: 4.286A pdb=" N GLU A 753 " --> pdb=" O LYS A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 765 Processing helix chain 'A' and resid 774 through 792 Processing helix chain 'A' and resid 797 through 805 removed outlier: 3.539A pdb=" N ASN A 803 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 827 removed outlier: 3.585A pdb=" N LYS A 812 " --> pdb=" O SER A 808 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN A 821 " --> pdb=" O THR A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 834 Processing helix chain 'A' and resid 835 through 847 removed outlier: 3.636A pdb=" N LEU A 847 " --> pdb=" O ARG A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 Processing helix chain 'A' and resid 865 through 870 Processing helix chain 'A' and resid 882 through 899 removed outlier: 3.958A pdb=" N GLU A 898 " --> pdb=" O ILE A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 918 Processing helix chain 'A' and resid 921 through 929 Processing helix chain 'A' and resid 930 through 933 Processing helix chain 'A' and resid 935 through 942 Processing helix chain 'A' and resid 944 through 949 removed outlier: 4.609A pdb=" N ASP A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 20 removed outlier: 3.585A pdb=" N SER A 16 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 28 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG A 36 " --> pdb=" O THR A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 59 removed outlier: 3.687A pdb=" N GLU A 58 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL A 81 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 215 381 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.27 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2495 1.34 - 1.46: 2042 1.46 - 1.57: 4588 1.57 - 1.69: 157 1.69 - 1.81: 48 Bond restraints: 9330 Sorted by residual: bond pdb=" C TYR A 910 " pdb=" O TYR A 910 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.19e-02 7.06e+03 1.24e+01 bond pdb=" C LYS A 906 " pdb=" O LYS A 906 " ideal model delta sigma weight residual 1.236 1.273 -0.037 1.15e-02 7.56e+03 1.03e+01 bond pdb=" N ASN A 915 " pdb=" CA ASN A 915 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.21e-02 6.83e+03 8.91e+00 bond pdb=" CA SER A 908 " pdb=" CB SER A 908 " ideal model delta sigma weight residual 1.529 1.490 0.039 1.55e-02 4.16e+03 6.27e+00 bond pdb=" N VAL A 907 " pdb=" CA VAL A 907 " ideal model delta sigma weight residual 1.460 1.490 -0.030 1.26e-02 6.30e+03 5.56e+00 ... (remaining 9325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.87: 12950 6.87 - 13.75: 4 13.75 - 20.62: 0 20.62 - 27.50: 2 27.50 - 34.37: 1 Bond angle restraints: 12957 Sorted by residual: angle pdb=" O3' C B -1 " pdb=" P G B 1 " pdb=" O5' G B 1 " ideal model delta sigma weight residual 104.00 131.43 -27.43 1.90e+00 2.77e-01 2.08e+02 angle pdb=" O3' C B -1 " pdb=" P G B 1 " pdb=" OP2 G B 1 " ideal model delta sigma weight residual 108.00 73.63 34.37 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C3' C B 2 " pdb=" O3' C B 2 " pdb=" P C B 3 " ideal model delta sigma weight residual 119.70 108.97 10.73 1.20e+00 6.94e-01 8.00e+01 angle pdb=" C3' C B -1 " pdb=" O3' C B -1 " pdb=" P G B 1 " ideal model delta sigma weight residual 119.70 109.42 10.28 1.20e+00 6.94e-01 7.34e+01 angle pdb=" OP2 G B 1 " pdb=" P G B 1 " pdb=" O5' G B 1 " ideal model delta sigma weight residual 108.00 86.23 21.77 3.00e+00 1.11e-01 5.27e+01 ... (remaining 12952 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.30: 5075 20.30 - 40.59: 475 40.59 - 60.89: 117 60.89 - 81.18: 77 81.18 - 101.48: 2 Dihedral angle restraints: 5746 sinusoidal: 3072 harmonic: 2674 Sorted by residual: dihedral pdb=" CA ASN A 290 " pdb=" C ASN A 290 " pdb=" N SER A 291 " pdb=" CA SER A 291 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C4' C B 2 " pdb=" O4' C B 2 " pdb=" C1' C B 2 " pdb=" C2' C B 2 " ideal model delta sinusoidal sigma weight residual -21.00 6.33 -27.33 1 8.00e+00 1.56e-02 1.67e+01 dihedral pdb=" C4' C B -1 " pdb=" O4' C B -1 " pdb=" C1' C B -1 " pdb=" C2' C B -1 " ideal model delta sinusoidal sigma weight residual -21.00 3.73 -24.73 1 8.00e+00 1.56e-02 1.38e+01 ... (remaining 5743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1452 0.134 - 0.268: 30 0.268 - 0.403: 0 0.403 - 0.537: 3 0.537 - 0.671: 1 Chirality restraints: 1486 Sorted by residual: chirality pdb=" P G B 1 " pdb=" OP1 G B 1 " pdb=" OP2 G B 1 " pdb=" O5' G B 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.08 -0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" P C B -1 " pdb=" OP1 C B -1 " pdb=" OP2 C B -1 " pdb=" O5' C B -1 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" P C B 2 " pdb=" OP1 C B 2 " pdb=" OP2 C B 2 " pdb=" O5' C B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.82 -0.41 2.00e-01 2.50e+01 4.27e+00 ... (remaining 1483 not shown) Planarity restraints: 1373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 904 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C SER A 904 " 0.036 2.00e-02 2.50e+03 pdb=" O SER A 904 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY A 905 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 16 " -0.027 2.00e-02 2.50e+03 1.13e-02 3.86e+00 pdb=" N9 G B 16 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G B 16 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G B 16 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 16 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G B 16 " -0.006 2.00e-02 2.50e+03 pdb=" O6 G B 16 " -0.007 2.00e-02 2.50e+03 pdb=" N1 G B 16 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G B 16 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 16 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G B 16 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G B 16 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 936 " 0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO A 937 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 937 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 937 " 0.027 5.00e-02 4.00e+02 ... (remaining 1370 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 438 2.72 - 3.26: 9080 3.26 - 3.81: 14548 3.81 - 4.35: 17717 4.35 - 4.90: 28639 Nonbonded interactions: 70422 Sorted by model distance: nonbonded pdb=" O TYR A 164 " pdb=" OH TYR A 229 " model vdw 2.169 3.040 nonbonded pdb=" OG SER A 214 " pdb=" OD1 ASN A 223 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASN A 590 " pdb=" ND2 ASN A 594 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG A 254 " pdb=" OH TYR A 515 " model vdw 2.246 3.120 nonbonded pdb=" O GLY A 326 " pdb=" O2' A B 4 " model vdw 2.247 3.040 ... (remaining 70417 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=0.01 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 8.500 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9330 Z= 0.221 Angle : 0.838 34.369 12957 Z= 0.504 Chirality : 0.055 0.671 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.714 101.477 4024 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.27), residues: 894 helix: 0.70 (0.22), residues: 509 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 546 TYR 0.023 0.002 TYR A 297 PHE 0.016 0.002 PHE A 884 TRP 0.009 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.22 ( 9330) covalent geometry : angle 0.83776 / 0.50 (12957) hydrogen bonds : bond 0.16427 / 11.00 ( 409) hydrogen bonds : angle 7.25282 / 5.12 ( 1163) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.290 Fit side-chains REVERT: A 19 VAL cc_start: 0.8123 (t) cc_final: 0.7867 (p) REVERT: A 173 GLU cc_start: 0.7744 (mp0) cc_final: 0.7454 (mp0) REVERT: A 277 ASP cc_start: 0.6566 (m-30) cc_final: 0.6206 (m-30) REVERT: A 334 GLU cc_start: 0.5209 (mm-30) cc_final: 0.4758 (mm-30) REVERT: A 734 GLU cc_start: 0.7063 (tp30) cc_final: 0.6652 (tp30) REVERT: A 832 TYR cc_start: 0.7266 (m-80) cc_final: 0.6616 (m-80) REVERT: A 833 LEU cc_start: 0.8519 (mt) cc_final: 0.8308 (mp) REVERT: A 865 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5592 (mm-30) REVERT: A 908 SER cc_start: 0.8284 (t) cc_final: 0.7872 (m) REVERT: A 928 LEU cc_start: 0.7008 (mt) cc_final: 0.6762 (mp) REVERT: A 944 ILE cc_start: 0.8425 (mm) cc_final: 0.8134 (mm) REVERT: A 949 ASP cc_start: 0.6775 (t70) cc_final: 0.6268 (t70) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.0915 time to fit residues: 17.8716 Evaluate side-chains 133 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 916 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.179839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.159205 restraints weight = 13384.129| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 2.05 r_work: 0.3840 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3843 r_free = 0.3843 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9330 Z= 0.197 Angle : 0.618 9.281 12957 Z= 0.346 Chirality : 0.043 0.361 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.738 83.392 2243 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.77 % Allowed : 9.16 % Favored : 90.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.27), residues: 894 helix: 0.67 (0.22), residues: 529 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 648 TYR 0.022 0.002 TYR A 678 PHE 0.018 0.002 PHE A 465 TRP 0.008 0.002 TRP A 241 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 ( 9330) covalent geometry : angle 0.61835 / 0.35 (12957) hydrogen bonds : bond 0.08128 / 5.48 ( 409) hydrogen bonds : angle 5.33604 / 3.78 ( 1163) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.173 Fit side-chains REVERT: A 96 MET cc_start: 0.4700 (mmt) cc_final: 0.4223 (mmt) REVERT: A 173 GLU cc_start: 0.7805 (mp0) cc_final: 0.7453 (mp0) REVERT: A 256 TRP cc_start: 0.6406 (t60) cc_final: 0.5911 (t60) REVERT: A 277 ASP cc_start: 0.7074 (m-30) cc_final: 0.6682 (m-30) REVERT: A 334 GLU cc_start: 0.5409 (mm-30) cc_final: 0.4774 (mm-30) REVERT: A 734 GLU cc_start: 0.7462 (tp30) cc_final: 0.7118 (tp30) REVERT: A 832 TYR cc_start: 0.7586 (m-80) cc_final: 0.6863 (m-80) REVERT: A 865 GLU cc_start: 0.6484 (mm-30) cc_final: 0.6146 (mm-30) REVERT: A 908 SER cc_start: 0.8439 (t) cc_final: 0.7868 (m) REVERT: A 909 GLU cc_start: 0.6408 (tm-30) cc_final: 0.6179 (tm-30) REVERT: A 928 LEU cc_start: 0.7259 (mt) cc_final: 0.7044 (mp) REVERT: A 944 ILE cc_start: 0.8260 (mm) cc_final: 0.7983 (mm) outliers start: 6 outliers final: 4 residues processed: 139 average time/residue: 0.0864 time to fit residues: 16.3323 Evaluate side-chains 140 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 873 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.0000 chunk 57 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 ASN A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.180188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.160321 restraints weight = 13388.289| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.93 r_work: 0.3863 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3709 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3712 r_free = 0.3712 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9330 Z= 0.142 Angle : 0.526 7.022 12957 Z= 0.298 Chirality : 0.039 0.301 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.630 74.792 2241 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.42 % Allowed : 12.65 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.28), residues: 894 helix: 0.87 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.65 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 546 TYR 0.019 0.002 TYR A 920 PHE 0.015 0.001 PHE A 465 TRP 0.009 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 ( 9330) covalent geometry : angle 0.52633 / 0.30 (12957) hydrogen bonds : bond 0.07276 / 4.98 ( 409) hydrogen bonds : angle 4.98112 / 3.53 ( 1163) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6870 (m-30) cc_final: 0.6660 (m-30) REVERT: A 173 GLU cc_start: 0.7960 (mp0) cc_final: 0.7586 (mp0) REVERT: A 256 TRP cc_start: 0.6483 (t60) cc_final: 0.5944 (t60) REVERT: A 277 ASP cc_start: 0.7208 (m-30) cc_final: 0.6841 (m-30) REVERT: A 334 GLU cc_start: 0.5426 (mm-30) cc_final: 0.4474 (mm-30) REVERT: A 496 GLN cc_start: 0.7360 (pp30) cc_final: 0.7115 (pp30) REVERT: A 819 GLN cc_start: 0.8379 (tp40) cc_final: 0.8112 (tp-100) REVERT: A 832 TYR cc_start: 0.7702 (m-80) cc_final: 0.7040 (m-80) REVERT: A 865 GLU cc_start: 0.6684 (mm-30) cc_final: 0.6330 (mm-30) REVERT: A 908 SER cc_start: 0.8573 (t) cc_final: 0.8002 (m) REVERT: A 909 GLU cc_start: 0.6827 (tm-30) cc_final: 0.6491 (tm-30) REVERT: A 932 PHE cc_start: 0.7532 (m-10) cc_final: 0.7314 (m-10) outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 0.0925 time to fit residues: 17.0835 Evaluate side-chains 135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 873 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.2980 chunk 88 optimal weight: 0.0020 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.177978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.157451 restraints weight = 13456.136| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.06 r_work: 0.3822 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3821 r_free = 0.3821 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9330 Z= 0.187 Angle : 0.555 9.898 12957 Z= 0.311 Chirality : 0.040 0.202 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.680 74.631 2241 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.68 % Allowed : 14.19 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.28), residues: 894 helix: 0.86 (0.22), residues: 533 sheet: -3.41 (2.17), residues: 6 loop : -1.64 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 333 TYR 0.019 0.002 TYR A 873 PHE 0.018 0.002 PHE A 465 TRP 0.009 0.002 TRP A 423 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.19 ( 9330) covalent geometry : angle 0.55473 / 0.31 (12957) hydrogen bonds : bond 0.07351 / 5.00 ( 409) hydrogen bonds : angle 4.97497 / 3.51 ( 1163) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.4686 (mmt) cc_final: 0.4284 (mmt) REVERT: A 128 ASP cc_start: 0.6649 (m-30) cc_final: 0.6400 (m-30) REVERT: A 173 GLU cc_start: 0.7906 (mp0) cc_final: 0.7533 (mp0) REVERT: A 254 ARG cc_start: 0.6313 (ttp80) cc_final: 0.6048 (ttp80) REVERT: A 256 TRP cc_start: 0.6519 (t60) cc_final: 0.5904 (t60) REVERT: A 277 ASP cc_start: 0.7073 (m-30) cc_final: 0.6674 (m-30) REVERT: A 334 GLU cc_start: 0.5533 (mm-30) cc_final: 0.4871 (mm-30) REVERT: A 496 GLN cc_start: 0.7161 (pp30) cc_final: 0.6901 (pp30) REVERT: A 832 TYR cc_start: 0.7613 (m-80) cc_final: 0.6868 (m-80) REVERT: A 865 GLU cc_start: 0.6496 (mm-30) cc_final: 0.6159 (mm-30) REVERT: A 895 ILE cc_start: 0.7477 (mm) cc_final: 0.7231 (mt) REVERT: A 908 SER cc_start: 0.8525 (t) cc_final: 0.7988 (m) REVERT: A 909 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6357 (tm-30) REVERT: A 932 PHE cc_start: 0.7369 (m-10) cc_final: 0.7162 (m-10) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.0877 time to fit residues: 17.2381 Evaluate side-chains 143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 916 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 90 optimal weight: 4.9990 chunk 21 optimal weight: 0.0370 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 885 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.179402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.159517 restraints weight = 13474.871| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.97 r_work: 0.3847 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9330 Z= 0.138 Angle : 0.523 14.369 12957 Z= 0.291 Chirality : 0.038 0.177 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.691 74.742 2241 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.19 % Allowed : 16.00 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.28), residues: 894 helix: 0.94 (0.22), residues: 532 sheet: -3.44 (2.04), residues: 6 loop : -1.63 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 278 TYR 0.017 0.001 TYR A 873 PHE 0.014 0.001 PHE A 465 TRP 0.011 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 9330) covalent geometry : angle 0.52334 / 0.29 (12957) hydrogen bonds : bond 0.06930 / 4.75 ( 409) hydrogen bonds : angle 4.83360 / 3.43 ( 1163) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7607 (tm-30) REVERT: A 96 MET cc_start: 0.4711 (mmt) cc_final: 0.4351 (mmt) REVERT: A 128 ASP cc_start: 0.6563 (m-30) cc_final: 0.6317 (m-30) REVERT: A 162 THR cc_start: 0.5737 (OUTLIER) cc_final: 0.5484 (t) REVERT: A 173 GLU cc_start: 0.7920 (mp0) cc_final: 0.7569 (mp0) REVERT: A 256 TRP cc_start: 0.6410 (t60) cc_final: 0.5717 (t60) REVERT: A 334 GLU cc_start: 0.5474 (mm-30) cc_final: 0.4822 (mm-30) REVERT: A 474 MET cc_start: 0.8412 (ttm) cc_final: 0.8164 (ttm) REVERT: A 496 GLN cc_start: 0.7124 (pp30) cc_final: 0.6883 (pp30) REVERT: A 660 LYS cc_start: 0.7975 (mttp) cc_final: 0.7672 (mtmm) REVERT: A 676 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5927 (tpp) REVERT: A 717 LYS cc_start: 0.6547 (mmtm) cc_final: 0.6279 (mmtp) REVERT: A 734 GLU cc_start: 0.7454 (tp30) cc_final: 0.7097 (tp30) REVERT: A 832 TYR cc_start: 0.7525 (m-80) cc_final: 0.6890 (m-80) REVERT: A 865 GLU cc_start: 0.6412 (mm-30) cc_final: 0.5974 (mm-30) REVERT: A 895 ILE cc_start: 0.7556 (mm) cc_final: 0.7352 (mt) REVERT: A 909 GLU cc_start: 0.6737 (tm-30) cc_final: 0.6328 (tm-30) outliers start: 17 outliers final: 12 residues processed: 146 average time/residue: 0.0982 time to fit residues: 19.3103 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 676 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 949 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 30 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.178576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.159283 restraints weight = 13451.737| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.85 r_work: 0.3852 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3705 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3705 r_free = 0.3705 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3705 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9330 Z= 0.152 Angle : 0.539 14.337 12957 Z= 0.297 Chirality : 0.038 0.188 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.735 74.641 2241 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.81 % Allowed : 18.06 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 894 helix: 1.00 (0.22), residues: 531 sheet: -3.44 (2.01), residues: 6 loop : -1.63 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 254 TYR 0.020 0.002 TYR A 873 PHE 0.016 0.002 PHE A 465 TRP 0.012 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 ( 9330) covalent geometry : angle 0.53896 / 0.30 (12957) hydrogen bonds : bond 0.06876 / 4.70 ( 409) hydrogen bonds : angle 4.79203 / 3.39 ( 1163) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 96 MET cc_start: 0.5108 (mmt) cc_final: 0.4633 (mmt) REVERT: A 128 ASP cc_start: 0.6827 (m-30) cc_final: 0.6595 (m-30) REVERT: A 173 GLU cc_start: 0.8006 (mp0) cc_final: 0.7615 (mp0) REVERT: A 256 TRP cc_start: 0.6535 (t60) cc_final: 0.5849 (t60) REVERT: A 325 LEU cc_start: 0.4715 (OUTLIER) cc_final: 0.4451 (pt) REVERT: A 334 GLU cc_start: 0.5457 (mm-30) cc_final: 0.4444 (tp30) REVERT: A 339 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6913 (mtp-110) REVERT: A 496 GLN cc_start: 0.7372 (pp30) cc_final: 0.7134 (pp30) REVERT: A 588 MET cc_start: 0.6285 (OUTLIER) cc_final: 0.5700 (tmm) REVERT: A 734 GLU cc_start: 0.7672 (tp30) cc_final: 0.7345 (tp30) REVERT: A 832 TYR cc_start: 0.7619 (m-80) cc_final: 0.7036 (m-80) REVERT: A 865 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6416 (mm-30) REVERT: A 909 GLU cc_start: 0.6942 (tm-30) cc_final: 0.6511 (tm-30) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.1046 time to fit residues: 20.5012 Evaluate side-chains 153 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.0010 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.175997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156007 restraints weight = 13582.781| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.97 r_work: 0.3803 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9330 Z= 0.229 Angle : 0.613 13.882 12957 Z= 0.335 Chirality : 0.042 0.206 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.877 74.554 2241 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 2.45 % Allowed : 18.97 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.28), residues: 894 helix: 0.83 (0.22), residues: 532 sheet: -3.48 (1.96), residues: 6 loop : -1.64 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 725 TYR 0.019 0.002 TYR A 873 PHE 0.022 0.002 PHE A 465 TRP 0.010 0.003 TRP A 423 HIS 0.011 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.23 ( 9330) covalent geometry : angle 0.61299 / 0.33 (12957) hydrogen bonds : bond 0.07602 / 5.18 ( 409) hydrogen bonds : angle 5.00114 / 3.51 ( 1163) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7681 (tm-30) REVERT: A 128 ASP cc_start: 0.6614 (m-30) cc_final: 0.6362 (m-30) REVERT: A 173 GLU cc_start: 0.7932 (mp0) cc_final: 0.7556 (mp0) REVERT: A 256 TRP cc_start: 0.6475 (t60) cc_final: 0.5921 (t60) REVERT: A 334 GLU cc_start: 0.5415 (mm-30) cc_final: 0.4890 (mm-30) REVERT: A 496 GLN cc_start: 0.7233 (pp30) cc_final: 0.6913 (pp30) REVERT: A 832 TYR cc_start: 0.7500 (m-80) cc_final: 0.7018 (m-80) REVERT: A 865 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6039 (mm-30) REVERT: A 895 ILE cc_start: 0.7679 (mm) cc_final: 0.7432 (mt) REVERT: A 909 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6343 (tm-30) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.0948 time to fit residues: 19.0275 Evaluate side-chains 150 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 916 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.0470 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.4980 chunk 51 optimal weight: 0.0770 chunk 7 optimal weight: 0.0670 chunk 58 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 82 optimal weight: 0.0770 overall best weight: 0.1132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 ASN A 117 ASN A 285 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN A 885 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.180451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.161710 restraints weight = 13539.721| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.84 r_work: 0.3879 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9330 Z= 0.122 Angle : 0.557 14.713 12957 Z= 0.301 Chirality : 0.037 0.163 1486 Planarity : 0.004 0.047 1373 Dihedral : 17.758 74.632 2241 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.68 % Allowed : 20.00 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.28), residues: 894 helix: 1.02 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 546 TYR 0.018 0.001 TYR A 920 PHE 0.012 0.001 PHE A 534 TRP 0.012 0.002 TRP A 423 HIS 0.003 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 9330) covalent geometry : angle 0.55707 / 0.30 (12957) hydrogen bonds : bond 0.06698 / 4.64 ( 409) hydrogen bonds : angle 4.73228 / 3.35 ( 1163) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7696 (tm-30) REVERT: A 173 GLU cc_start: 0.8000 (mp0) cc_final: 0.7706 (mp0) REVERT: A 256 TRP cc_start: 0.6491 (t60) cc_final: 0.5730 (t60) REVERT: A 496 GLN cc_start: 0.7389 (pp30) cc_final: 0.7157 (pp30) REVERT: A 588 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5542 (tmm) REVERT: A 734 GLU cc_start: 0.7681 (tp30) cc_final: 0.7365 (tp30) REVERT: A 753 GLU cc_start: 0.7311 (tp30) cc_final: 0.7085 (tp30) REVERT: A 832 TYR cc_start: 0.7611 (m-80) cc_final: 0.7127 (m-80) REVERT: A 865 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6216 (mm-30) REVERT: A 909 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6526 (tm-30) outliers start: 13 outliers final: 11 residues processed: 151 average time/residue: 0.0943 time to fit residues: 19.1488 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.179085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.159198 restraints weight = 13375.751| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.94 r_work: 0.3848 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9330 Z= 0.152 Angle : 0.567 14.143 12957 Z= 0.306 Chirality : 0.038 0.189 1486 Planarity : 0.004 0.066 1373 Dihedral : 17.789 74.416 2241 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.06 % Allowed : 20.00 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.28), residues: 894 helix: 0.98 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.64 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 546 TYR 0.025 0.002 TYR A 678 PHE 0.013 0.002 PHE A 73 TRP 0.012 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9330) covalent geometry : angle 0.56669 / 0.31 (12957) hydrogen bonds : bond 0.06615 / 4.52 ( 409) hydrogen bonds : angle 4.76148 / 3.34 ( 1163) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7787 (tm-30) REVERT: A 173 GLU cc_start: 0.7984 (mp0) cc_final: 0.7661 (mp0) REVERT: A 256 TRP cc_start: 0.6499 (t60) cc_final: 0.5824 (t60) REVERT: A 496 GLN cc_start: 0.7464 (pp30) cc_final: 0.7200 (pp30) REVERT: A 588 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5636 (tmm) REVERT: A 734 GLU cc_start: 0.7695 (tp30) cc_final: 0.7311 (tp30) REVERT: A 753 GLU cc_start: 0.7398 (tp30) cc_final: 0.7181 (tp30) REVERT: A 832 TYR cc_start: 0.7622 (m-80) cc_final: 0.7127 (m-80) REVERT: A 865 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6261 (mm-30) REVERT: A 909 GLU cc_start: 0.7006 (tm-30) cc_final: 0.6536 (tm-30) outliers start: 16 outliers final: 12 residues processed: 145 average time/residue: 0.0970 time to fit residues: 18.7593 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.158996 restraints weight = 13462.837| |-----------------------------------------------------------------------------| r_work (start): 0.3952 rms_B_bonded: 1.89 r_work: 0.3848 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9330 Z= 0.156 Angle : 0.576 14.202 12957 Z= 0.309 Chirality : 0.039 0.182 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.809 74.549 2241 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.81 % Allowed : 20.00 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.28), residues: 894 helix: 0.97 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 339 TYR 0.026 0.002 TYR A 678 PHE 0.013 0.002 PHE A 73 TRP 0.013 0.002 TRP A 423 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 ( 9330) covalent geometry : angle 0.57560 / 0.31 (12957) hydrogen bonds : bond 0.06649 / 4.54 ( 409) hydrogen bonds : angle 4.74845 / 3.34 ( 1163) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 173 GLU cc_start: 0.7977 (mp0) cc_final: 0.7658 (mp0) REVERT: A 256 TRP cc_start: 0.6489 (t60) cc_final: 0.5817 (t60) REVERT: A 496 GLN cc_start: 0.7436 (pp30) cc_final: 0.7168 (pp30) REVERT: A 588 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.5632 (tmm) REVERT: A 753 GLU cc_start: 0.7416 (tp30) cc_final: 0.7203 (tp30) REVERT: A 832 TYR cc_start: 0.7613 (m-80) cc_final: 0.7131 (m-80) REVERT: A 847 LEU cc_start: 0.8067 (mt) cc_final: 0.7853 (mp) REVERT: A 865 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6248 (mm-30) REVERT: A 909 GLU cc_start: 0.7037 (tm-30) cc_final: 0.6561 (tm-30) outliers start: 14 outliers final: 11 residues processed: 144 average time/residue: 0.0940 time to fit residues: 18.1957 Evaluate side-chains 155 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 0.0050 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.178625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158687 restraints weight = 13372.560| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.96 r_work: 0.3841 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 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 0.037 9330 Z= 0.155 Angle : 0.573 14.211 12957 Z= 0.310 Chirality : 0.038 0.181 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.831 74.485 2241 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.81 % Allowed : 19.87 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.28), residues: 894 helix: 0.97 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.027 0.002 TYR A 678 PHE 0.013 0.001 PHE A 73 TRP 0.011 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 ( 9330) covalent geometry : angle 0.57274 / 0.31 (12957) hydrogen bonds : bond 0.06668 / 4.56 ( 409) hydrogen bonds : angle 4.79714 / 3.37 ( 1163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1972.57 seconds wall clock time: 34 minutes 31.31 seconds (2071.31 seconds total)