Starting phenix.real_space_refine on Thu Jul 2 16:14:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8q_63718/07_2026/9m8q_63718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8q_63718/07_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_63718/07_2026/9m8q_63718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8q_63718/07_2026/9m8q_63718.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8q_63718/07_2026/9m8q_63718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8q_63718/07_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-dev-6108/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: 1.37, per 1000 atoms: 0.15 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: 0.59 Conformation dependent library (CDL) restraints added in 251.7 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: 0.93 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: 1.61 Time building geometry restraints manager: 0.79 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: 12949 6.87 - 13.75: 5 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 1.50e+00 4.44e-01 3.35e+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 120.20 108.97 11.23 1.50e+00 4.44e-01 5.61e+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 angle pdb=" C3' C B -1 " pdb=" O3' C B -1 " pdb=" P G B 1 " ideal model delta sigma weight residual 120.20 109.42 10.78 1.50e+00 4.44e-01 5.17e+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: 1469 0.134 - 0.268: 13 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: 1.800 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.110 ------------------------------------------------------------------------------- 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= 0.210 Angle : 0.783 34.369 12957 Z= 0.450 Chirality : 0.047 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 0.00357 / 0.21 ( 9330) covalent geometry : angle 0.78296 / 0.45 (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 : 0.336 Fit side-chains REVERT: A 19 VAL cc_start: 0.8123 (t) cc_final: 0.7868 (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: 0.6207 (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: 0.6650 (tp30) REVERT: A 832 TYR cc_start: 0.7266 (m-80) cc_final: 0.6651 (m-80) REVERT: A 833 LEU cc_start: 0.8519 (mt) cc_final: 0.8306 (mp) REVERT: A 865 GLU cc_start: 0.6073 (mm-30) cc_final: 0.5593 (mm-30) REVERT: A 908 SER cc_start: 0.8284 (t) cc_final: 0.7873 (m) REVERT: A 928 LEU cc_start: 0.7008 (mt) cc_final: 0.6765 (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: 0.6263 (t70) outliers start: 2 outliers final: 1 residues processed: 143 average time/residue: 0.1136 time to fit residues: 21.7783 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 : 0.298 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.179754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160417 restraints weight = 13383.295| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.86 r_work: 0.3853 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3704 r_free = 0.3704 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-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: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1087 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= 0.198 Angle : 0.597 7.744 12957 Z= 0.342 Chirality : 0.041 0.247 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.786 86.477 2243 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 0.77 % Allowed : 9.55 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.27), residues: 894 helix: 0.69 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.72 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 648 TYR 0.021 0.002 TYR A 678 PHE 0.018 0.002 PHE A 465 TRP 0.008 0.003 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 0.59708 / 0.34 (12957) hydrogen bonds : bond 0.08021 / 5.41 ( 409) hydrogen bonds : angle 5.33619 / 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 145 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.278 Fit side-chains REVERT: A 173 GLU cc_start: 0.7850 (mp0) cc_final: 0.7486 (mp0) REVERT: A 256 TRP cc_start: 0.6497 (t60) cc_final: 0.6042 (t60) REVERT: A 277 ASP cc_start: 0.7215 (m-30) cc_final: 0.6851 (m-30) REVERT: A 334 GLU cc_start: 0.5474 (mm-30) cc_final: 0.4760 (mm-30) REVERT: A 734 GLU cc_start: 0.7684 (tp30) cc_final: 0.7358 (tp30) REVERT: A 832 TYR cc_start: 0.7724 (m-80) cc_final: 0.6985 (m-80) REVERT: A 865 GLU cc_start: 0.6665 (mm-30) cc_final: 0.6337 (mm-30) REVERT: A 908 SER cc_start: 0.8469 (t) cc_final: 0.7916 (m) REVERT: A 928 LEU cc_start: 0.7410 (mt) cc_final: 0.7195 (mp) REVERT: A 944 ILE cc_start: 0.8338 (mm) cc_final: 0.8059 (mm) outliers start: 6 outliers final: 4 residues processed: 140 average time/residue: 0.0925 time to fit residues: 17.4153 Evaluate side-chains 136 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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: 0.6980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 885 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.178281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.157622 restraints weight = 13390.630| |-----------------------------------------------------------------------------| r_work (start): 0.3936 rms_B_bonded: 2.07 r_work: 0.3825 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9330 Z= 0.172 Angle : 0.548 6.121 12957 Z= 0.314 Chirality : 0.040 0.236 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.739 75.022 2241 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.55 % Allowed : 12.65 % Favored : 85.81 % 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: -0.29 (0.27), residues: 894 helix: 0.78 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.69 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 546 TYR 0.019 0.002 TYR A 920 PHE 0.017 0.002 PHE A 465 TRP 0.008 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 9330) covalent geometry : angle 0.54831 / 0.31 (12957) hydrogen bonds : bond 0.07408 / 5.05 ( 409) hydrogen bonds : angle 5.07773 / 3.59 ( 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 143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7472 (tm-30) REVERT: A 128 ASP cc_start: 0.6652 (m-30) cc_final: 0.6410 (m-30) REVERT: A 173 GLU cc_start: 0.7904 (mp0) cc_final: 0.7620 (mp0) REVERT: A 256 TRP cc_start: 0.6454 (t60) cc_final: 0.5893 (t60) REVERT: A 277 ASP cc_start: 0.7076 (m-30) cc_final: 0.6684 (m-30) REVERT: A 496 GLN cc_start: 0.7149 (pp30) cc_final: 0.6901 (pp30) REVERT: A 819 GLN cc_start: 0.8312 (tp40) cc_final: 0.8068 (tp-100) REVERT: A 832 TYR cc_start: 0.7507 (m-80) cc_final: 0.6843 (m-80) REVERT: A 865 GLU cc_start: 0.6507 (mm-30) cc_final: 0.6155 (mm-30) REVERT: A 908 SER cc_start: 0.8546 (t) cc_final: 0.7999 (m) REVERT: A 928 LEU cc_start: 0.7287 (mt) cc_final: 0.7058 (mp) outliers start: 12 outliers final: 6 residues processed: 135 average time/residue: 0.1007 time to fit residues: 18.1874 Evaluate side-chains 134 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.210 ------------------------------------------------------------------------------- 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: 3.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 88 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4161 r_free = 0.4161 target = 0.177248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.156560 restraints weight = 13476.112| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.09 r_work: 0.3807 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3809 r_free = 0.3809 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9330 Z= 0.204 Angle : 0.571 10.714 12957 Z= 0.325 Chirality : 0.041 0.236 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.801 74.882 2241 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.94 % Allowed : 14.84 % Favored : 83.23 % 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: -0.33 (0.27), residues: 894 helix: 0.78 (0.22), residues: 532 sheet: -3.42 (2.17), residues: 6 loop : -1.72 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 333 TYR 0.030 0.002 TYR A 832 PHE 0.019 0.002 PHE A 465 TRP 0.009 0.002 TRP A 838 HIS 0.009 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 9330) covalent geometry : angle 0.57100 / 0.33 (12957) hydrogen bonds : bond 0.07518 / 5.11 ( 409) hydrogen bonds : angle 5.05228 / 3.56 ( 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 146 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 131 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7496 (tm-30) REVERT: A 128 ASP cc_start: 0.6640 (m-30) cc_final: 0.6408 (m-30) REVERT: A 173 GLU cc_start: 0.7888 (mp0) cc_final: 0.7596 (mp0) REVERT: A 254 ARG cc_start: 0.6326 (ttp80) cc_final: 0.6051 (ttp80) REVERT: A 256 TRP cc_start: 0.6498 (t60) cc_final: 0.5813 (t60) REVERT: A 277 ASP cc_start: 0.7115 (m-30) cc_final: 0.6725 (m-30) REVERT: A 496 GLN cc_start: 0.7187 (pp30) cc_final: 0.6906 (pp30) REVERT: A 832 TYR cc_start: 0.7448 (m-80) cc_final: 0.7043 (m-80) REVERT: A 865 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6195 (mm-30) REVERT: A 908 SER cc_start: 0.8548 (t) cc_final: 0.8005 (m) REVERT: A 928 LEU cc_start: 0.7337 (mt) cc_final: 0.7126 (mp) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.0845 time to fit residues: 15.8151 Evaluate side-chains 141 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 132 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 45 SER Chi-restraints excluded: chain A residue 132 ILE 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 873 TYR Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4184 r_free = 0.4184 target = 0.178683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159347 restraints weight = 13504.856| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 1.88 r_work: 0.3846 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- 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: 6 | |-----------------------------------------------------------------------------| |-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: 0.7051 moved from start: 0.1795 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= 0.145 Angle : 0.535 14.975 12957 Z= 0.299 Chirality : 0.038 0.230 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.751 74.993 2241 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.06 % Allowed : 17.16 % Favored : 80.77 % 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: -0.19 (0.28), residues: 894 helix: 0.88 (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 0.007 0.000 ARG A 546 TYR 0.017 0.002 TYR A 873 PHE 0.016 0.001 PHE A 884 TRP 0.010 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9330) covalent geometry : angle 0.53542 / 0.30 (12957) hydrogen bonds : bond 0.06943 / 4.75 ( 409) hydrogen bonds : angle 4.88458 / 3.46 ( 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 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 128 ASP cc_start: 0.6849 (m-30) cc_final: 0.6613 (m-30) REVERT: A 173 GLU cc_start: 0.7949 (mp0) cc_final: 0.7649 (mp0) REVERT: A 256 TRP cc_start: 0.6551 (t60) cc_final: 0.5867 (t60) REVERT: A 277 ASP cc_start: 0.7219 (m-30) cc_final: 0.6835 (m-30) REVERT: A 490 ASN cc_start: 0.7867 (m-40) cc_final: 0.7660 (m-40) REVERT: A 496 GLN cc_start: 0.7360 (pp30) cc_final: 0.7131 (pp30) REVERT: A 734 GLU cc_start: 0.7723 (tp30) cc_final: 0.7262 (tp30) REVERT: A 819 GLN cc_start: 0.8422 (tp40) cc_final: 0.8083 (tp-100) REVERT: A 832 TYR cc_start: 0.7518 (m-80) cc_final: 0.7209 (m-80) REVERT: A 865 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6384 (mm-30) REVERT: A 892 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: A 895 ILE cc_start: 0.7720 (mm) cc_final: 0.7502 (mt) REVERT: A 947 LEU cc_start: 0.8118 (mt) cc_final: 0.7850 (mp) outliers start: 16 outliers final: 10 residues processed: 141 average time/residue: 0.0888 time to fit residues: 16.7155 Evaluate side-chains 143 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 337 LEU 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 892 GLN Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159148 restraints weight = 13432.173| |-----------------------------------------------------------------------------| r_work (start): 0.3948 rms_B_bonded: 1.81 r_work: 0.3846 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 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 = 0.3703 r_free = 0.3703 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 (5 function evaluations) r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9330 Z= 0.164 Angle : 0.559 14.633 12957 Z= 0.307 Chirality : 0.039 0.218 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.797 74.859 2241 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.19 % Allowed : 18.84 % Favored : 78.97 % 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: -0.20 (0.28), residues: 894 helix: 0.91 (0.22), residues: 530 sheet: -3.44 (2.01), residues: 6 loop : -1.68 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 546 TYR 0.019 0.002 TYR A 873 PHE 0.017 0.002 PHE A 465 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 0.00349 / 0.16 ( 9330) covalent geometry : angle 0.55880 / 0.31 (12957) hydrogen bonds : bond 0.06982 / 4.77 ( 409) hydrogen bonds : angle 4.84685 / 3.42 ( 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: 17 poor density : 137 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7868 (tm-30) REVERT: A 128 ASP cc_start: 0.6845 (m-30) cc_final: 0.6607 (m-30) REVERT: A 162 THR cc_start: 0.6033 (OUTLIER) cc_final: 0.5752 (t) REVERT: A 173 GLU cc_start: 0.7977 (mp0) cc_final: 0.7592 (mp0) REVERT: A 256 TRP cc_start: 0.6568 (t60) cc_final: 0.5861 (t60) REVERT: A 277 ASP cc_start: 0.7220 (m-30) cc_final: 0.6825 (m-30) REVERT: A 325 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4368 (pt) REVERT: A 334 GLU cc_start: 0.5465 (mm-30) cc_final: 0.4887 (mm-30) REVERT: A 339 ARG cc_start: 0.7216 (mtp-110) cc_final: 0.6947 (mtp-110) REVERT: A 490 ASN cc_start: 0.7869 (m-40) cc_final: 0.7666 (m-40) REVERT: A 496 GLN cc_start: 0.7401 (pp30) cc_final: 0.7130 (pp30) REVERT: A 588 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5616 (tmm) REVERT: A 819 GLN cc_start: 0.8398 (tp40) cc_final: 0.8085 (tp-100) REVERT: A 832 TYR cc_start: 0.7537 (m-80) cc_final: 0.7054 (m-80) REVERT: A 865 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6240 (mm-30) REVERT: A 895 ILE cc_start: 0.7749 (mm) cc_final: 0.7519 (mt) REVERT: A 947 LEU cc_start: 0.8099 (mt) cc_final: 0.7821 (mp) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 0.0920 time to fit residues: 17.8064 Evaluate side-chains 149 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 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 755 LYS Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 873 TYR 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: 0.6980 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN A 851 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151608 restraints weight = 13614.114| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 1.88 r_work: 0.3765 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3609 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3612 r_free = 0.3612 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 9330 Z= 0.344 Angle : 0.736 13.714 12957 Z= 0.402 Chirality : 0.049 0.283 1486 Planarity : 0.005 0.051 1373 Dihedral : 18.137 74.708 2241 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 2.84 % Allowed : 19.35 % Favored : 77.81 % 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: -0.77 (0.27), residues: 894 helix: 0.41 (0.22), residues: 532 sheet: -3.67 (1.86), residues: 6 loop : -1.88 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 735 TYR 0.041 0.003 TYR A 832 PHE 0.034 0.003 PHE A 465 TRP 0.014 0.004 TRP A 838 HIS 0.016 0.002 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00763 / 0.34 ( 9330) covalent geometry : angle 0.73612 / 0.40 (12957) hydrogen bonds : bond 0.08807 / 5.99 ( 409) hydrogen bonds : angle 5.34647 / 3.74 ( 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 165 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7956 (tm-30) REVERT: A 36 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7426 (ttp-170) REVERT: A 128 ASP cc_start: 0.6897 (m-30) cc_final: 0.6664 (m-30) REVERT: A 146 ASN cc_start: 0.7794 (m-40) cc_final: 0.7418 (t0) REVERT: A 173 GLU cc_start: 0.7923 (mp0) cc_final: 0.7591 (mp0) REVERT: A 277 ASP cc_start: 0.7483 (m-30) cc_final: 0.7092 (m-30) REVERT: A 339 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.7065 (mtp-110) REVERT: A 490 ASN cc_start: 0.7917 (m-40) cc_final: 0.7689 (m-40) REVERT: A 819 GLN cc_start: 0.8536 (tp40) cc_final: 0.8208 (tp-100) REVERT: A 845 ASP cc_start: 0.7938 (m-30) cc_final: 0.7707 (m-30) REVERT: A 865 GLU cc_start: 0.6771 (mm-30) cc_final: 0.6300 (mm-30) REVERT: A 892 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7241 (mp10) REVERT: A 895 ILE cc_start: 0.7978 (mm) cc_final: 0.7709 (mt) outliers start: 22 outliers final: 16 residues processed: 148 average time/residue: 0.0903 time to fit residues: 17.8579 Evaluate side-chains 158 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 328 ASN 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 631 ILE Chi-restraints excluded: chain A residue 755 LYS Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP 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: 0.5980 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.175247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.156057 restraints weight = 13476.890| |-----------------------------------------------------------------------------| r_work (start): 0.3930 rms_B_bonded: 1.87 r_work: 0.3825 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3673 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3677 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3677 r_free = 0.3677 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3677 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2226 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= 0.144 Angle : 0.569 14.940 12957 Z= 0.315 Chirality : 0.039 0.228 1486 Planarity : 0.004 0.048 1373 Dihedral : 17.919 74.908 2241 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.71 % Allowed : 20.13 % Favored : 77.16 % 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: -0.47 (0.28), residues: 894 helix: 0.63 (0.22), residues: 540 sheet: -3.48 (1.86), residues: 6 loop : -1.77 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.018 0.002 TYR A 920 PHE 0.016 0.002 PHE A 465 TRP 0.011 0.002 TRP A 256 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 9330) covalent geometry : angle 0.56917 / 0.32 (12957) hydrogen bonds : bond 0.07239 / 5.00 ( 409) hydrogen bonds : angle 4.96077 / 3.50 ( 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: 21 poor density : 136 time to evaluate : 0.255 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 36 ARG cc_start: 0.7594 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: A 128 ASP cc_start: 0.6845 (m-30) cc_final: 0.6581 (m-30) REVERT: A 173 GLU cc_start: 0.7937 (mp0) cc_final: 0.7624 (mp0) REVERT: A 256 TRP cc_start: 0.6504 (t60) cc_final: 0.5987 (t60) REVERT: A 277 ASP cc_start: 0.7376 (m-30) cc_final: 0.6980 (m-30) REVERT: A 325 LEU cc_start: 0.4701 (OUTLIER) cc_final: 0.4366 (pt) REVERT: A 496 GLN cc_start: 0.7397 (pp30) cc_final: 0.7160 (pp30) REVERT: A 819 GLN cc_start: 0.8464 (tp40) cc_final: 0.8161 (tp-100) REVERT: A 865 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6237 (mm-30) REVERT: A 892 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: A 895 ILE cc_start: 0.7750 (mm) cc_final: 0.7484 (mt) REVERT: A 947 LEU cc_start: 0.8089 (mt) cc_final: 0.7795 (mp) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.1101 time to fit residues: 21.5036 Evaluate side-chains 151 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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 96 MET 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 571 THR 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 892 GLN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP Chi-restraints excluded: chain A residue 917 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.0770 chunk 75 optimal weight: 0.0270 chunk 62 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 69 optimal weight: 0.0040 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.3008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN A 285 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.176765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.157095 restraints weight = 13352.049| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.98 r_work: 0.3833 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3685 r_free = 0.3685 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 = 0.3685 r_free = 0.3685 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: 0.3685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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 0.032 9330 Z= 0.131 Angle : 0.555 14.828 12957 Z= 0.310 Chirality : 0.038 0.223 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.844 74.746 2241 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.58 % Allowed : 20.39 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.37 (0.28), residues: 894 helix: 0.76 (0.22), residues: 536 sheet: -3.35 (1.92), residues: 6 loop : -1.79 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 546 TYR 0.016 0.001 TYR A 920 PHE 0.013 0.001 PHE A 465 TRP 0.012 0.002 TRP A 423 HIS 0.005 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 ( 9330) covalent geometry : angle 0.55497 / 0.31 (12957) hydrogen bonds : bond 0.06748 / 4.64 ( 409) hydrogen bonds : angle 4.90008 / 3.43 ( 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 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 36 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.7364 (ttp-170) REVERT: A 128 ASP cc_start: 0.6941 (m-30) cc_final: 0.6659 (m-30) REVERT: A 173 GLU cc_start: 0.7929 (mp0) cc_final: 0.7512 (mp0) REVERT: A 277 ASP cc_start: 0.7369 (m-30) cc_final: 0.6964 (m-30) REVERT: A 325 LEU cc_start: 0.4478 (OUTLIER) cc_final: 0.4161 (pt) REVERT: A 334 GLU cc_start: 0.5435 (mm-30) cc_final: 0.5002 (mm-30) REVERT: A 496 GLN cc_start: 0.7415 (pp30) cc_final: 0.7200 (pp30) REVERT: A 865 GLU cc_start: 0.6685 (mm-30) cc_final: 0.6189 (mm-30) REVERT: A 892 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7273 (mp10) outliers start: 20 outliers final: 13 residues processed: 146 average time/residue: 0.1106 time to fit residues: 21.7347 Evaluate side-chains 150 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 316 PHE 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 814 GLU Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 892 GLN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.0040 chunk 85 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 chunk 77 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 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 = 0.4176 r_free = 0.4176 target = 0.177185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.157563 restraints weight = 13398.151| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.98 r_work: 0.3843 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 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 = 0.3693 r_free = 0.3693 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: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9330 Z= 0.132 Angle : 0.557 14.607 12957 Z= 0.306 Chirality : 0.038 0.220 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.796 74.739 2241 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.32 % Allowed : 20.65 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.25 (0.28), residues: 894 helix: 0.87 (0.22), residues: 534 sheet: -3.13 (1.93), residues: 6 loop : -1.75 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.025 0.001 TYR A 678 PHE 0.013 0.002 PHE A 465 TRP 0.013 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 9330) covalent geometry : angle 0.55708 / 0.31 (12957) hydrogen bonds : bond 0.06470 / 4.43 ( 409) hydrogen bonds : angle 4.79142 / 3.37 ( 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 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7729 (tm-30) REVERT: A 36 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7324 (ttp-170) REVERT: A 108 PHE cc_start: 0.7468 (m-10) cc_final: 0.7242 (m-10) REVERT: A 128 ASP cc_start: 0.6975 (m-30) cc_final: 0.6689 (m-30) REVERT: A 173 GLU cc_start: 0.7949 (mp0) cc_final: 0.7632 (mp0) REVERT: A 256 TRP cc_start: 0.6498 (t60) cc_final: 0.5784 (t60) REVERT: A 325 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4207 (pt) REVERT: A 496 GLN cc_start: 0.7429 (pp30) cc_final: 0.7214 (pp30) REVERT: A 588 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5525 (tmm) REVERT: A 865 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6225 (mm-30) REVERT: A 892 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7243 (mp10) outliers start: 18 outliers final: 12 residues processed: 146 average time/residue: 0.1163 time to fit residues: 22.6958 Evaluate side-chains 152 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 548 MET 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 892 GLN Chi-restraints excluded: chain A residue 896 MET Chi-restraints excluded: chain A residue 912 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 95 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 64 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 ASN ** 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 = 0.4191 r_free = 0.4191 target = 0.178992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.159877 restraints weight = 13331.695| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.85 r_work: 0.3856 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3705 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3709 r_free = 0.3709 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.2360 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= 0.132 Angle : 0.552 14.519 12957 Z= 0.303 Chirality : 0.038 0.219 1486 Planarity : 0.004 0.062 1373 Dihedral : 17.800 74.679 2241 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.71 % Allowed : 20.52 % Favored : 76.77 % 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: 0.89 (0.22), residues: 535 sheet: -3.02 (1.95), residues: 6 loop : -1.78 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 278 TYR 0.026 0.002 TYR A 678 PHE 0.013 0.001 PHE A 534 TRP 0.013 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9330) covalent geometry : angle 0.55181 / 0.30 (12957) hydrogen bonds : bond 0.06331 / 4.33 ( 409) hydrogen bonds : angle 4.76225 / 3.34 ( 1163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2159.34 seconds wall clock time: 37 minutes 50.72 seconds (2270.72 seconds total)