Starting phenix.real_space_refine on Wed Feb 4 06:21:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m8q_63718/02_2026/9m8q_63718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m8q_63718/02_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_63718/02_2026/9m8q_63718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m8q_63718/02_2026/9m8q_63718.map" model { file = "/net/cci-nas-00/data/ceres_data/9m8q_63718/02_2026/9m8q_63718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m8q_63718/02_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-2.0-5952/lib/python3.9/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: 2.14, per 1000 atoms: 0.24 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: 0.79 Conformation dependent library (CDL) restraints added in 359.2 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: 1.12 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: 1.60 Time building geometry restraints manager: 1.07 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: 2.540 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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.330 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 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= 0.195 Angle : 0.783 34.369 12957 Z= 0.434 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 covalent geometry : bond 0.00357 ( 9330) covalent geometry : angle 0.78293 (12957) hydrogen bonds : bond 0.16427 ( 409) hydrogen bonds : angle 7.25282 ( 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 : 0.231 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: 0.0924 time to fit residues: 17.6575 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 : 0.232 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 915 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.158042 restraints weight = 13398.586| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.06 r_work: 0.3826 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.1445 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= 0.200 Angle : 0.629 6.870 12957 Z= 0.336 Chirality : 0.041 0.245 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.742 74.842 2243 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.77 % Allowed : 10.32 % Favored : 88.90 % 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: -0.35 (0.27), residues: 894 helix: 0.73 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.70 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.024 0.002 TYR A 678 PHE 0.020 0.002 PHE A 465 TRP 0.010 0.002 TRP A 423 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9330) covalent geometry : angle 0.62941 (12957) hydrogen bonds : bond 0.07602 ( 409) hydrogen bonds : angle 5.13166 ( 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 142 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6671 (m-30) cc_final: 0.6439 (m-30) REVERT: A 173 GLU cc_start: 0.7908 (mp0) cc_final: 0.7568 (mp0) REVERT: A 256 TRP cc_start: 0.6471 (t60) cc_final: 0.5739 (t60) REVERT: A 277 ASP cc_start: 0.7141 (m-30) cc_final: 0.6735 (m-30) REVERT: A 334 GLU cc_start: 0.5437 (mm-30) cc_final: 0.4751 (mm-30) REVERT: A 496 GLN cc_start: 0.7177 (pp30) cc_final: 0.6895 (pp30) REVERT: A 832 TYR cc_start: 0.7545 (m-80) cc_final: 0.6988 (m-80) REVERT: A 865 GLU cc_start: 0.6482 (mm-30) cc_final: 0.6164 (mm-30) REVERT: A 895 ILE cc_start: 0.7514 (mm) cc_final: 0.7272 (mt) REVERT: A 908 SER cc_start: 0.8495 (t) cc_final: 0.7990 (m) REVERT: A 909 GLU cc_start: 0.6613 (tm-30) cc_final: 0.6409 (tm-30) REVERT: A 928 LEU cc_start: 0.7371 (mt) cc_final: 0.7139 (mp) REVERT: A 949 ASP cc_start: 0.7383 (t70) cc_final: 0.6966 (t70) outliers start: 6 outliers final: 4 residues processed: 138 average time/residue: 0.0905 time to fit residues: 17.0112 Evaluate side-chains 135 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 131 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 132 ILE 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: 2.9990 chunk 55 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 431 HIS A 885 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.173541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.153400 restraints weight = 13441.328| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.04 r_work: 0.3788 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9330 Z= 0.230 Angle : 0.636 7.273 12957 Z= 0.339 Chirality : 0.042 0.247 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.877 74.634 2241 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.68 % Allowed : 14.71 % Favored : 83.61 % 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: -0.38 (0.27), residues: 894 helix: 0.73 (0.22), residues: 530 sheet: -3.39 (2.33), residues: 6 loop : -1.70 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 735 TYR 0.025 0.002 TYR A 678 PHE 0.021 0.002 PHE A 465 TRP 0.010 0.002 TRP A 838 HIS 0.010 0.002 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 9330) covalent geometry : angle 0.63602 (12957) hydrogen bonds : bond 0.07707 ( 409) hydrogen bonds : angle 5.09478 ( 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 153 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 36 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7142 (ttp-170) REVERT: A 45 SER cc_start: 0.6838 (p) cc_final: 0.6602 (m) REVERT: A 128 ASP cc_start: 0.6628 (m-30) cc_final: 0.6370 (m-30) REVERT: A 173 GLU cc_start: 0.7900 (mp0) cc_final: 0.7532 (mp0) REVERT: A 277 ASP cc_start: 0.7222 (m-30) cc_final: 0.6810 (m-30) REVERT: A 334 GLU cc_start: 0.5601 (mm-30) cc_final: 0.4607 (mm-30) REVERT: A 474 MET cc_start: 0.8596 (ttm) cc_final: 0.8367 (ttm) REVERT: A 490 ASN cc_start: 0.7784 (m-40) cc_final: 0.7562 (m-40) REVERT: A 496 GLN cc_start: 0.7160 (pp30) cc_final: 0.6886 (pp30) REVERT: A 676 MET cc_start: 0.6520 (OUTLIER) cc_final: 0.6159 (tpp) REVERT: A 753 GLU cc_start: 0.7544 (tp30) cc_final: 0.7258 (tp30) REVERT: A 832 TYR cc_start: 0.7399 (m-80) cc_final: 0.7040 (m-80) REVERT: A 865 GLU cc_start: 0.6515 (mm-30) cc_final: 0.6194 (mm-30) REVERT: A 895 ILE cc_start: 0.7619 (mm) cc_final: 0.7403 (mt) REVERT: A 908 SER cc_start: 0.8603 (t) cc_final: 0.8064 (m) REVERT: A 909 GLU cc_start: 0.6807 (tm-30) cc_final: 0.6525 (tm-30) REVERT: A 928 LEU cc_start: 0.7364 (mt) cc_final: 0.7113 (mp) outliers start: 13 outliers final: 7 residues processed: 145 average time/residue: 0.0857 time to fit residues: 16.9223 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 : 0.181 ------------------------------------------------------------------------------- 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 555 ILE Chi-restraints excluded: chain A residue 676 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 916 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4144 r_free = 0.4144 target = 0.174712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.155128 restraints weight = 13552.415| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 1.91 r_work: 0.3815 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9330 Z= 0.187 Angle : 0.588 8.878 12957 Z= 0.313 Chirality : 0.040 0.238 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.815 74.376 2241 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.45 % Allowed : 16.65 % Favored : 80.90 % 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: -0.26 (0.28), residues: 894 helix: 0.83 (0.22), residues: 532 sheet: -3.43 (2.12), residues: 6 loop : -1.66 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 254 TYR 0.020 0.002 TYR A 678 PHE 0.019 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 covalent geometry : bond 0.00402 ( 9330) covalent geometry : angle 0.58824 (12957) hydrogen bonds : bond 0.07004 ( 409) hydrogen bonds : angle 4.90397 ( 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 157 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7745 (tm-30) REVERT: A 36 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7443 (ttp-170) REVERT: A 128 ASP cc_start: 0.6871 (m-30) cc_final: 0.6631 (m-30) REVERT: A 173 GLU cc_start: 0.7935 (mp0) cc_final: 0.7633 (mp0) REVERT: A 277 ASP cc_start: 0.7415 (m-30) cc_final: 0.7028 (m-30) REVERT: A 300 GLU cc_start: 0.6005 (mp0) cc_final: 0.5645 (mp0) REVERT: A 496 GLN cc_start: 0.7439 (pp30) cc_final: 0.7183 (pp30) REVERT: A 819 GLN cc_start: 0.8462 (tp40) cc_final: 0.8158 (tp-100) REVERT: A 865 GLU cc_start: 0.6679 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 895 ILE cc_start: 0.7821 (mm) cc_final: 0.7564 (mt) REVERT: A 909 GLU cc_start: 0.6970 (tm-30) cc_final: 0.6588 (tm-30) REVERT: A 928 LEU cc_start: 0.7447 (mt) cc_final: 0.7239 (mp) REVERT: A 932 PHE cc_start: 0.7523 (m-10) cc_final: 0.7265 (m-10) REVERT: A 947 LEU cc_start: 0.8133 (mt) cc_final: 0.7842 (mp) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 0.0966 time to fit residues: 18.5659 Evaluate side-chains 147 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 TYR 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: 0.0770 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.3980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 680 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.177023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.157816 restraints weight = 13459.508| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 1.86 r_work: 0.3849 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3699 rms_B_bonded: 4.81 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: 7 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.2341 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= 0.141 Angle : 0.547 12.929 12957 Z= 0.288 Chirality : 0.037 0.247 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.716 74.341 2241 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.06 % Allowed : 18.45 % Favored : 79.48 % 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: -0.04 (0.28), residues: 894 helix: 1.01 (0.22), residues: 533 sheet: -3.42 (2.04), residues: 6 loop : -1.59 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.028 0.001 TYR A 678 PHE 0.015 0.001 PHE A 465 TRP 0.010 0.002 TRP A 423 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 9330) covalent geometry : angle 0.54659 (12957) hydrogen bonds : bond 0.06281 ( 409) hydrogen bonds : angle 4.65716 ( 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 155 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 173 GLU cc_start: 0.7938 (mp0) cc_final: 0.7634 (mp0) REVERT: A 256 TRP cc_start: 0.6560 (t60) cc_final: 0.5848 (t60) REVERT: A 300 GLU cc_start: 0.6191 (mp0) cc_final: 0.5801 (mp0) REVERT: A 588 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5870 (tmm) REVERT: A 753 GLU cc_start: 0.7471 (tp30) cc_final: 0.7214 (tp30) REVERT: A 847 LEU cc_start: 0.8055 (mp) cc_final: 0.7838 (mp) REVERT: A 865 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6230 (mm-30) REVERT: A 909 GLU cc_start: 0.7046 (tm-30) cc_final: 0.6594 (tm-30) REVERT: A 932 PHE cc_start: 0.7481 (m-10) cc_final: 0.7265 (m-10) outliers start: 16 outliers final: 11 residues processed: 147 average time/residue: 0.1184 time to fit residues: 23.0474 Evaluate side-chains 148 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 674 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 72 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN A 117 ASN A 885 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.173047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.153228 restraints weight = 13376.531| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 1.90 r_work: 0.3799 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9330 Z= 0.225 Angle : 0.643 12.966 12957 Z= 0.336 Chirality : 0.042 0.249 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.964 74.498 2241 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % 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: -0.20 (0.28), residues: 894 helix: 0.86 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.68 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 546 TYR 0.026 0.002 TYR A 678 PHE 0.021 0.002 PHE A 465 TRP 0.010 0.002 TRP A 838 HIS 0.010 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 9330) covalent geometry : angle 0.64286 (12957) hydrogen bonds : bond 0.07309 ( 409) hydrogen bonds : angle 4.91132 ( 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 163 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 128 ASP cc_start: 0.6885 (m-30) cc_final: 0.6664 (m-30) REVERT: A 173 GLU cc_start: 0.7909 (mp0) cc_final: 0.7615 (mp0) REVERT: A 277 ASP cc_start: 0.7452 (m-30) cc_final: 0.7121 (m-30) REVERT: A 300 GLU cc_start: 0.6226 (mp0) cc_final: 0.6010 (mp0) REVERT: A 865 GLU cc_start: 0.6733 (mm-30) cc_final: 0.6287 (mm-30) REVERT: A 895 ILE cc_start: 0.7879 (mm) cc_final: 0.7603 (mt) REVERT: A 909 GLU cc_start: 0.6969 (tm-30) cc_final: 0.6547 (tm-30) REVERT: A 952 GLU cc_start: 0.7651 (tp30) cc_final: 0.7190 (tp30) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.1194 time to fit residues: 24.2839 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 : 0.285 ------------------------------------------------------------------------------- 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 316 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 755 LYS 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 916 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 42 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 0.3980 chunk 91 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 175 HIS A 285 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.157956 restraints weight = 13484.950| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.01 r_work: 0.3833 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2637 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= 0.141 Angle : 0.563 13.264 12957 Z= 0.298 Chirality : 0.038 0.263 1486 Planarity : 0.004 0.050 1373 Dihedral : 17.830 74.328 2241 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.35 % Allowed : 19.48 % 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: -0.13 (0.28), residues: 894 helix: 0.93 (0.22), residues: 538 sheet: -3.32 (1.96), residues: 6 loop : -1.66 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.024 0.001 TYR A 678 PHE 0.015 0.001 PHE A 465 TRP 0.012 0.002 TRP A 256 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9330) covalent geometry : angle 0.56285 (12957) hydrogen bonds : bond 0.06416 ( 409) hydrogen bonds : angle 4.70568 ( 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 166 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7858 (mp0) cc_final: 0.7566 (mp0) REVERT: A 300 GLU cc_start: 0.5950 (mp0) cc_final: 0.5706 (mp0) REVERT: A 493 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.5935 (m-30) REVERT: A 588 MET cc_start: 0.5978 (OUTLIER) cc_final: 0.5114 (tmm) REVERT: A 699 GLU cc_start: 0.5136 (tm-30) cc_final: 0.4897 (tm-30) REVERT: A 810 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4841 (tm-30) REVERT: A 829 LEU cc_start: 0.8335 (mt) cc_final: 0.8105 (mp) REVERT: A 847 LEU cc_start: 0.8076 (mt) cc_final: 0.7863 (mp) REVERT: A 865 GLU cc_start: 0.6506 (mm-30) cc_final: 0.6050 (mm-30) REVERT: A 895 ILE cc_start: 0.7539 (mm) cc_final: 0.7285 (mt) REVERT: A 909 GLU cc_start: 0.6839 (tm-30) cc_final: 0.6357 (tm-30) REVERT: A 952 GLU cc_start: 0.7463 (tp30) cc_final: 0.7049 (tp30) outliers start: 26 outliers final: 17 residues processed: 151 average time/residue: 0.1030 time to fit residues: 21.1158 Evaluate side-chains 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 342 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 810 GLU Chi-restraints excluded: chain A residue 814 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 869 TYR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 949 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 51 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN A 322 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.177843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158049 restraints weight = 13389.650| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 1.95 r_work: 0.3834 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9330 Z= 0.152 Angle : 0.584 13.183 12957 Z= 0.305 Chirality : 0.038 0.267 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.838 74.325 2241 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.35 % Allowed : 20.00 % Favored : 76.65 % 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: 0.96 (0.22), residues: 539 sheet: -3.31 (1.92), residues: 6 loop : -1.71 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 546 TYR 0.027 0.001 TYR A 678 PHE 0.013 0.001 PHE A 73 TRP 0.009 0.002 TRP A 256 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9330) covalent geometry : angle 0.58442 (12957) hydrogen bonds : bond 0.06386 ( 409) hydrogen bonds : angle 4.69856 ( 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 165 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 139 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 128 ASP cc_start: 0.6888 (m-30) cc_final: 0.6628 (m-30) REVERT: A 147 ILE cc_start: 0.8030 (mm) cc_final: 0.7736 (tp) REVERT: A 173 GLU cc_start: 0.7914 (mp0) cc_final: 0.7598 (mp0) REVERT: A 300 GLU cc_start: 0.6184 (mp0) cc_final: 0.5905 (mp0) REVERT: A 493 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.6561 (m-30) REVERT: A 588 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5557 (tmm) REVERT: A 734 GLU cc_start: 0.7760 (tp30) cc_final: 0.7303 (tp30) REVERT: A 810 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5064 (tm-30) REVERT: A 829 LEU cc_start: 0.8327 (mt) cc_final: 0.8091 (mp) REVERT: A 847 LEU cc_start: 0.8060 (mt) cc_final: 0.7854 (mp) REVERT: A 848 ARG cc_start: 0.7298 (mtt180) cc_final: 0.7091 (mtt-85) REVERT: A 865 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6303 (mm-30) REVERT: A 895 ILE cc_start: 0.7727 (mm) cc_final: 0.7443 (mt) REVERT: A 909 GLU cc_start: 0.6973 (tm-30) cc_final: 0.6507 (tm-30) REVERT: A 952 GLU cc_start: 0.7665 (tp30) cc_final: 0.7125 (tp30) outliers start: 26 outliers final: 18 residues processed: 154 average time/residue: 0.1051 time to fit residues: 21.9173 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 : 0.331 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 295 VAL 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 342 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 810 GLU 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 949 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 7 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 10 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4166 r_free = 0.4166 target = 0.177265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.157954 restraints weight = 13334.360| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 1.85 r_work: 0.3834 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3678 r_free = 0.3678 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9330 Z= 0.168 Angle : 0.595 12.997 12957 Z= 0.312 Chirality : 0.039 0.270 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.870 74.338 2241 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.52 % Rotamer: Outliers : 3.10 % Allowed : 20.52 % Favored : 76.39 % 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: 0.90 (0.22), residues: 540 sheet: -3.26 (1.91), residues: 6 loop : -1.73 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 546 TYR 0.027 0.002 TYR A 678 PHE 0.013 0.002 PHE A 73 TRP 0.009 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 9330) covalent geometry : angle 0.59497 (12957) hydrogen bonds : bond 0.06571 ( 409) hydrogen bonds : angle 4.72991 ( 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 159 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 45 SER cc_start: 0.8072 (m) cc_final: 0.7766 (m) REVERT: A 128 ASP cc_start: 0.6809 (m-30) cc_final: 0.6557 (m-30) REVERT: A 173 GLU cc_start: 0.7880 (mp0) cc_final: 0.7579 (mp0) REVERT: A 300 GLU cc_start: 0.6605 (mp0) cc_final: 0.6370 (mp0) REVERT: A 493 ASP cc_start: 0.7682 (OUTLIER) cc_final: 0.6044 (m-30) REVERT: A 588 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5578 (tmm) REVERT: A 660 LYS cc_start: 0.8078 (mptt) cc_final: 0.7854 (mtmm) REVERT: A 753 GLU cc_start: 0.7498 (tp30) cc_final: 0.7239 (tp30) REVERT: A 810 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.5026 (tm-30) REVERT: A 829 LEU cc_start: 0.8352 (mt) cc_final: 0.8134 (mp) REVERT: A 848 ARG cc_start: 0.7316 (mtt180) cc_final: 0.7107 (mtt-85) REVERT: A 865 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6315 (mm-30) REVERT: A 895 ILE cc_start: 0.7801 (mm) cc_final: 0.7492 (mt) REVERT: A 909 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6496 (tm-30) REVERT: A 952 GLU cc_start: 0.7650 (tp30) cc_final: 0.7170 (tp30) outliers start: 24 outliers final: 19 residues processed: 145 average time/residue: 0.1119 time to fit residues: 21.8545 Evaluate side-chains 161 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 111 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 295 VAL 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 342 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 810 GLU 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 916 ASP Chi-restraints excluded: chain A residue 949 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 57 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 88 optimal weight: 0.0970 chunk 41 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4163 r_free = 0.4163 target = 0.177246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.156341 restraints weight = 13351.091| |-----------------------------------------------------------------------------| r_work (start): 0.3923 rms_B_bonded: 2.07 r_work: 0.3811 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9330 Z= 0.174 Angle : 0.605 13.100 12957 Z= 0.317 Chirality : 0.040 0.274 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.893 74.332 2241 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.15 % Favored : 93.74 % Rotamer: Outliers : 3.10 % Allowed : 20.39 % Favored : 76.52 % 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: -0.26 (0.28), residues: 894 helix: 0.84 (0.22), residues: 540 sheet: -3.28 (1.92), residues: 6 loop : -1.75 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 546 TYR 0.028 0.002 TYR A 678 PHE 0.033 0.002 PHE A 517 TRP 0.009 0.002 TRP A 423 HIS 0.007 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 9330) covalent geometry : angle 0.60510 (12957) hydrogen bonds : bond 0.06620 ( 409) hydrogen bonds : angle 4.76648 ( 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 167 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 36 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7263 (ttp-170) REVERT: A 45 SER cc_start: 0.8070 (m) cc_final: 0.7767 (m) REVERT: A 147 ILE cc_start: 0.7956 (mm) cc_final: 0.7678 (tp) REVERT: A 300 GLU cc_start: 0.6429 (mp0) cc_final: 0.5965 (mp0) REVERT: A 334 GLU cc_start: 0.5205 (mm-30) cc_final: 0.4837 (mm-30) REVERT: A 493 ASP cc_start: 0.7550 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: A 588 MET cc_start: 0.5842 (OUTLIER) cc_final: 0.5195 (tmm) REVERT: A 660 LYS cc_start: 0.7988 (mptt) cc_final: 0.7714 (mtmm) REVERT: A 699 GLU cc_start: 0.5141 (tm-30) cc_final: 0.4855 (tm-30) REVERT: A 753 GLU cc_start: 0.7425 (tp30) cc_final: 0.7198 (tp30) REVERT: A 810 GLU cc_start: 0.5434 (OUTLIER) cc_final: 0.4904 (tm-30) REVERT: A 829 LEU cc_start: 0.8360 (mt) cc_final: 0.8150 (mp) REVERT: A 848 ARG cc_start: 0.7123 (mtt180) cc_final: 0.6905 (mtt-85) REVERT: A 865 GLU cc_start: 0.6495 (mm-30) cc_final: 0.6041 (mm-30) REVERT: A 895 ILE cc_start: 0.7501 (mm) cc_final: 0.7201 (mt) REVERT: A 909 GLU cc_start: 0.6872 (tm-30) cc_final: 0.6403 (tm-30) REVERT: A 952 GLU cc_start: 0.7498 (tp30) cc_final: 0.7050 (tp30) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.1094 time to fit residues: 22.9496 Evaluate side-chains 163 residues out of total 785 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 111 SER Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 295 VAL 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 342 MET Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 496 GLN Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 555 ILE Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 810 GLU 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 916 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 88 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4167 r_free = 0.4167 target = 0.177372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.157227 restraints weight = 13255.468| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 1.90 r_work: 0.3826 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 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 = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3027 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= 0.172 Angle : 0.619 13.028 12957 Z= 0.320 Chirality : 0.039 0.277 1486 Planarity : 0.004 0.049 1373 Dihedral : 17.891 74.333 2241 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.48 % Favored : 94.41 % Rotamer: Outliers : 3.10 % Allowed : 20.39 % Favored : 76.52 % 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: -0.27 (0.28), residues: 894 helix: 0.82 (0.22), residues: 541 sheet: -3.26 (1.92), residues: 6 loop : -1.75 (0.31), residues: 347 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 0.033 0.002 PHE A 517 TRP 0.009 0.002 TRP A 423 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9330) covalent geometry : angle 0.61891 (12957) hydrogen bonds : bond 0.06599 ( 409) hydrogen bonds : angle 4.78255 ( 1163) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.26 seconds wall clock time: 39 minutes 11.72 seconds (2351.72 seconds total)