Starting phenix.real_space_refine on Wed Aug 5 23:29:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge4_51289/08_2026/9ge4_51289.map" } resolution = 3.52 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= 0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 304 5.49 5 S 14 5.16 5 C 6662 2.51 5 N 2265 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12121 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3132 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "L" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 3100 Classifications: {'DNA': 152} Link IDs: {'rna3p': 151} Chain: "M" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 739 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "O" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 803 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 819 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "T" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 2.19, per 1000 atoms: 0.18 Number of scatterers: 12121 At special positions: 0 Unit cell: (117.875, 130.134, 115.046, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 304 15.00 O 2876 8.00 N 2265 7.00 C 6662 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: 0.78 Conformation dependent library (CDL) restraints added in 372.5 milliseconds 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 66.8% alpha, 2.1% beta 127 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'M' and resid 45 through 55 removed outlier: 3.908A pdb=" N ILE M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 removed outlier: 3.602A pdb=" N GLN M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.590A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA M 95 " --> pdb=" O ALA M 91 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 98 " --> pdb=" O GLU M 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY M 102 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N CYS M 110 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 24 through 29 Processing helix chain 'N' and resid 30 through 42 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.572A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 4.022A pdb=" N GLN N 93 " --> pdb=" O ALA N 89 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 22 removed outlier: 3.603A pdb=" N ARG O 20 " --> pdb=" O SER O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 33 removed outlier: 3.919A pdb=" N ARG O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 34 through 37 Processing helix chain 'O' and resid 44 through 52 removed outlier: 4.094A pdb=" N ALA O 48 " --> pdb=" O VAL O 44 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA O 49 " --> pdb=" O GLY O 45 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL O 50 " --> pdb=" O ALA O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 64 through 69 Processing helix chain 'O' and resid 70 through 74 Processing helix chain 'P' and resid 37 through 49 removed outlier: 3.952A pdb=" N TYR P 42 " --> pdb=" O SER P 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN P 47 " --> pdb=" O LYS P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 85 removed outlier: 3.720A pdb=" N GLY P 60 " --> pdb=" O SER P 56 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ARG P 79 " --> pdb=" O GLY P 75 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU P 80 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 101 Processing helix chain 'P' and resid 103 through 123 removed outlier: 3.976A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 55 removed outlier: 3.520A pdb=" N ARG Q 52 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 77 removed outlier: 3.896A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 114 removed outlier: 3.520A pdb=" N ALA Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA Q 98 " --> pdb=" O GLU Q 94 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY Q 102 " --> pdb=" O ALA Q 98 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N CYS Q 110 " --> pdb=" O ASP Q 106 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.729A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 29 Processing helix chain 'R' and resid 30 through 42 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.536A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA R 76 " --> pdb=" O TYR R 72 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 35 Processing helix chain 'S' and resid 45 through 62 removed outlier: 3.767A pdb=" N ALA S 49 " --> pdb=" O GLY S 45 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR S 51 " --> pdb=" O THR S 47 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ALA S 54 " --> pdb=" O VAL S 50 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE S 55 " --> pdb=" O TYR S 51 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR S 58 " --> pdb=" O ALA S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 71 Processing helix chain 'S' and resid 80 through 88 removed outlier: 3.785A pdb=" N LEU S 84 " --> pdb=" O THR S 80 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU S 86 " --> pdb=" O ARG S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 37 through 49 removed outlier: 3.613A pdb=" N TYR T 42 " --> pdb=" O SER T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 84 removed outlier: 4.007A pdb=" N ILE T 61 " --> pdb=" O LYS T 57 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N MET T 62 " --> pdb=" O ALA T 58 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 102 removed outlier: 4.053A pdb=" N ALA T 97 " --> pdb=" O GLU T 93 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.788A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS T 116 " --> pdb=" O SER T 112 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR T 119 " --> pdb=" O THR T 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.616A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'N' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'O' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.063A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'S' and resid 77 through 78 308 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 320 hydrogen bonds 640 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1526 1.32 - 1.44: 4627 1.44 - 1.57: 6163 1.57 - 1.69: 617 1.69 - 1.82: 24 Bond restraints: 12957 Sorted by residual: bond pdb=" CG HIS O 83 " pdb=" CD2 HIS O 83 " ideal model delta sigma weight residual 1.354 1.280 0.074 1.10e-02 8.26e+03 4.49e+01 bond pdb=" C THR O 80 " pdb=" N PRO O 81 " ideal model delta sigma weight residual 1.337 1.389 -0.052 1.11e-02 8.12e+03 2.21e+01 bond pdb=" N1 DC L -42 " pdb=" C6 DC L -42 " ideal model delta sigma weight residual 1.367 1.340 0.027 6.00e-03 2.78e+04 2.09e+01 bond pdb=" CG HIS R 75 " pdb=" CD2 HIS R 75 " ideal model delta sigma weight residual 1.354 1.304 0.050 1.10e-02 8.26e+03 2.05e+01 bond pdb=" CG HIS S 31 " pdb=" CD2 HIS S 31 " ideal model delta sigma weight residual 1.354 1.305 0.049 1.10e-02 8.26e+03 2.01e+01 ... (remaining 12952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 16512 2.98 - 5.95: 2050 5.95 - 8.93: 204 8.93 - 11.90: 22 11.90 - 14.88: 9 Bond angle restraints: 18797 Sorted by residual: angle pdb=" O4' DT K 53 " pdb=" C1' DT K 53 " pdb=" N1 DT K 53 " ideal model delta sigma weight residual 108.00 114.81 -6.81 7.00e-01 2.04e+00 9.47e+01 angle pdb=" O4' DC L -51 " pdb=" C1' DC L -51 " pdb=" N1 DC L -51 " ideal model delta sigma weight residual 108.00 114.17 -6.17 7.00e-01 2.04e+00 7.77e+01 angle pdb=" N LEU O 64 " pdb=" CA LEU O 64 " pdb=" CB LEU O 64 " ideal model delta sigma weight residual 110.49 125.37 -14.88 1.69e+00 3.50e-01 7.75e+01 angle pdb=" O4' DT K -24 " pdb=" C1' DT K -24 " pdb=" N1 DT K -24 " ideal model delta sigma weight residual 108.00 113.75 -5.75 7.00e-01 2.04e+00 6.74e+01 angle pdb=" N VAL O 50 " pdb=" CA VAL O 50 " pdb=" CB VAL O 50 " ideal model delta sigma weight residual 112.33 121.59 -9.26 1.19e+00 7.06e-01 6.06e+01 ... (remaining 18792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.97: 5654 33.97 - 67.94: 1284 67.94 - 101.91: 50 101.91 - 135.88: 0 135.88 - 169.86: 4 Dihedral angle restraints: 6992 sinusoidal: 4837 harmonic: 2155 Sorted by residual: dihedral pdb=" CA ILE O 55 " pdb=" C ILE O 55 " pdb=" N LEU O 56 " pdb=" CA LEU O 56 " ideal model delta harmonic sigma weight residual 180.00 146.73 33.27 0 5.00e+00 4.00e-02 4.43e+01 dihedral pdb=" CA VAL P 98 " pdb=" C VAL P 98 " pdb=" N ARG P 99 " pdb=" CA ARG P 99 " ideal model delta harmonic sigma weight residual 180.00 148.00 32.00 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA THR O 60 " pdb=" C THR O 60 " pdb=" N ALA O 61 " pdb=" CA ALA O 61 " ideal model delta harmonic sigma weight residual 180.00 148.88 31.12 0 5.00e+00 4.00e-02 3.87e+01 ... (remaining 6989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 1644 0.131 - 0.262: 408 0.262 - 0.393: 80 0.393 - 0.524: 10 0.524 - 0.655: 2 Chirality restraints: 2144 Sorted by residual: chirality pdb=" P DT L -81 " pdb=" OP1 DT L -81 " pdb=" OP2 DT L -81 " pdb=" O5' DT L -81 " both_signs ideal model delta sigma weight residual True 2.34 -2.99 -0.66 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" P DC K -70 " pdb=" OP1 DC K -70 " pdb=" OP2 DC K -70 " pdb=" O5' DC K -70 " both_signs ideal model delta sigma weight residual True 2.34 -2.94 -0.60 2.00e-01 2.50e+01 9.12e+00 chirality pdb=" P DA K 38 " pdb=" OP1 DA K 38 " pdb=" OP2 DA K 38 " pdb=" O5' DA K 38 " both_signs ideal model delta sigma weight residual True 2.34 -2.79 -0.46 2.00e-01 2.50e+01 5.25e+00 ... (remaining 2141 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG L -56 " 0.158 2.00e-02 2.50e+03 6.47e-02 1.25e+02 pdb=" N9 DG L -56 " -0.033 2.00e-02 2.50e+03 pdb=" C8 DG L -56 " -0.060 2.00e-02 2.50e+03 pdb=" N7 DG L -56 " -0.048 2.00e-02 2.50e+03 pdb=" C5 DG L -56 " -0.032 2.00e-02 2.50e+03 pdb=" C6 DG L -56 " 0.017 2.00e-02 2.50e+03 pdb=" O6 DG L -56 " 0.112 2.00e-02 2.50e+03 pdb=" N1 DG L -56 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG L -56 " -0.023 2.00e-02 2.50e+03 pdb=" N2 DG L -56 " -0.013 2.00e-02 2.50e+03 pdb=" N3 DG L -56 " -0.030 2.00e-02 2.50e+03 pdb=" C4 DG L -56 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K -14 " -0.149 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" N9 DG K -14 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG K -14 " 0.088 2.00e-02 2.50e+03 pdb=" N7 DG K -14 " 0.049 2.00e-02 2.50e+03 pdb=" C5 DG K -14 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DG K -14 " -0.044 2.00e-02 2.50e+03 pdb=" O6 DG K -14 " -0.074 2.00e-02 2.50e+03 pdb=" N1 DG K -14 " -0.017 2.00e-02 2.50e+03 pdb=" C2 DG K -14 " 0.008 2.00e-02 2.50e+03 pdb=" N2 DG K -14 " 0.052 2.00e-02 2.50e+03 pdb=" N3 DG K -14 " 0.022 2.00e-02 2.50e+03 pdb=" C4 DG K -14 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K -35 " -0.136 2.00e-02 2.50e+03 6.39e-02 1.02e+02 pdb=" N1 DT K -35 " 0.032 2.00e-02 2.50e+03 pdb=" C2 DT K -35 " 0.043 2.00e-02 2.50e+03 pdb=" O2 DT K -35 " 0.049 2.00e-02 2.50e+03 pdb=" N3 DT K -35 " 0.023 2.00e-02 2.50e+03 pdb=" C4 DT K -35 " -0.015 2.00e-02 2.50e+03 pdb=" O4 DT K -35 " -0.109 2.00e-02 2.50e+03 pdb=" C5 DT K -35 " 0.043 2.00e-02 2.50e+03 pdb=" C7 DT K -35 " 0.030 2.00e-02 2.50e+03 pdb=" C6 DT K -35 " 0.040 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 90 2.62 - 3.19: 9381 3.19 - 3.76: 19892 3.76 - 4.33: 28962 4.33 - 4.90: 40863 Nonbonded interactions: 99188 Sorted by model distance: nonbonded pdb=" OP1 DG K -13 " pdb=" NH2 ARG N 36 " model vdw 2.050 3.120 nonbonded pdb=" OE1 GLU Q 50 " pdb=" NH1 ARG R 39 " model vdw 2.117 3.120 nonbonded pdb=" OP1 DG K 26 " pdb=" NZ LYS R 79 " model vdw 2.174 3.120 nonbonded pdb=" N2 DG K 51 " pdb=" O2 DC L -51 " model vdw 2.214 3.120 nonbonded pdb=" OP1 DA L 39 " pdb=" CE LYS O 35 " model vdw 2.221 3.440 ... (remaining 99183 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 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 133) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = (chain 'O' and (resid 13 through 107 or resid 109 through 118)) selection = (chain 'S' and (resid 13 through 107 or resid 109 through 118)) } ncs_group { reference = (chain 'P' and resid 32 through 123) selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.220 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.100 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 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 : 0.012 0.093 12957 Z= 0.880 Angle : 1.991 14.880 18797 Z= 1.468 Chirality : 0.122 0.655 2144 Planarity : 0.028 0.247 1317 Dihedral : 27.603 169.856 5604 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.65 % Favored : 91.53 % Rotamer: Outliers : 3.06 % Allowed : 7.58 % Favored : 89.35 % Cbeta Deviations : 1.73 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.41 % 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: -4.02 (0.24), residues: 732 helix: -2.59 (0.18), residues: 499 sheet: None (None), residues: 0 loop : -2.39 (0.35), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.008 ARG R 67 TYR 0.104 0.015 TYR O 51 PHE 0.053 0.014 PHE P 70 HIS 0.021 0.007 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.01247 / 0.88 (12957) covalent geometry : angle 1.99124 / 1.47 (18797) hydrogen bonds : bond 0.20935 / 22.55 ( 628) hydrogen bonds : angle 7.83408 / 10.35 ( 1528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8953 (mttt) cc_final: 0.8670 (ttpt) REVERT: M 59 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7773 (pt0) REVERT: M 87 SER cc_start: 0.9261 (m) cc_final: 0.9043 (t) REVERT: M 94 GLU cc_start: 0.9247 (mm-30) cc_final: 0.8984 (tp30) REVERT: N 25 ASN cc_start: 0.9272 (m110) cc_final: 0.9045 (m-40) REVERT: N 27 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8161 (tm-30) REVERT: N 74 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8511 (mt-10) REVERT: O 16 SER cc_start: 0.8626 (t) cc_final: 0.8390 (p) REVERT: O 84 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7788 (tp) REVERT: O 85 GLN cc_start: 0.7373 (mt0) cc_final: 0.7154 (mt0) REVERT: O 91 ASP cc_start: 0.8480 (p0) cc_final: 0.8182 (t70) REVERT: O 92 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8287 (pm20) REVERT: P 40 TYR cc_start: 0.8904 (m-80) cc_final: 0.8699 (m-80) REVERT: P 116 LYS cc_start: 0.8549 (mmmt) cc_final: 0.8345 (mtpp) REVERT: Q 41 TYR cc_start: 0.8913 (m-80) cc_final: 0.8608 (m-80) REVERT: Q 42 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7825 (ttm-80) REVERT: Q 77 ASP cc_start: 0.9339 (m-30) cc_final: 0.9081 (t0) REVERT: Q 94 GLU cc_start: 0.8862 (mm-30) cc_final: 0.8554 (tp30) REVERT: Q 129 ARG cc_start: 0.8676 (ttt-90) cc_final: 0.8283 (ttm110) REVERT: R 63 GLU cc_start: 0.9181 (tp30) cc_final: 0.8893 (mt-10) REVERT: R 84 MET cc_start: 0.8744 (mmm) cc_final: 0.8387 (tpp) REVERT: S 89 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8754 (tpm170) REVERT: S 113 LYS cc_start: 0.7645 (tmmm) cc_final: 0.7440 (tppt) REVERT: T 33 ARG cc_start: 0.7330 (mtm180) cc_final: 0.6749 (mtt90) REVERT: T 35 GLU cc_start: 0.8955 (tt0) cc_final: 0.8648 (tt0) REVERT: T 41 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8642 (p) REVERT: T 59 MET cc_start: 0.8992 (tpp) cc_final: 0.8729 (tpp) REVERT: T 86 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7892 (tpp80) outliers start: 19 outliers final: 5 residues processed: 198 average time/residue: 0.1434 time to fit residues: 37.4453 Evaluate side-chains 149 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 43 VAL Chi-restraints excluded: chain O residue 84 LEU Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0050 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 75 HIS O 83 HIS P 82 HIS S 85 GLN T 49 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.144970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102479 restraints weight = 19313.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105543 restraints weight = 10700.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.107134 restraints weight = 7723.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108376 restraints weight = 5868.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.108542 restraints weight = 5701.628| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 12957 Z= 0.211 Angle : 0.942 10.017 18797 Z= 0.528 Chirality : 0.064 0.384 2144 Planarity : 0.006 0.102 1317 Dihedral : 31.239 171.671 4167 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.10 % Favored : 95.49 % Rotamer: Outliers : 4.19 % Allowed : 13.71 % Favored : 82.10 % 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: -2.19 (0.28), residues: 732 helix: -0.90 (0.22), residues: 495 sheet: None (None), residues: 0 loop : -2.46 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG R 67 TYR 0.036 0.003 TYR N 88 PHE 0.028 0.002 PHE Q 78 HIS 0.005 0.001 HIS S 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.21 (12957) covalent geometry : angle 0.94245 / 0.53 (18797) hydrogen bonds : bond 0.07432 / 8.09 ( 628) hydrogen bonds : angle 3.75992 / 5.06 ( 1528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8426 (tpp80) cc_final: 0.8210 (ttm-80) REVERT: N 25 ASN cc_start: 0.8648 (m110) cc_final: 0.8386 (m-40) REVERT: N 46 ILE cc_start: 0.9205 (mm) cc_final: 0.8929 (mm) REVERT: P 68 ASP cc_start: 0.8741 (t0) cc_final: 0.8535 (t0) REVERT: Q 86 SER cc_start: 0.9088 (m) cc_final: 0.8788 (m) REVERT: Q 129 ARG cc_start: 0.7940 (ttt-90) cc_final: 0.7731 (ttm110) REVERT: T 33 ARG cc_start: 0.7594 (mtm180) cc_final: 0.7070 (mtt90) outliers start: 26 outliers final: 16 residues processed: 182 average time/residue: 0.1426 time to fit residues: 34.6207 Evaluate side-chains 158 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 114 SER Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 20.0000 chunk 86 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 10.9990 chunk 10 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 33 HIS O 85 GLN Q 108 ASN R 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.144769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102031 restraints weight = 19567.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.105136 restraints weight = 10762.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106701 restraints weight = 7705.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107475 restraints weight = 5828.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.107739 restraints weight = 5838.171| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12957 Z= 0.186 Angle : 0.796 8.318 18797 Z= 0.462 Chirality : 0.054 0.394 2144 Planarity : 0.005 0.057 1317 Dihedral : 31.406 168.786 4161 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.05 % Favored : 94.54 % Rotamer: Outliers : 4.19 % Allowed : 15.48 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.30), residues: 732 helix: -0.25 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -2.29 (0.37), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 42 TYR 0.031 0.003 TYR P 83 PHE 0.029 0.001 PHE Q 78 HIS 0.009 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 (12957) covalent geometry : angle 0.79617 / 0.46 (18797) hydrogen bonds : bond 0.06235 / 6.81 ( 628) hydrogen bonds : angle 3.35266 / 4.51 ( 1528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8196 (ttm-80) REVERT: M 94 GLU cc_start: 0.7991 (tp30) cc_final: 0.7771 (tp30) REVERT: M 120 MET cc_start: 0.8043 (mtp) cc_final: 0.7478 (mtp) REVERT: N 64 ASN cc_start: 0.8564 (m-40) cc_final: 0.8122 (t0) REVERT: O 88 ILE cc_start: 0.7527 (mt) cc_final: 0.7151 (mm) REVERT: Q 86 SER cc_start: 0.9126 (m) cc_final: 0.8826 (m) REVERT: T 33 ARG cc_start: 0.7618 (mtm180) cc_final: 0.7178 (mtt90) REVERT: T 57 LYS cc_start: 0.8852 (mtpp) cc_final: 0.8635 (mtmm) REVERT: T 93 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7109 (mp0) REVERT: T 119 THR cc_start: 0.9166 (t) cc_final: 0.8833 (t) outliers start: 26 outliers final: 14 residues processed: 167 average time/residue: 0.1327 time to fit residues: 30.0397 Evaluate side-chains 150 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 70 optimal weight: 0.2980 chunk 35 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 41 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN P 82 HIS ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.147212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.104870 restraints weight = 19415.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107821 restraints weight = 10641.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109188 restraints weight = 7700.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.110654 restraints weight = 5911.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110798 restraints weight = 5662.402| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12957 Z= 0.165 Angle : 0.734 8.121 18797 Z= 0.427 Chirality : 0.051 0.366 2144 Planarity : 0.005 0.046 1317 Dihedral : 31.421 170.358 4161 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.23 % Favored : 95.49 % Rotamer: Outliers : 3.55 % Allowed : 17.26 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.30), residues: 732 helix: 0.11 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -2.45 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG S 82 TYR 0.048 0.002 TYR P 83 PHE 0.027 0.001 PHE Q 78 HIS 0.009 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (12957) covalent geometry : angle 0.73399 / 0.43 (18797) hydrogen bonds : bond 0.05430 / 5.87 ( 628) hydrogen bonds : angle 3.08577 / 4.15 ( 1528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8489 (tpp80) cc_final: 0.8153 (ttm-80) REVERT: N 64 ASN cc_start: 0.8530 (m-40) cc_final: 0.8248 (t0) REVERT: O 88 ILE cc_start: 0.7220 (mt) cc_final: 0.6680 (mm) REVERT: Q 86 SER cc_start: 0.9087 (m) cc_final: 0.8804 (m) REVERT: T 33 ARG cc_start: 0.7652 (mtm180) cc_final: 0.7254 (mtt90) REVERT: T 87 SER cc_start: 0.8201 (t) cc_final: 0.7625 (p) REVERT: T 90 THR cc_start: 0.8675 (t) cc_final: 0.8163 (t) REVERT: T 93 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: T 119 THR cc_start: 0.9169 (t) cc_final: 0.8833 (t) outliers start: 22 outliers final: 16 residues processed: 163 average time/residue: 0.1256 time to fit residues: 28.1426 Evaluate side-chains 150 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 133 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 41 HIS Chi-restraints excluded: chain S residue 85 GLN Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.6980 chunk 19 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 chunk 90 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 0.0870 chunk 9 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.159775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120301 restraints weight = 21685.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.123373 restraints weight = 11328.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125307 restraints weight = 7757.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126418 restraints weight = 6312.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.126964 restraints weight = 5672.939| |-----------------------------------------------------------------------------| r_work (final): 0.3931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12957 Z= 0.161 Angle : 0.697 9.082 18797 Z= 0.409 Chirality : 0.048 0.360 2144 Planarity : 0.005 0.042 1317 Dihedral : 31.289 171.485 4160 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.19 % Favored : 94.54 % Rotamer: Outliers : 4.03 % Allowed : 18.39 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.31), residues: 732 helix: 0.37 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -2.27 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 92 TYR 0.062 0.003 TYR N 88 PHE 0.017 0.001 PHE Q 78 HIS 0.006 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (12957) covalent geometry : angle 0.69707 / 0.41 (18797) hydrogen bonds : bond 0.05066 / 5.47 ( 628) hydrogen bonds : angle 2.95000 / 4.01 ( 1528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8473 (tpp80) cc_final: 0.8133 (ttm-80) REVERT: N 64 ASN cc_start: 0.8445 (m-40) cc_final: 0.8219 (t0) REVERT: N 88 TYR cc_start: 0.7896 (m-80) cc_final: 0.7617 (m-80) REVERT: Q 86 SER cc_start: 0.9054 (m) cc_final: 0.8798 (m) REVERT: Q 94 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7178 (tp30) REVERT: R 63 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7878 (mt-10) REVERT: T 40 TYR cc_start: 0.8739 (m-80) cc_final: 0.8488 (m-80) REVERT: T 90 THR cc_start: 0.8711 (t) cc_final: 0.8127 (t) REVERT: T 93 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: T 119 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8749 (t) outliers start: 25 outliers final: 17 residues processed: 156 average time/residue: 0.1323 time to fit residues: 28.3792 Evaluate side-chains 148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 41 HIS Chi-restraints excluded: chain S residue 85 GLN Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 79 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 82 HIS ** R 75 HIS ** 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 = 0.4283 r_free = 0.4283 target = 0.158447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.118515 restraints weight = 21515.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.121544 restraints weight = 11356.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.123409 restraints weight = 7821.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.124521 restraints weight = 6403.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.125117 restraints weight = 5747.960| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 12957 Z= 0.172 Angle : 0.703 9.177 18797 Z= 0.408 Chirality : 0.048 0.355 2144 Planarity : 0.005 0.040 1317 Dihedral : 31.334 172.045 4160 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 4.19 % Allowed : 18.06 % Favored : 77.74 % 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: -0.65 (0.31), residues: 732 helix: 0.44 (0.24), residues: 498 sheet: None (None), residues: 0 loop : -2.32 (0.36), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 92 TYR 0.045 0.002 TYR N 88 PHE 0.014 0.001 PHE Q 78 HIS 0.012 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.17 (12957) covalent geometry : angle 0.70261 / 0.41 (18797) hydrogen bonds : bond 0.05260 / 5.72 ( 628) hydrogen bonds : angle 3.00021 / 4.06 ( 1528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 88 TYR cc_start: 0.7999 (m-80) cc_final: 0.7631 (m-80) REVERT: P 76 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7733 (tm-30) REVERT: Q 86 SER cc_start: 0.9025 (m) cc_final: 0.8736 (m) REVERT: Q 94 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7239 (tp30) REVERT: T 93 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: T 119 THR cc_start: 0.9163 (t) cc_final: 0.8843 (t) outliers start: 26 outliers final: 18 residues processed: 152 average time/residue: 0.1192 time to fit residues: 25.0624 Evaluate side-chains 146 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 84 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 0.0980 chunk 17 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 82 HIS ** Q 108 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 = 0.4220 r_free = 0.4220 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.112829 restraints weight = 21578.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.115519 restraints weight = 12282.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117178 restraints weight = 8834.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.118153 restraints weight = 7393.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.118547 restraints weight = 6712.726| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12957 Z= 0.263 Angle : 0.813 8.495 18797 Z= 0.458 Chirality : 0.053 0.370 2144 Planarity : 0.006 0.049 1317 Dihedral : 31.485 171.819 4160 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.78 % Favored : 94.95 % Rotamer: Outliers : 5.32 % Allowed : 18.87 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.01 (0.30), residues: 732 helix: 0.15 (0.24), residues: 492 sheet: None (None), residues: 0 loop : -2.35 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 79 TYR 0.046 0.004 TYR N 88 PHE 0.014 0.002 PHE Q 78 HIS 0.014 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 (12957) covalent geometry : angle 0.81251 / 0.46 (18797) hydrogen bonds : bond 0.06815 / 7.42 ( 628) hydrogen bonds : angle 3.56380 / 4.80 ( 1528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8212 (ttm-80) REVERT: M 94 GLU cc_start: 0.8090 (tp30) cc_final: 0.7811 (tp30) REVERT: N 88 TYR cc_start: 0.8077 (m-80) cc_final: 0.7688 (m-80) REVERT: Q 86 SER cc_start: 0.8990 (m) cc_final: 0.8657 (m) REVERT: Q 94 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7359 (tp30) REVERT: T 93 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: T 119 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8902 (t) REVERT: T 120 LYS cc_start: 0.8809 (ttpp) cc_final: 0.8579 (ttpp) outliers start: 33 outliers final: 24 residues processed: 157 average time/residue: 0.1263 time to fit residues: 27.2836 Evaluate side-chains 156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain P residue 122 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 41 HIS Chi-restraints excluded: chain S residue 64 LEU Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 51 ASP Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 31 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 85 optimal weight: 0.5980 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 85 GLN P 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.159351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.119054 restraints weight = 21560.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122211 restraints weight = 11194.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.124182 restraints weight = 7631.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.125332 restraints weight = 6201.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.125873 restraints weight = 5556.682| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12957 Z= 0.159 Angle : 0.699 9.172 18797 Z= 0.407 Chirality : 0.047 0.353 2144 Planarity : 0.004 0.039 1317 Dihedral : 31.297 173.306 4160 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.08 % Rotamer: Outliers : 3.23 % Allowed : 21.45 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.31), residues: 732 helix: 0.53 (0.24), residues: 490 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 92 TYR 0.038 0.003 TYR T 83 PHE 0.010 0.001 PHE Q 78 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.16 (12957) covalent geometry : angle 0.69906 / 0.41 (18797) hydrogen bonds : bond 0.04984 / 5.32 ( 628) hydrogen bonds : angle 2.99464 / 3.98 ( 1528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8167 (ttm-80) REVERT: N 88 TYR cc_start: 0.7971 (m-80) cc_final: 0.7686 (m-80) REVERT: Q 86 SER cc_start: 0.9008 (m) cc_final: 0.8715 (m) REVERT: Q 94 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7200 (tp30) REVERT: T 90 THR cc_start: 0.8756 (t) cc_final: 0.8302 (t) REVERT: T 93 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: T 119 THR cc_start: 0.9184 (t) cc_final: 0.8969 (t) outliers start: 20 outliers final: 18 residues processed: 151 average time/residue: 0.1407 time to fit residues: 28.9033 Evaluate side-chains 152 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 41 HIS Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 10.0000 chunk 86 optimal weight: 0.5980 chunk 5 optimal weight: 10.9990 chunk 8 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 82 HIS ** Q 108 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 = 0.4181 r_free = 0.4181 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.109212 restraints weight = 21499.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.111808 restraints weight = 12396.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.113418 restraints weight = 8993.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.114364 restraints weight = 7548.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.114773 restraints weight = 6869.623| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.083 12957 Z= 0.409 Angle : 0.953 9.626 18797 Z= 0.521 Chirality : 0.059 0.381 2144 Planarity : 0.007 0.047 1317 Dihedral : 31.551 172.093 4160 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.60 % Favored : 93.99 % Rotamer: Outliers : 4.52 % Allowed : 20.65 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.66 (0.29), residues: 732 helix: -0.32 (0.23), residues: 491 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG R 92 TYR 0.043 0.004 TYR N 88 PHE 0.014 0.002 PHE Q 78 HIS 0.011 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00931 / 0.41 (12957) covalent geometry : angle 0.95341 / 0.52 (18797) hydrogen bonds : bond 0.08199 / 8.99 ( 628) hydrogen bonds : angle 4.02538 / 5.35 ( 1528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 94 GLU cc_start: 0.8064 (tp30) cc_final: 0.7786 (tp30) REVERT: N 88 TYR cc_start: 0.8137 (m-80) cc_final: 0.7896 (m-80) REVERT: Q 86 SER cc_start: 0.8989 (m) cc_final: 0.8745 (m) REVERT: Q 94 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7390 (tp30) REVERT: T 93 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7353 (mt-10) outliers start: 28 outliers final: 24 residues processed: 149 average time/residue: 0.1255 time to fit residues: 25.4553 Evaluate side-chains 147 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 80 THR Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 115 THR Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain P residue 119 THR Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 117 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 51 ASP Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 87 SER Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 16 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 93 GLN O 83 HIS P 82 HIS ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.156789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.116525 restraints weight = 21608.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.119672 restraints weight = 11231.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.121637 restraints weight = 7656.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.122715 restraints weight = 6214.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.123267 restraints weight = 5592.019| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12957 Z= 0.165 Angle : 0.743 9.795 18797 Z= 0.426 Chirality : 0.049 0.366 2144 Planarity : 0.005 0.037 1317 Dihedral : 31.315 173.674 4160 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.22 % Rotamer: Outliers : 3.23 % Allowed : 23.39 % Favored : 73.39 % 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: -0.97 (0.30), residues: 732 helix: 0.23 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -2.45 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 82 TYR 0.039 0.003 TYR N 88 PHE 0.010 0.001 PHE S 25 HIS 0.007 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.17 (12957) covalent geometry : angle 0.74296 / 0.43 (18797) hydrogen bonds : bond 0.05518 / 5.88 ( 628) hydrogen bonds : angle 3.19319 / 4.25 ( 1528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1464 Ramachandran restraints generated. 732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8176 (ttm-80) REVERT: N 88 TYR cc_start: 0.7980 (m-80) cc_final: 0.7758 (m-80) REVERT: P 40 TYR cc_start: 0.8680 (m-80) cc_final: 0.8224 (m-80) REVERT: Q 86 SER cc_start: 0.8964 (m) cc_final: 0.8640 (m) REVERT: Q 94 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7265 (tp30) REVERT: T 93 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7284 (mt-10) REVERT: T 120 LYS cc_start: 0.8625 (ttpp) cc_final: 0.8357 (tttm) outliers start: 20 outliers final: 14 residues processed: 137 average time/residue: 0.1224 time to fit residues: 22.7543 Evaluate side-chains 138 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain O residue 76 VAL Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 118 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 41 HIS Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 83 HIS P 82 HIS S 83 HIS T 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.156647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.116356 restraints weight = 21592.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.119488 restraints weight = 11298.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.121405 restraints weight = 7730.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122508 restraints weight = 6294.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.123137 restraints weight = 5648.764| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12957 Z= 0.177 Angle : 0.729 10.581 18797 Z= 0.417 Chirality : 0.049 0.365 2144 Planarity : 0.005 0.042 1317 Dihedral : 31.183 174.117 4160 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.74 % Favored : 93.99 % Rotamer: Outliers : 2.58 % Allowed : 23.55 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.79 (0.30), residues: 732 helix: 0.39 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -2.42 (0.34), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG S 78 TYR 0.037 0.002 TYR N 88 PHE 0.010 0.001 PHE M 67 HIS 0.009 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (12957) covalent geometry : angle 0.72869 / 0.42 (18797) hydrogen bonds : bond 0.05527 / 5.96 ( 628) hydrogen bonds : angle 3.16454 / 4.19 ( 1528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.01 seconds wall clock time: 33 minutes 47.40 seconds (2027.40 seconds total)