Starting phenix.real_space_refine on Fri Jul 3 05:18:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ge4_51289/07_2026/9ge4_51289.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ge4_51289/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ge4_51289/07_2026/9ge4_51289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ge4_51289/07_2026/9ge4_51289.map" model { file = "/net/cci-nas-00/data/ceres_data/9ge4_51289/07_2026/9ge4_51289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ge4_51289/07_2026/9ge4_51289.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.60, per 1000 atoms: 0.21 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: 0.80 Conformation dependent library (CDL) restraints added in 150.6 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: 1.72 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: 2.15 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: 16565 2.98 - 5.95: 2000 5.95 - 8.93: 201 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=" O3' DG K -44 " pdb=" P DT K -43 " pdb=" O5' DT K -43 " ideal model delta sigma weight residual 104.00 91.73 12.27 1.50e+00 4.44e-01 6.69e+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: 9.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.840 Find NCS groups from input model: 0.190 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.540 ------------------------------------------------------------------------------- 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= 0.879 Angle : 1.982 14.880 18797 Z= 1.458 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 1.98163 / 1.46 (18797) hydrogen bonds : bond 0.20935 / 22.41 ( 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 : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 56 LYS cc_start: 0.8953 (mttt) cc_final: 0.8669 (ttpt) REVERT: M 59 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7777 (pt0) REVERT: M 87 SER cc_start: 0.9261 (m) cc_final: 0.9042 (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: 0.8162 (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: 0.7789 (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: 0.8181 (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 87 SER cc_start: 0.9149 (m) cc_final: 0.8842 (p) 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: 0.7826 (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: 0.8284 (ttm110) REVERT: R 30 THR cc_start: 0.8836 (p) cc_final: 0.8633 (t) 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: 0.8388 (tpp) REVERT: S 89 ARG cc_start: 0.9064 (ttt180) cc_final: 0.8753 (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: 0.6750 (mtt90) REVERT: T 35 GLU cc_start: 0.8955 (tt0) cc_final: 0.8647 (tt0) REVERT: T 41 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8644 (p) REVERT: T 59 MET cc_start: 0.8992 (tpp) cc_final: 0.8736 (tpp) REVERT: T 86 ARG cc_start: 0.8138 (mmt90) cc_final: 0.7885 (tpp80) REVERT: T 87 SER cc_start: 0.8993 (m) cc_final: 0.8634 (p) outliers start: 19 outliers final: 5 residues processed: 198 average time/residue: 0.1398 time to fit residues: 36.3506 Evaluate side-chains 151 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 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: 0.5194 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.144625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102195 restraints weight = 19353.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.105342 restraints weight = 10713.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106903 restraints weight = 7683.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108269 restraints weight = 5843.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108432 restraints weight = 5641.789| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12957 Z= 0.209 Angle : 0.929 10.205 18797 Z= 0.524 Chirality : 0.063 0.350 2144 Planarity : 0.006 0.096 1317 Dihedral : 31.315 173.344 4167 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.10 % Favored : 95.49 % Rotamer: Outliers : 4.19 % Allowed : 13.39 % Favored : 82.42 % 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: -2.23 (0.28), residues: 732 helix: -0.92 (0.22), residues: 495 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 67 TYR 0.034 0.003 TYR N 88 PHE 0.025 0.003 PHE Q 78 HIS 0.005 0.001 HIS O 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.21 (12957) covalent geometry : angle 0.92936 / 0.52 (18797) hydrogen bonds : bond 0.07429 / 8.04 ( 628) hydrogen bonds : angle 3.76624 / 5.08 ( 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 197 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 25 ASN cc_start: 0.8651 (m110) cc_final: 0.8395 (m-40) REVERT: N 46 ILE cc_start: 0.9195 (mm) cc_final: 0.8922 (mm) REVERT: P 68 ASP cc_start: 0.8749 (t0) cc_final: 0.8542 (t0) REVERT: P 87 SER cc_start: 0.8823 (m) cc_final: 0.8530 (p) REVERT: P 108 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8612 (ttmm) REVERT: Q 86 SER cc_start: 0.9090 (m) cc_final: 0.8782 (m) REVERT: Q 129 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7739 (ttm110) REVERT: T 33 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7056 (mtt90) REVERT: T 87 SER cc_start: 0.8804 (m) cc_final: 0.8225 (p) REVERT: T 93 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7274 (mp0) outliers start: 26 outliers final: 13 residues processed: 186 average time/residue: 0.1212 time to fit residues: 30.2276 Evaluate side-chains 156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 117 VAL 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 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 93 GLU 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: 0.7980 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3931 r_free = 0.3931 target = 0.143749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.100984 restraints weight = 19554.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.103863 restraints weight = 10798.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.105456 restraints weight = 7871.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.106665 restraints weight = 5930.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.106824 restraints weight = 5797.012| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 12957 Z= 0.200 Angle : 0.809 8.481 18797 Z= 0.469 Chirality : 0.054 0.372 2144 Planarity : 0.006 0.054 1317 Dihedral : 31.546 168.132 4161 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.19 % Favored : 94.40 % Rotamer: Outliers : 4.84 % Allowed : 15.16 % Favored : 80.00 % 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: -1.59 (0.30), residues: 732 helix: -0.40 (0.23), residues: 499 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG S 43 TYR 0.036 0.004 TYR N 88 PHE 0.028 0.002 PHE Q 78 HIS 0.011 0.002 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.20 (12957) covalent geometry : angle 0.80946 / 0.47 (18797) hydrogen bonds : bond 0.06550 / 7.15 ( 628) hydrogen bonds : angle 3.47057 / 4.66 ( 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 180 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8207 (ttm-80) REVERT: Q 86 SER cc_start: 0.9130 (m) cc_final: 0.8837 (m) REVERT: Q 94 GLU cc_start: 0.7893 (tp30) cc_final: 0.7631 (tp30) REVERT: T 33 ARG cc_start: 0.7532 (mtm180) cc_final: 0.7135 (mtt90) REVERT: T 57 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8678 (mtmm) REVERT: T 86 ARG cc_start: 0.8429 (tpp80) cc_final: 0.8062 (ttm-80) REVERT: T 87 SER cc_start: 0.8747 (m) cc_final: 0.8124 (p) REVERT: T 119 THR cc_start: 0.9175 (t) cc_final: 0.8855 (t) outliers start: 30 outliers final: 16 residues processed: 173 average time/residue: 0.1133 time to fit residues: 26.7650 Evaluate side-chains 151 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 44 LYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain P residue 56 SER 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 96 THR 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 66 VAL 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: 0.8980 chunk 35 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103816 restraints weight = 19377.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.106787 restraints weight = 10703.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.108208 restraints weight = 7732.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.108960 restraints weight = 5884.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109202 restraints weight = 5881.846| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3469 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= 0.178 Angle : 0.737 7.770 18797 Z= 0.430 Chirality : 0.050 0.348 2144 Planarity : 0.005 0.051 1317 Dihedral : 31.576 169.825 4161 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.51 % Favored : 95.22 % Rotamer: Outliers : 3.71 % Allowed : 18.06 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.30), residues: 732 helix: -0.06 (0.23), residues: 497 sheet: None (None), residues: 0 loop : -2.53 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 92 TYR 0.041 0.003 TYR N 88 PHE 0.027 0.001 PHE Q 78 HIS 0.009 0.001 HIS O 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (12957) covalent geometry : angle 0.73734 / 0.43 (18797) hydrogen bonds : bond 0.05653 / 6.10 ( 628) hydrogen bonds : angle 3.16419 / 4.22 ( 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 169 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8504 (tpp80) cc_final: 0.8175 (ttm-80) REVERT: N 64 ASN cc_start: 0.8575 (m-40) cc_final: 0.8100 (t0) REVERT: N 88 TYR cc_start: 0.7963 (m-80) cc_final: 0.7738 (m-80) REVERT: Q 86 SER cc_start: 0.9101 (m) cc_final: 0.8805 (m) REVERT: Q 94 GLU cc_start: 0.7877 (tp30) cc_final: 0.7502 (tp30) REVERT: T 86 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8046 (ttm-80) REVERT: T 87 SER cc_start: 0.8673 (m) cc_final: 0.8122 (p) REVERT: T 93 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7888 (mm-30) REVERT: T 119 THR cc_start: 0.9172 (t) cc_final: 0.8837 (t) outliers start: 23 outliers final: 17 residues processed: 161 average time/residue: 0.1020 time to fit residues: 22.9179 Evaluate side-chains 150 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 27 VAL 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 12 THR Chi-restraints excluded: chain S residue 23 LEU 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 54 ILE 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: 0.7980 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 0.3980 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4201 r_free = 0.4201 target = 0.153371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.111347 restraints weight = 21161.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114448 restraints weight = 11209.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.116415 restraints weight = 7770.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.117515 restraints weight = 6346.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.117942 restraints weight = 5724.014| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12957 Z= 0.165 Angle : 0.703 8.776 18797 Z= 0.411 Chirality : 0.048 0.346 2144 Planarity : 0.005 0.042 1317 Dihedral : 31.439 170.766 4160 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.08 % Rotamer: Outliers : 3.23 % Allowed : 19.68 % Favored : 77.10 % 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: -0.86 (0.31), residues: 732 helix: 0.28 (0.24), residues: 497 sheet: None (None), residues: 0 loop : -2.38 (0.35), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 92 TYR 0.050 0.003 TYR N 88 PHE 0.022 0.001 PHE Q 78 HIS 0.009 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (12957) covalent geometry : angle 0.70276 / 0.41 (18797) hydrogen bonds : bond 0.05317 / 5.74 ( 628) hydrogen bonds : angle 3.00695 / 4.08 ( 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 157 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8486 (tpp80) cc_final: 0.8140 (ttm-80) REVERT: N 64 ASN cc_start: 0.8431 (m-40) cc_final: 0.8224 (t0) REVERT: N 84 MET cc_start: 0.7686 (tpp) cc_final: 0.7371 (tpp) REVERT: N 88 TYR cc_start: 0.7998 (m-80) cc_final: 0.7588 (m-80) REVERT: Q 86 SER cc_start: 0.9057 (m) cc_final: 0.8776 (m) REVERT: Q 94 GLU cc_start: 0.7878 (tp30) cc_final: 0.7472 (tp30) REVERT: T 87 SER cc_start: 0.8603 (m) cc_final: 0.8077 (p) REVERT: T 119 THR cc_start: 0.9084 (t) cc_final: 0.8766 (t) outliers start: 20 outliers final: 16 residues processed: 153 average time/residue: 0.1127 time to fit residues: 23.9171 Evaluate side-chains 141 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain P residue 52 THR 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 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 94 ILE 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: 1.9990 chunk 10 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.157540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.117530 restraints weight = 21532.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120568 restraints weight = 11498.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.122437 restraints weight = 7920.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.123510 restraints weight = 6479.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.124143 restraints weight = 5824.395| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12957 Z= 0.175 Angle : 0.703 9.008 18797 Z= 0.410 Chirality : 0.048 0.339 2144 Planarity : 0.005 0.041 1317 Dihedral : 31.449 171.448 4160 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.19 % Favored : 94.54 % Rotamer: Outliers : 3.55 % Allowed : 20.81 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.30), residues: 732 helix: 0.35 (0.24), residues: 496 sheet: None (None), residues: 0 loop : -2.44 (0.34), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 92 TYR 0.041 0.003 TYR P 83 PHE 0.016 0.001 PHE Q 78 HIS 0.012 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (12957) covalent geometry : angle 0.70267 / 0.41 (18797) hydrogen bonds : bond 0.05373 / 5.81 ( 628) hydrogen bonds : angle 3.04234 / 4.12 ( 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 157 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8120 (ttm-80) REVERT: M 60 LEU cc_start: 0.8752 (mt) cc_final: 0.8478 (mt) REVERT: M 61 LEU cc_start: 0.8674 (mt) cc_final: 0.8447 (mp) REVERT: Q 86 SER cc_start: 0.9043 (m) cc_final: 0.8739 (m) REVERT: Q 94 GLU cc_start: 0.7888 (tp30) cc_final: 0.7494 (tp30) REVERT: T 86 ARG cc_start: 0.8363 (tpp80) cc_final: 0.8072 (ttm-80) REVERT: T 87 SER cc_start: 0.8593 (m) cc_final: 0.8143 (p) REVERT: T 93 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: T 119 THR cc_start: 0.9072 (t) cc_final: 0.8791 (t) outliers start: 22 outliers final: 19 residues processed: 152 average time/residue: 0.1101 time to fit residues: 23.2574 Evaluate side-chains 146 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 SER 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 60 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 11.9990 chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 80 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 = 0.4188 r_free = 0.4188 target = 0.150849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109774 restraints weight = 21577.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112739 restraints weight = 11595.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.114558 restraints weight = 8066.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.115610 restraints weight = 6614.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116163 restraints weight = 5957.333| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 12957 Z= 0.315 Angle : 0.863 12.719 18797 Z= 0.482 Chirality : 0.055 0.364 2144 Planarity : 0.006 0.053 1317 Dihedral : 31.668 171.072 4160 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.87 % Favored : 93.85 % Rotamer: Outliers : 6.45 % Allowed : 18.55 % Favored : 75.00 % 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: -1.46 (0.29), residues: 732 helix: -0.15 (0.23), residues: 488 sheet: None (None), residues: 0 loop : -2.59 (0.33), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 92 TYR 0.066 0.004 TYR N 88 PHE 0.016 0.002 PHE Q 78 HIS 0.010 0.002 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00695 / 0.31 (12957) covalent geometry : angle 0.86325 / 0.48 (18797) hydrogen bonds : bond 0.07589 / 8.22 ( 628) hydrogen bonds : angle 3.79195 / 5.11 ( 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 170 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 84 MET cc_start: 0.7961 (tpp) cc_final: 0.7684 (tpp) REVERT: N 88 TYR cc_start: 0.7890 (m-80) cc_final: 0.7596 (m-80) REVERT: Q 86 SER cc_start: 0.8995 (m) cc_final: 0.8655 (m) REVERT: Q 94 GLU cc_start: 0.8106 (tp30) cc_final: 0.7651 (tp30) REVERT: T 87 SER cc_start: 0.8767 (m) cc_final: 0.8311 (p) REVERT: T 93 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7438 (mt-10) outliers start: 40 outliers final: 29 residues processed: 160 average time/residue: 0.1124 time to fit residues: 25.0292 Evaluate side-chains 155 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain N residue 30 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 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 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 60 VAL Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 86 VAL 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 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 54 ILE Chi-restraints excluded: chain T residue 93 GLU Chi-restraints excluded: chain T residue 94 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 60 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 27 optimal weight: 9.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 93 GLN O 83 HIS O 85 GLN P 82 HIS ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.156392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.115854 restraints weight = 21531.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.118960 restraints weight = 11326.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120942 restraints weight = 7772.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.122012 restraints weight = 6318.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.122600 restraints weight = 5694.429| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12957 Z= 0.172 Angle : 0.712 9.020 18797 Z= 0.415 Chirality : 0.048 0.346 2144 Planarity : 0.005 0.039 1317 Dihedral : 31.508 172.436 4160 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.64 % Favored : 95.08 % Rotamer: Outliers : 3.71 % Allowed : 21.94 % Favored : 74.35 % 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: -0.92 (0.30), residues: 732 helix: 0.30 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -2.48 (0.33), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG S 82 TYR 0.053 0.003 TYR N 88 PHE 0.011 0.001 PHE Q 78 HIS 0.008 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (12957) covalent geometry : angle 0.71170 / 0.42 (18797) hydrogen bonds : bond 0.05536 / 5.89 ( 628) hydrogen bonds : angle 3.13111 / 4.21 ( 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 152 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8203 (ttm-80) REVERT: N 84 MET cc_start: 0.7684 (tpp) cc_final: 0.7477 (tpp) REVERT: N 88 TYR cc_start: 0.7685 (m-80) cc_final: 0.7291 (m-80) REVERT: P 40 TYR cc_start: 0.8662 (m-80) cc_final: 0.8186 (m-80) REVERT: P 76 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7592 (tm-30) REVERT: Q 86 SER cc_start: 0.8949 (m) cc_final: 0.8644 (m) REVERT: Q 94 GLU cc_start: 0.7956 (tp30) cc_final: 0.7486 (tp30) REVERT: T 40 TYR cc_start: 0.8810 (m-80) cc_final: 0.8563 (m-80) REVERT: T 86 ARG cc_start: 0.8392 (tpp80) cc_final: 0.8039 (ttm-80) REVERT: T 87 SER cc_start: 0.8668 (m) cc_final: 0.8173 (p) REVERT: T 93 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7356 (mt-10) REVERT: T 120 LYS cc_start: 0.8821 (tmmt) cc_final: 0.8522 (ttpt) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.1218 time to fit residues: 24.8878 Evaluate side-chains 149 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 56 SER Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 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 60 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 20 optimal weight: 10.9990 chunk 82 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 82 HIS ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 69 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 = 0.4148 r_free = 0.4148 target = 0.147495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.106706 restraints weight = 21556.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.109239 restraints weight = 12588.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.110796 restraints weight = 9201.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111726 restraints weight = 7762.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112224 restraints weight = 7063.055| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.094 12957 Z= 0.477 Angle : 1.001 10.027 18797 Z= 0.550 Chirality : 0.061 0.386 2144 Planarity : 0.008 0.059 1317 Dihedral : 31.810 171.128 4160 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.97 % Favored : 92.62 % Rotamer: Outliers : 4.68 % Allowed : 21.94 % Favored : 73.39 % 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: -2.13 (0.28), residues: 732 helix: -0.64 (0.22), residues: 491 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 92 TYR 0.063 0.005 TYR N 88 PHE 0.016 0.003 PHE M 78 HIS 0.010 0.003 HIS S 83 Details of bonding type rmsd/Z covalent geometry : bond 0.01076 / 0.48 (12957) covalent geometry : angle 1.00101 / 0.55 (18797) hydrogen bonds : bond 0.09053 / 9.83 ( 628) hydrogen bonds : angle 4.27423 / 5.72 ( 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 157 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 87 SER cc_start: 0.9062 (t) cc_final: 0.8702 (t) REVERT: M 94 GLU cc_start: 0.8052 (tp30) cc_final: 0.7777 (tp30) REVERT: M 97 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7707 (mp0) REVERT: N 46 ILE cc_start: 0.9196 (mm) cc_final: 0.8947 (mm) REVERT: N 88 TYR cc_start: 0.7996 (m-80) cc_final: 0.7706 (m-80) REVERT: Q 94 GLU cc_start: 0.8250 (tp30) cc_final: 0.7772 (tp30) REVERT: T 93 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: T 120 LYS cc_start: 0.9077 (tmmt) cc_final: 0.8715 (ttpp) outliers start: 29 outliers final: 23 residues processed: 151 average time/residue: 0.1267 time to fit residues: 26.2428 Evaluate side-chains 148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 M residue 117 VAL Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 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 23 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 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: 0.8980 chunk 8 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 83 HIS P 82 HIS ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 69 ASN T 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.150520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.108313 restraints weight = 21173.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.111316 restraints weight = 11491.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.113165 restraints weight = 8045.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.114265 restraints weight = 6644.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.114851 restraints weight = 5994.071| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12957 Z= 0.179 Angle : 0.745 11.177 18797 Z= 0.430 Chirality : 0.049 0.371 2144 Planarity : 0.005 0.039 1317 Dihedral : 31.500 172.961 4160 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.37 % Favored : 95.36 % Rotamer: Outliers : 3.23 % Allowed : 24.03 % Favored : 72.74 % 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: -1.29 (0.30), residues: 732 helix: 0.04 (0.24), residues: 489 sheet: None (None), residues: 0 loop : -2.70 (0.32), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 82 TYR 0.050 0.003 TYR N 88 PHE 0.013 0.002 PHE S 25 HIS 0.010 0.001 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.18 (12957) covalent geometry : angle 0.74472 / 0.43 (18797) hydrogen bonds : bond 0.05721 / 6.07 ( 628) hydrogen bonds : angle 3.26673 / 4.36 ( 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 152 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8200 (ttm-80) REVERT: P 40 TYR cc_start: 0.8664 (m-80) cc_final: 0.8193 (m-80) REVERT: Q 86 SER cc_start: 0.9003 (m) cc_final: 0.8705 (m) REVERT: Q 94 GLU cc_start: 0.8004 (tp30) cc_final: 0.7535 (tp30) REVERT: T 86 ARG cc_start: 0.8416 (tpp80) cc_final: 0.8040 (ttm-80) REVERT: T 93 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7442 (mt-10) outliers start: 20 outliers final: 17 residues processed: 147 average time/residue: 0.1352 time to fit residues: 26.9762 Evaluate side-chains 148 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 96 CYS Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 112 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 60 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 8 optimal weight: 10.0000 chunk 31 optimal weight: 0.0870 chunk 38 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 53 optimal weight: 0.5980 chunk 22 optimal weight: 10.0000 overall best weight: 0.6360 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.156495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.116111 restraints weight = 21517.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.119205 restraints weight = 11249.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121142 restraints weight = 7725.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122215 restraints weight = 6289.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.122781 restraints weight = 5667.191| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12957 Z= 0.169 Angle : 0.700 10.808 18797 Z= 0.409 Chirality : 0.047 0.367 2144 Planarity : 0.005 0.043 1317 Dihedral : 31.275 173.863 4160 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.19 % Favored : 94.54 % Rotamer: Outliers : 3.06 % Allowed : 22.90 % Favored : 74.03 % 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: -0.96 (0.30), residues: 732 helix: 0.28 (0.24), residues: 490 sheet: None (None), residues: 0 loop : -2.53 (0.33), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 92 TYR 0.047 0.003 TYR N 88 PHE 0.010 0.001 PHE Q 78 HIS 0.009 0.001 HIS P 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12957) covalent geometry : angle 0.70047 / 0.41 (18797) hydrogen bonds : bond 0.05425 / 5.82 ( 628) hydrogen bonds : angle 3.14220 / 4.20 ( 1528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.79 seconds wall clock time: 32 minutes 32.29 seconds (1952.29 seconds total)