Starting phenix.real_space_refine on Fri Jul 3 21:48:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.map" model { file = "/net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gel_51294/07_2026/9gel_51294.cif" } resolution = 4.86 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 226 5.49 5 S 12 5.16 5 C 4923 2.51 5 N 1679 2.21 5 O 2119 1.98 5 H 7108 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 63 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: 16067 Number of models: 1 Model: "" Number of chains: 8 Chain: "K" Number of atoms: 3601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 3601 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "L" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 3568 Classifications: {'DNA': 113} Link IDs: {'rna3p': 112} Chain: "M" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1516 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "N" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1334 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "Q" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1575 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 1279 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "S" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "T" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 3.07, per 1000 atoms: 0.19 Number of scatterers: 16067 At special positions: 0 Unit cell: (117.047, 133.768, 84.332, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 226 15.00 O 2119 8.00 N 1679 7.00 C 4923 6.00 H 7108 1.00 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: 1.44 Conformation dependent library (CDL) restraints added in 408.6 milliseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1012 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 7 sheets defined 70.0% alpha, 2.6% beta 86 base pairs and 163 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'M' and resid 46 through 57 Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 Processing helix chain 'M' and resid 120 through 132 removed outlier: 5.530A pdb=" N ALA M 127 " --> pdb=" O ASP M 123 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG M 129 " --> pdb=" O GLN M 125 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY M 132 " --> pdb=" O ARG M 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 4.327A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ARG N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA N 76 " --> pdb=" O TYR N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.635A pdb=" N ALA N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 55 removed outlier: 4.098A pdb=" N GLN Q 55 " --> pdb=" O ILE Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 76 removed outlier: 3.699A pdb=" N PHE Q 67 " --> pdb=" O ARG Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 102 Processing helix chain 'Q' and resid 106 through 114 Processing helix chain 'Q' and resid 121 through 131 removed outlier: 3.515A pdb=" N GLN Q 125 " --> pdb=" O PRO Q 121 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG Q 129 " --> pdb=" O GLN Q 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 removed outlier: 3.681A pdb=" N GLY R 28 " --> pdb=" O ASN R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 4.544A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR R 72 " --> pdb=" O ASP R 68 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR R 73 " --> pdb=" O ALA R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 removed outlier: 3.635A pdb=" N ARG R 92 " --> pdb=" O TYR R 88 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN R 93 " --> pdb=" O ALA R 89 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 22 removed outlier: 4.019A pdb=" N ARG S 20 " --> pdb=" O THR S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 3.732A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA S 53 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE S 62 " --> pdb=" O LEU S 58 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 removed outlier: 3.836A pdb=" N LEU S 83 " --> pdb=" O ILE S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 90 through 98 removed outlier: 4.229A pdb=" N LEU S 96 " --> pdb=" O GLU S 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 47 removed outlier: 3.681A pdb=" N LYS T 46 " --> pdb=" O TYR T 42 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN T 47 " --> pdb=" O LYS T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 84 removed outlier: 4.303A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY T 75 " --> pdb=" O GLU T 71 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN T 84 " --> pdb=" O LEU T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 100 Processing helix chain 'T' and resid 104 through 123 removed outlier: 4.176A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 7.002A 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 96 through 97 removed outlier: 7.555A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.200A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'S' and resid 42 through 43 removed outlier: 7.129A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'S' and resid 77 through 78 250 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 219 hydrogen bonds 430 hydrogen bond angles 0 basepair planarities 86 basepair parallelities 163 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 7104 1.13 - 1.30: 1130 1.30 - 1.47: 4373 1.47 - 1.65: 4056 1.65 - 1.82: 20 Bond restraints: 16683 Sorted by residual: bond pdb=" N1 DG K -22 " pdb=" H1 DG K -22 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N2 DG K -23 " pdb=" H22 DG K -23 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" C8 DA K 21 " pdb=" H8 DA K 21 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD1 TYR R 88 " pdb=" HD1 TYR R 88 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" NH2 ARG M 83 " pdb="HH21 ARG M 83 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 16678 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 25627 2.67 - 5.33: 3879 5.33 - 8.00: 692 8.00 - 10.66: 34 10.66 - 13.33: 8 Bond angle restraints: 30240 Sorted by residual: angle pdb=" O4' DC K -32 " pdb=" C1' DC K -32 " pdb=" N1 DC K -32 " ideal model delta sigma weight residual 108.00 118.96 -10.96 7.00e-01 2.04e+00 2.45e+02 angle pdb=" O5' DT K 57 " pdb=" C5' DT K 57 " pdb=" C4' DT K 57 " ideal model delta sigma weight residual 109.40 120.46 -11.06 8.00e-01 1.56e+00 1.91e+02 angle pdb=" O4' DT L 38 " pdb=" C1' DT L 38 " pdb=" N1 DT L 38 " ideal model delta sigma weight residual 108.00 116.38 -8.38 7.00e-01 2.04e+00 1.43e+02 angle pdb=" O4' DT K 55 " pdb=" C1' DT K 55 " pdb=" N1 DT K 55 " ideal model delta sigma weight residual 108.00 116.13 -8.13 7.00e-01 2.04e+00 1.35e+02 angle pdb=" O5' DT K -28 " pdb=" C5' DT K -28 " pdb=" C4' DT K -28 " ideal model delta sigma weight residual 109.40 118.36 -8.96 8.00e-01 1.56e+00 1.25e+02 ... (remaining 30235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.63: 5713 34.63 - 69.26: 1108 69.26 - 103.89: 54 103.89 - 138.52: 3 138.52 - 173.16: 3 Dihedral angle restraints: 6881 sinusoidal: 5129 harmonic: 1752 Sorted by residual: dihedral pdb=" CA THR T 88 " pdb=" C THR T 88 " pdb=" N ILE T 89 " pdb=" CA ILE T 89 " ideal model delta harmonic sigma weight residual 180.00 150.68 29.32 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ARG Q 42 " pdb=" C ARG Q 42 " pdb=" N PRO Q 43 " pdb=" CA PRO Q 43 " ideal model delta harmonic sigma weight residual 180.00 150.94 29.06 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLY Q 44 " pdb=" C GLY Q 44 " pdb=" N THR Q 45 " pdb=" CA THR Q 45 " ideal model delta harmonic sigma weight residual 180.00 151.36 28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 6878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 1124 0.094 - 0.187: 395 0.187 - 0.281: 50 0.281 - 0.374: 10 0.374 - 0.468: 3 Chirality restraints: 1582 Sorted by residual: chirality pdb=" C4' DC K -32 " pdb=" C5' DC K -32 " pdb=" O4' DC K -32 " pdb=" C3' DC K -32 " both_signs ideal model delta sigma weight residual False -2.53 -2.06 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" C3' DC L -72 " pdb=" C4' DC L -72 " pdb=" O3' DC L -72 " pdb=" C2' DC L -72 " both_signs ideal model delta sigma weight residual False -2.73 -2.26 -0.47 2.00e-01 2.50e+01 5.43e+00 chirality pdb=" C3' DC L 20 " pdb=" C4' DC L 20 " pdb=" O3' DC L 20 " pdb=" C2' DC L 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.28 -0.45 2.00e-01 2.50e+01 4.98e+00 ... (remaining 1579 not shown) Planarity restraints: 1676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT L -9 " 0.545 2.00e-02 2.50e+03 2.28e-01 1.56e+03 pdb=" N1 DT L -9 " -0.024 2.00e-02 2.50e+03 pdb=" C2 DT L -9 " -0.184 2.00e-02 2.50e+03 pdb=" O2 DT L -9 " -0.237 2.00e-02 2.50e+03 pdb=" N3 DT L -9 " -0.071 2.00e-02 2.50e+03 pdb=" C4 DT L -9 " 0.081 2.00e-02 2.50e+03 pdb=" O4 DT L -9 " 0.407 2.00e-02 2.50e+03 pdb=" C5 DT L -9 " -0.081 2.00e-02 2.50e+03 pdb=" C7 DT L -9 " -0.151 2.00e-02 2.50e+03 pdb=" C6 DT L -9 " -0.105 2.00e-02 2.50e+03 pdb=" H3 DT L -9 " -0.052 2.00e-02 2.50e+03 pdb=" H6 DT L -9 " -0.129 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K -1 " 0.344 2.00e-02 2.50e+03 1.62e-01 7.87e+02 pdb=" N1 DT K -1 " 0.051 2.00e-02 2.50e+03 pdb=" C2 DT K -1 " -0.065 2.00e-02 2.50e+03 pdb=" O2 DT K -1 " -0.300 2.00e-02 2.50e+03 pdb=" N3 DT K -1 " 0.034 2.00e-02 2.50e+03 pdb=" C4 DT K -1 " 0.091 2.00e-02 2.50e+03 pdb=" O4 DT K -1 " 0.221 2.00e-02 2.50e+03 pdb=" C5 DT K -1 " -0.029 2.00e-02 2.50e+03 pdb=" C7 DT K -1 " -0.157 2.00e-02 2.50e+03 pdb=" C6 DT K -1 " -0.040 2.00e-02 2.50e+03 pdb=" H3 DT K -1 " -0.039 2.00e-02 2.50e+03 pdb=" H6 DT K -1 " -0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG L -23 " 0.391 2.00e-02 2.50e+03 1.39e-01 6.80e+02 pdb=" N9 DG L -23 " 0.011 2.00e-02 2.50e+03 pdb=" C8 DG L -23 " -0.107 2.00e-02 2.50e+03 pdb=" N7 DG L -23 " -0.068 2.00e-02 2.50e+03 pdb=" C5 DG L -23 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DG L -23 " 0.063 2.00e-02 2.50e+03 pdb=" O6 DG L -23 " 0.161 2.00e-02 2.50e+03 pdb=" N1 DG L -23 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DG L -23 " -0.098 2.00e-02 2.50e+03 pdb=" N2 DG L -23 " -0.111 2.00e-02 2.50e+03 pdb=" N3 DG L -23 " -0.123 2.00e-02 2.50e+03 pdb=" C4 DG L -23 " -0.063 2.00e-02 2.50e+03 pdb=" H8 DG L -23 " -0.154 2.00e-02 2.50e+03 pdb=" H1 DG L -23 " 0.094 2.00e-02 2.50e+03 ... (remaining 1673 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 890 2.19 - 2.79: 24582 2.79 - 3.39: 42832 3.39 - 4.00: 58332 4.00 - 4.60: 82794 Nonbonded interactions: 209430 Sorted by model distance: nonbonded pdb=" HG1 THR R 73 " pdb=" OD2 ASP R 85 " model vdw 1.583 2.450 nonbonded pdb=" HH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 1.612 2.450 nonbonded pdb=" HG SER M 57 " pdb=" OE1 GLU M 59 " model vdw 1.614 2.450 nonbonded pdb=" HH TYR N 98 " pdb=" OD2 ASP T 68 " model vdw 1.619 2.450 nonbonded pdb=" OP1 DA K 7 " pdb=" HG SER R 47 " model vdw 1.622 2.450 ... (remaining 209425 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 25 through 102) selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.540 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 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 : 0.014 0.052 9575 Z= 1.328 Angle : 2.028 11.231 13895 Z= 2.090 Chirality : 0.093 0.468 1582 Planarity : 0.038 0.245 976 Dihedral : 28.237 173.155 4161 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.26 % Favored : 94.36 % Rotamer: Outliers : 1.55 % Allowed : 4.42 % Favored : 94.04 % 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: -2.11 (0.33), residues: 532 helix: -1.11 (0.24), residues: 364 sheet: None (None), residues: 0 loop : -1.72 (0.47), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 67 TYR 0.155 0.020 TYR S 50 PHE 0.042 0.014 PHE N 100 HIS 0.017 0.004 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.01369 / 1.33 ( 9575) covalent geometry : angle 2.02790 / 2.09 (13895) hydrogen bonds : bond 0.13762 / 14.69 ( 469) hydrogen bonds : angle 7.37831 / 9.94 ( 1171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 200 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 61 LEU cc_start: 0.8767 (mt) cc_final: 0.8499 (mt) REVERT: M 90 MET cc_start: 0.8826 (mmm) cc_final: 0.8488 (tmm) REVERT: N 24 ASP cc_start: 0.6964 (m-30) cc_final: 0.6761 (m-30) REVERT: N 27 GLN cc_start: 0.7418 (mt0) cc_final: 0.7103 (tt0) REVERT: N 39 ARG cc_start: 0.9333 (mmt-90) cc_final: 0.9010 (mmt180) REVERT: N 70 VAL cc_start: 0.9066 (t) cc_final: 0.8694 (t) REVERT: N 100 PHE cc_start: 0.6518 (m-80) cc_final: 0.5878 (m-80) REVERT: Q 63 ARG cc_start: 0.8184 (mmt90) cc_final: 0.7419 (mmt90) REVERT: Q 94 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8899 (tp30) REVERT: R 31 LYS cc_start: 0.7625 (tttt) cc_final: 0.7322 (mttt) REVERT: R 54 THR cc_start: 0.7487 (m) cc_final: 0.6985 (p) REVERT: S 59 THR cc_start: 0.9671 (m) cc_final: 0.9280 (p) REVERT: T 44 VAL cc_start: 0.9336 (t) cc_final: 0.9099 (m) REVERT: T 100 LEU cc_start: 0.9357 (mm) cc_final: 0.9117 (mm) REVERT: T 105 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8892 (pm20) outliers start: 7 outliers final: 4 residues processed: 202 average time/residue: 0.2517 time to fit residues: 65.1114 Evaluate side-chains 156 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 152 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 25 ASN T 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121173 restraints weight = 68888.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.126433 restraints weight = 48518.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.129207 restraints weight = 16370.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.130987 restraints weight = 9507.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.131049 restraints weight = 6620.889| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9575 Z= 0.289 Angle : 1.033 9.111 13895 Z= 0.622 Chirality : 0.063 0.381 1582 Planarity : 0.009 0.083 976 Dihedral : 31.843 175.885 3078 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.20 % Favored : 96.24 % Rotamer: Outliers : 0.44 % Allowed : 2.21 % Favored : 97.35 % 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: -2.14 (0.32), residues: 532 helix: -1.05 (0.24), residues: 363 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 39 TYR 0.020 0.002 TYR T 40 PHE 0.032 0.003 PHE S 25 HIS 0.008 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.29 ( 9575) covalent geometry : angle 1.03339 / 0.62 (13895) hydrogen bonds : bond 0.10134 / 11.20 ( 469) hydrogen bonds : angle 5.37921 / 7.18 ( 1171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 58 THR cc_start: 0.7724 (p) cc_final: 0.7455 (p) REVERT: M 94 GLU cc_start: 0.8705 (tp30) cc_final: 0.8461 (tp30) REVERT: N 27 GLN cc_start: 0.8401 (mt0) cc_final: 0.7609 (tt0) REVERT: N 39 ARG cc_start: 0.8544 (mmt-90) cc_final: 0.8206 (mmt-90) REVERT: N 84 MET cc_start: 0.8412 (mmm) cc_final: 0.7430 (tmm) REVERT: N 100 PHE cc_start: 0.8241 (m-80) cc_final: 0.7407 (m-80) REVERT: Q 80 THR cc_start: 0.7541 (t) cc_final: 0.7291 (t) REVERT: Q 120 MET cc_start: 0.8720 (mtp) cc_final: 0.8188 (mtp) REVERT: Q 129 ARG cc_start: 0.7377 (tpp-160) cc_final: 0.7160 (tpp-160) REVERT: R 67 ARG cc_start: 0.6698 (mmt90) cc_final: 0.6204 (tmm-80) REVERT: S 23 LEU cc_start: 0.9165 (mt) cc_final: 0.8658 (mt) REVERT: S 56 GLU cc_start: 0.9277 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: S 89 ASN cc_start: 0.8816 (m-40) cc_final: 0.8604 (m110) REVERT: T 76 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8806 (tm-30) REVERT: T 80 LEU cc_start: 0.9439 (mt) cc_final: 0.9230 (mt) REVERT: T 105 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8030 (pm20) outliers start: 2 outliers final: 1 residues processed: 177 average time/residue: 0.2616 time to fit residues: 58.6367 Evaluate side-chains 147 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.136902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120397 restraints weight = 71549.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125407 restraints weight = 53477.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.128188 restraints weight = 19378.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.129159 restraints weight = 11090.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129319 restraints weight = 9125.920| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 9575 Z= 0.274 Angle : 0.928 9.812 13895 Z= 0.572 Chirality : 0.056 0.288 1582 Planarity : 0.009 0.101 976 Dihedral : 31.936 174.670 3078 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.76 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.33), residues: 532 helix: -0.96 (0.25), residues: 349 sheet: None (None), residues: 0 loop : -1.68 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG M 53 TYR 0.021 0.002 TYR R 72 PHE 0.040 0.003 PHE S 25 HIS 0.005 0.002 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.27 ( 9575) covalent geometry : angle 0.92844 / 0.57 (13895) hydrogen bonds : bond 0.10132 / 10.72 ( 469) hydrogen bonds : angle 5.14971 / 6.85 ( 1171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8453 (mt0) cc_final: 0.7795 (tt0) REVERT: N 84 MET cc_start: 0.8551 (mmm) cc_final: 0.7676 (tmm) REVERT: N 97 LEU cc_start: 0.8932 (tp) cc_final: 0.8701 (tp) REVERT: N 100 PHE cc_start: 0.8061 (m-80) cc_final: 0.7367 (m-80) REVERT: Q 62 ILE cc_start: 0.8894 (mm) cc_final: 0.8663 (mm) REVERT: Q 94 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8060 (tp30) REVERT: Q 120 MET cc_start: 0.8779 (mtp) cc_final: 0.8507 (mtp) REVERT: R 67 ARG cc_start: 0.6932 (mmt90) cc_final: 0.6168 (tmm-80) REVERT: T 76 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8476 (tm-30) REVERT: T 105 GLU cc_start: 0.8223 (mm-30) cc_final: 0.8009 (pm20) REVERT: T 115 THR cc_start: 0.8094 (t) cc_final: 0.7849 (t) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2329 time to fit residues: 47.6910 Evaluate side-chains 133 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.138575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.120932 restraints weight = 68787.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126603 restraints weight = 47647.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.129893 restraints weight = 16952.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130345 restraints weight = 10655.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.131481 restraints weight = 8233.436| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9575 Z= 0.227 Angle : 0.848 9.022 13895 Z= 0.522 Chirality : 0.052 0.285 1582 Planarity : 0.007 0.065 976 Dihedral : 32.049 174.746 3078 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.01 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % 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: -1.50 (0.33), residues: 532 helix: -0.56 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -1.66 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 32 TYR 0.015 0.002 TYR R 72 PHE 0.030 0.002 PHE S 25 HIS 0.006 0.002 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.23 ( 9575) covalent geometry : angle 0.84757 / 0.52 (13895) hydrogen bonds : bond 0.09283 / 9.69 ( 469) hydrogen bonds : angle 4.77798 / 6.26 ( 1171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8482 (mt0) cc_final: 0.7722 (tt0) REVERT: N 100 PHE cc_start: 0.8131 (m-80) cc_final: 0.7752 (m-80) REVERT: Q 94 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8092 (tp30) REVERT: Q 120 MET cc_start: 0.8922 (mtp) cc_final: 0.8573 (mtp) REVERT: Q 122 LYS cc_start: 0.8911 (pptt) cc_final: 0.8646 (pptt) REVERT: R 67 ARG cc_start: 0.7014 (mmt90) cc_final: 0.6154 (tmm-80) REVERT: T 33 ARG cc_start: 0.7105 (mtm180) cc_final: 0.6827 (ptp-170) REVERT: T 76 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8486 (tm-30) REVERT: T 105 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7897 (pm20) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2401 time to fit residues: 44.4137 Evaluate side-chains 129 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 8.9990 chunk 52 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.138764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.120436 restraints weight = 72125.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126799 restraints weight = 52973.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.128905 restraints weight = 19193.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.129929 restraints weight = 14670.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.130625 restraints weight = 10802.816| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9575 Z= 0.228 Angle : 0.835 8.697 13895 Z= 0.515 Chirality : 0.050 0.284 1582 Planarity : 0.007 0.121 976 Dihedral : 32.076 175.087 3078 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: -1.26 (0.34), residues: 532 helix: -0.33 (0.25), residues: 351 sheet: None (None), residues: 0 loop : -1.67 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 35 TYR 0.019 0.002 TYR R 72 PHE 0.017 0.002 PHE S 25 HIS 0.012 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.23 ( 9575) covalent geometry : angle 0.83518 / 0.51 (13895) hydrogen bonds : bond 0.09042 / 9.34 ( 469) hydrogen bonds : angle 4.66219 / 6.17 ( 1171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8426 (mt0) cc_final: 0.7672 (tt0) REVERT: N 100 PHE cc_start: 0.8069 (m-80) cc_final: 0.7278 (m-80) REVERT: Q 62 ILE cc_start: 0.8789 (mm) cc_final: 0.8531 (mm) REVERT: Q 94 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8143 (tp30) REVERT: Q 120 MET cc_start: 0.9022 (mtp) cc_final: 0.8701 (mtp) REVERT: R 67 ARG cc_start: 0.7212 (mmt90) cc_final: 0.6217 (tmm-80) REVERT: S 94 ASN cc_start: 0.7861 (t0) cc_final: 0.7648 (t0) REVERT: T 33 ARG cc_start: 0.7245 (mtm180) cc_final: 0.6891 (ptp-170) REVERT: T 105 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7939 (pm20) REVERT: T 115 THR cc_start: 0.8104 (t) cc_final: 0.7691 (t) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2384 time to fit residues: 43.5407 Evaluate side-chains 130 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 44 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.135327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115708 restraints weight = 72230.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.122129 restraints weight = 55075.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.125569 restraints weight = 20318.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.125949 restraints weight = 13923.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.126877 restraints weight = 10550.009| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 9575 Z= 0.323 Angle : 0.934 9.150 13895 Z= 0.565 Chirality : 0.055 0.266 1582 Planarity : 0.008 0.113 976 Dihedral : 32.273 175.365 3078 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 35.23 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.70 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -1.96 (0.33), residues: 532 helix: -0.85 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -2.01 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 35 TYR 0.021 0.002 TYR T 40 PHE 0.018 0.003 PHE N 100 HIS 0.012 0.004 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.32 ( 9575) covalent geometry : angle 0.93385 / 0.57 (13895) hydrogen bonds : bond 0.11280 / 11.77 ( 469) hydrogen bonds : angle 5.23748 / 6.97 ( 1171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8387 (mt0) cc_final: 0.7700 (tt0) REVERT: N 100 PHE cc_start: 0.8095 (m-80) cc_final: 0.7254 (m-80) REVERT: Q 72 ARG cc_start: 0.8219 (mtp85) cc_final: 0.7978 (mtt180) REVERT: Q 94 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8204 (tp30) REVERT: R 67 ARG cc_start: 0.7459 (mmt90) cc_final: 0.6082 (tmm-80) REVERT: S 94 ASN cc_start: 0.8002 (t0) cc_final: 0.7801 (t0) REVERT: T 33 ARG cc_start: 0.7391 (mtm180) cc_final: 0.6974 (ptp-170) REVERT: T 76 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8583 (tm-30) REVERT: T 105 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7985 (pm20) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2561 time to fit residues: 44.4562 Evaluate side-chains 125 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.0070 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.141253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.122852 restraints weight = 70908.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129269 restraints weight = 51817.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.131924 restraints weight = 18789.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133360 restraints weight = 13221.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.133754 restraints weight = 9417.331| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.5297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9575 Z= 0.191 Angle : 0.804 8.789 13895 Z= 0.497 Chirality : 0.050 0.290 1582 Planarity : 0.008 0.135 976 Dihedral : 32.235 174.805 3078 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.38 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.34), residues: 532 helix: -0.20 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -1.64 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 129 TYR 0.017 0.002 TYR R 72 PHE 0.057 0.002 PHE S 25 HIS 0.026 0.004 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.19 ( 9575) covalent geometry : angle 0.80395 / 0.50 (13895) hydrogen bonds : bond 0.08318 / 8.39 ( 469) hydrogen bonds : angle 4.38515 / 5.80 ( 1171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8333 (mt0) cc_final: 0.7559 (tt0) REVERT: N 100 PHE cc_start: 0.8030 (m-80) cc_final: 0.7158 (m-80) REVERT: Q 94 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8172 (tp30) REVERT: R 67 ARG cc_start: 0.7359 (mmt90) cc_final: 0.5957 (tmm-80) REVERT: S 94 ASN cc_start: 0.7788 (t0) cc_final: 0.7582 (t0) REVERT: T 33 ARG cc_start: 0.7261 (mtm180) cc_final: 0.6893 (ptp-170) REVERT: T 105 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7737 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2342 time to fit residues: 40.3624 Evaluate side-chains 123 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 31 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.140033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121564 restraints weight = 71310.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128308 restraints weight = 50631.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.130428 restraints weight = 18297.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.132136 restraints weight = 13735.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.132542 restraints weight = 9419.751| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9575 Z= 0.207 Angle : 0.791 8.599 13895 Z= 0.489 Chirality : 0.048 0.291 1582 Planarity : 0.006 0.061 976 Dihedral : 32.202 174.855 3078 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.38 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.00 (0.34), residues: 532 helix: -0.11 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -1.63 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 128 TYR 0.017 0.002 TYR R 72 PHE 0.015 0.002 PHE S 25 HIS 0.009 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.21 ( 9575) covalent geometry : angle 0.79098 / 0.49 (13895) hydrogen bonds : bond 0.08314 / 8.43 ( 469) hydrogen bonds : angle 4.39914 / 5.81 ( 1171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8286 (mt0) cc_final: 0.7544 (tt0) REVERT: N 100 PHE cc_start: 0.8008 (m-80) cc_final: 0.7213 (m-80) REVERT: Q 94 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8184 (tp30) REVERT: R 67 ARG cc_start: 0.7375 (mmt90) cc_final: 0.5912 (tmm-80) REVERT: S 91 GLU cc_start: 0.8949 (pm20) cc_final: 0.8365 (pm20) REVERT: S 94 ASN cc_start: 0.7848 (t0) cc_final: 0.7630 (t0) REVERT: T 33 ARG cc_start: 0.7269 (mtm180) cc_final: 0.6927 (ptp-170) REVERT: T 105 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7778 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2179 time to fit residues: 38.4191 Evaluate side-chains 124 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.137934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119649 restraints weight = 72626.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.125724 restraints weight = 55404.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.128668 restraints weight = 20761.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.129493 restraints weight = 14355.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130377 restraints weight = 10684.921| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 9575 Z= 0.253 Angle : 0.826 8.385 13895 Z= 0.508 Chirality : 0.050 0.276 1582 Planarity : 0.007 0.085 976 Dihedral : 32.236 174.803 3078 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 26.27 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.51 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.33), residues: 532 helix: -0.32 (0.25), residues: 356 sheet: None (None), residues: 0 loop : -2.05 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 29 TYR 0.018 0.002 TYR R 72 PHE 0.020 0.002 PHE S 25 HIS 0.007 0.002 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.25 ( 9575) covalent geometry : angle 0.82553 / 0.51 (13895) hydrogen bonds : bond 0.09158 / 9.38 ( 469) hydrogen bonds : angle 4.66066 / 6.19 ( 1171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 59 GLU cc_start: 0.8349 (mp0) cc_final: 0.8094 (mp0) REVERT: N 27 GLN cc_start: 0.8323 (mt0) cc_final: 0.7626 (tt0) REVERT: N 100 PHE cc_start: 0.8088 (m-80) cc_final: 0.7501 (m-80) REVERT: Q 94 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8236 (tp30) REVERT: R 45 ARG cc_start: 0.7254 (mtp85) cc_final: 0.7041 (mtp85) REVERT: R 67 ARG cc_start: 0.7515 (mmt90) cc_final: 0.5875 (tmm-80) REVERT: S 91 GLU cc_start: 0.8984 (pm20) cc_final: 0.8469 (pm20) REVERT: S 94 ASN cc_start: 0.7824 (t0) cc_final: 0.7606 (t0) REVERT: T 33 ARG cc_start: 0.7263 (mtm180) cc_final: 0.6915 (ptp-170) REVERT: T 96 THR cc_start: 0.9266 (m) cc_final: 0.9042 (m) REVERT: T 105 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7821 (pm20) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2086 time to fit residues: 37.8687 Evaluate side-chains 120 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.142407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.123173 restraints weight = 70822.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.130435 restraints weight = 50946.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.132805 restraints weight = 18110.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.134106 restraints weight = 13642.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.134658 restraints weight = 9736.216| |-----------------------------------------------------------------------------| r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9575 Z= 0.182 Angle : 0.754 8.727 13895 Z= 0.469 Chirality : 0.047 0.290 1582 Planarity : 0.006 0.056 976 Dihedral : 32.194 174.176 3078 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.56 % Allowed : 2.26 % Favored : 97.18 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.35), residues: 532 helix: 0.21 (0.26), residues: 349 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 128 TYR 0.028 0.002 TYR T 37 PHE 0.016 0.001 PHE S 25 HIS 0.008 0.002 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.18 ( 9575) covalent geometry : angle 0.75379 / 0.47 (13895) hydrogen bonds : bond 0.07475 / 7.41 ( 469) hydrogen bonds : angle 4.19432 / 5.56 ( 1171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 27 GLN cc_start: 0.8177 (mt0) cc_final: 0.7472 (tt0) REVERT: N 100 PHE cc_start: 0.7835 (m-80) cc_final: 0.7428 (m-80) REVERT: Q 94 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8236 (tp30) REVERT: Q 120 MET cc_start: 0.8973 (mtp) cc_final: 0.8769 (mtp) REVERT: R 67 ARG cc_start: 0.7450 (mmt90) cc_final: 0.5832 (tmm-80) REVERT: R 78 ARG cc_start: 0.8271 (mtm180) cc_final: 0.8041 (mtm180) REVERT: S 91 GLU cc_start: 0.8891 (pm20) cc_final: 0.8381 (pm20) REVERT: T 33 ARG cc_start: 0.7365 (mtm180) cc_final: 0.7032 (ptp-170) REVERT: T 105 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7767 (pm20) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1879 time to fit residues: 33.8316 Evaluate side-chains 124 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 33 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.122184 restraints weight = 71803.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.129127 restraints weight = 52660.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.131887 restraints weight = 19765.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.132891 restraints weight = 14060.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.133166 restraints weight = 10197.083| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9575 Z= 0.189 Angle : 0.749 8.673 13895 Z= 0.466 Chirality : 0.047 0.293 1582 Planarity : 0.006 0.054 976 Dihedral : 32.165 174.258 3078 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.01 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.35), residues: 532 helix: 0.22 (0.26), residues: 355 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 45 TYR 0.017 0.002 TYR R 72 PHE 0.036 0.002 PHE Q 84 HIS 0.004 0.001 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.19 ( 9575) covalent geometry : angle 0.74947 / 0.47 (13895) hydrogen bonds : bond 0.07571 / 7.54 ( 469) hydrogen bonds : angle 4.16513 / 5.55 ( 1171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2567.84 seconds wall clock time: 44 minutes 29.74 seconds (2669.74 seconds total)