Starting phenix.real_space_refine on Thu Aug 6 17:25:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gel_51294/08_2026/9gel_51294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gel_51294/08_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_51294/08_2026/9gel_51294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gel_51294/08_2026/9gel_51294.map" model { file = "/net/cci-nas-00/data/ceres_data/9gel_51294/08_2026/9gel_51294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gel_51294/08_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-2.2rc3-6140/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: 3.21, per 1000 atoms: 0.20 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: 1.41 Conformation dependent library (CDL) restraints added in 332.1 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: 2.96 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: 3.42 Time building geometry restraints manager: 1.95 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: 25594 2.67 - 5.33: 3908 5.33 - 8.00: 695 8.00 - 10.66: 35 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: 5.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.100 Extract box with map and model: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.420 Find NCS groups from input model: 0.110 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.100 ------------------------------------------------------------------------------- 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= 1.329 Angle : 2.039 11.231 13895 Z= 2.103 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 2.03929 / 2.10 (13895) hydrogen bonds : bond 0.13762 / 14.72 ( 469) hydrogen bonds : angle 7.37831 / 9.95 ( 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 : 0.274 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: M 61 LEU cc_start: 0.8767 (mt) cc_final: 0.8496 (mt) REVERT: M 90 MET cc_start: 0.8826 (mmm) cc_final: 0.8488 (tmm) REVERT: N 39 ARG cc_start: 0.9333 (mmt-90) cc_final: 0.9012 (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 94 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8899 (tp30) REVERT: R 31 LYS cc_start: 0.7625 (tttt) cc_final: 0.7255 (mttt) REVERT: R 54 THR cc_start: 0.7487 (m) cc_final: 0.6986 (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: 0.8891 (pm20) outliers start: 7 outliers final: 4 residues processed: 202 average time/residue: 0.2275 time to fit residues: 59.1965 Evaluate side-chains 153 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 149 time to evaluate : 0.317 ------------------------------------------------------------------------------- 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: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.138209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.121317 restraints weight = 70397.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.126282 restraints weight = 50132.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129252 restraints weight = 18259.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130231 restraints weight = 10334.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.130367 restraints weight = 8709.703| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9575 Z= 0.298 Angle : 1.074 9.288 13895 Z= 0.636 Chirality : 0.065 0.407 1582 Planarity : 0.009 0.084 976 Dihedral : 31.825 175.077 3078 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 21.85 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.38 % Favored : 96.05 % 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: -2.12 (0.32), residues: 532 helix: -1.04 (0.24), residues: 356 sheet: None (None), residues: 0 loop : -1.91 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 39 TYR 0.022 0.002 TYR T 40 PHE 0.031 0.003 PHE S 25 HIS 0.007 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.30 ( 9575) covalent geometry : angle 1.07352 / 0.64 (13895) hydrogen bonds : bond 0.10321 / 11.51 ( 469) hydrogen bonds : angle 5.42067 / 7.23 ( 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 175 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 173 time to evaluate : 0.207 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: M 58 THR cc_start: 0.7747 (p) cc_final: 0.7481 (p) REVERT: M 94 GLU cc_start: 0.8720 (tp30) cc_final: 0.8462 (tp30) REVERT: N 27 GLN cc_start: 0.8417 (mt0) cc_final: 0.7749 (tt0) REVERT: N 39 ARG cc_start: 0.8534 (mmt-90) cc_final: 0.8252 (mmt-90) REVERT: N 84 MET cc_start: 0.8465 (mmm) cc_final: 0.7498 (tmm) REVERT: N 100 PHE cc_start: 0.8250 (m-80) cc_final: 0.7423 (m-80) REVERT: Q 80 THR cc_start: 0.7554 (t) cc_final: 0.7318 (t) REVERT: Q 120 MET cc_start: 0.8722 (mtp) cc_final: 0.8271 (mtp) REVERT: Q 129 ARG cc_start: 0.7366 (tpp-160) cc_final: 0.7147 (tpp-160) REVERT: R 67 ARG cc_start: 0.6737 (mmt90) cc_final: 0.6209 (tmm-80) REVERT: S 23 LEU cc_start: 0.9170 (mt) cc_final: 0.8683 (mt) REVERT: S 56 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.8361 (mt-10) REVERT: S 89 ASN cc_start: 0.8805 (m-40) cc_final: 0.8588 (m110) REVERT: T 76 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8814 (tm-30) REVERT: T 80 LEU cc_start: 0.9441 (mt) cc_final: 0.9240 (mt) REVERT: T 105 GLU cc_start: 0.8252 (mm-30) cc_final: 0.8021 (pm20) outliers start: 2 outliers final: 1 residues processed: 174 average time/residue: 0.1984 time to fit residues: 44.3275 Evaluate side-chains 145 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 143 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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: 0.8980 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... R 25 ASN T 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.137525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120926 restraints weight = 72110.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.126050 restraints weight = 52780.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.129254 restraints weight = 19161.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.129482 restraints weight = 11882.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.130340 restraints weight = 9394.964| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 9575 Z= 0.264 Angle : 0.931 10.124 13895 Z= 0.570 Chirality : 0.056 0.289 1582 Planarity : 0.008 0.079 976 Dihedral : 31.832 174.169 3078 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.57 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: -1.89 (0.33), residues: 532 helix: -0.89 (0.25), residues: 355 sheet: None (None), residues: 0 loop : -1.76 (0.44), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 53 TYR 0.020 0.002 TYR R 72 PHE 0.033 0.003 PHE S 25 HIS 0.005 0.002 HIS S 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.26 ( 9575) covalent geometry : angle 0.93061 / 0.57 (13895) hydrogen bonds : bond 0.09940 / 10.64 ( 469) hydrogen bonds : angle 5.12361 / 6.81 ( 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 156 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.298 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: M 94 GLU cc_start: 0.8884 (tp30) cc_final: 0.8472 (tp30) REVERT: N 27 GLN cc_start: 0.8476 (mt0) cc_final: 0.7794 (tt0) REVERT: N 84 MET cc_start: 0.8523 (mmm) cc_final: 0.7656 (tmm) REVERT: N 97 LEU cc_start: 0.8921 (tp) cc_final: 0.8706 (tp) REVERT: N 100 PHE cc_start: 0.8055 (m-80) cc_final: 0.7373 (m-80) REVERT: Q 62 ILE cc_start: 0.8909 (mm) cc_final: 0.8252 (mm) REVERT: Q 63 ARG cc_start: 0.8392 (mmt90) cc_final: 0.7153 (mmt90) REVERT: Q 120 MET cc_start: 0.8782 (mtp) cc_final: 0.8274 (mtp) REVERT: R 67 ARG cc_start: 0.6893 (mmt90) cc_final: 0.6214 (tmm-80) REVERT: S 24 GLN cc_start: 0.8770 (mp10) cc_final: 0.7986 (mp10) REVERT: T 76 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8454 (tm-30) REVERT: T 115 THR cc_start: 0.8080 (t) cc_final: 0.7856 (t) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1855 time to fit residues: 38.5507 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 : 0.272 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN T 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.140503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.121266 restraints weight = 67742.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127673 restraints weight = 48118.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.131726 restraints weight = 17454.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.131606 restraints weight = 11104.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132661 restraints weight = 8860.870| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9575 Z= 0.209 Angle : 0.831 10.223 13895 Z= 0.511 Chirality : 0.051 0.322 1582 Planarity : 0.007 0.132 976 Dihedral : 31.922 174.272 3078 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.56 % Allowed : 2.63 % Favored : 96.80 % 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: -1.31 (0.33), residues: 532 helix: -0.43 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -1.55 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG N 39 TYR 0.015 0.002 TYR R 72 PHE 0.042 0.003 PHE S 25 HIS 0.010 0.002 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.21 ( 9575) covalent geometry : angle 0.83078 / 0.51 (13895) hydrogen bonds : bond 0.08711 / 9.07 ( 469) hydrogen bonds : angle 4.57403 / 5.96 ( 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 141 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.328 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: N 27 GLN cc_start: 0.8474 (mt0) cc_final: 0.7792 (tt0) REVERT: N 100 PHE cc_start: 0.8119 (m-80) cc_final: 0.7755 (m-80) REVERT: Q 120 MET cc_start: 0.8928 (mtp) cc_final: 0.8540 (mtp) REVERT: Q 122 LYS cc_start: 0.8937 (pptt) cc_final: 0.8709 (pptt) REVERT: Q 129 ARG cc_start: 0.7791 (tpt170) cc_final: 0.7511 (tpp-160) REVERT: R 67 ARG cc_start: 0.6970 (mmt90) cc_final: 0.6205 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2259 time to fit residues: 41.6922 Evaluate side-chains 126 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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: 9.9990 chunk 52 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.138911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.121685 restraints weight = 71488.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.127334 restraints weight = 49103.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.130065 restraints weight = 17382.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.130834 restraints weight = 11619.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.131274 restraints weight = 8639.980| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.4835 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= 0.231 Angle : 0.841 10.629 13895 Z= 0.515 Chirality : 0.051 0.311 1582 Planarity : 0.006 0.075 976 Dihedral : 31.948 174.808 3078 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % 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: -1.12 (0.34), residues: 532 helix: -0.25 (0.26), residues: 350 sheet: None (None), residues: 0 loop : -1.56 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 39 TYR 0.018 0.002 TYR R 72 PHE 0.032 0.003 PHE S 25 HIS 0.014 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.23 ( 9575) covalent geometry : angle 0.84059 / 0.52 (13895) hydrogen bonds : bond 0.09139 / 9.53 ( 469) hydrogen bonds : angle 4.62095 / 6.11 ( 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 136 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.335 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: 0.8470 (mt0) cc_final: 0.7712 (tt0) REVERT: N 100 PHE cc_start: 0.8075 (m-80) cc_final: 0.7284 (m-10) REVERT: Q 120 MET cc_start: 0.9011 (mtp) cc_final: 0.8720 (mtp) REVERT: R 67 ARG cc_start: 0.7187 (mmt90) cc_final: 0.6208 (tmm-80) REVERT: T 115 THR cc_start: 0.8065 (t) cc_final: 0.7746 (t) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1996 time to fit residues: 36.0899 Evaluate side-chains 127 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.295 ------------------------------------------------------------------------------- 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: 9.9990 chunk 4 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 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 = 0.3958 r_free = 0.3958 target = 0.135001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.115282 restraints weight = 71388.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.121481 restraints weight = 53109.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.125700 restraints weight = 19416.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.125587 restraints weight = 12488.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.126068 restraints weight = 9697.606| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 9575 Z= 0.321 Angle : 0.946 10.715 13895 Z= 0.567 Chirality : 0.055 0.287 1582 Planarity : 0.008 0.100 976 Dihedral : 32.094 175.055 3078 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 35.48 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.51 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: -1.95 (0.33), residues: 532 helix: -0.83 (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 0.014 0.001 ARG S 35 TYR 0.020 0.002 TYR T 40 PHE 0.018 0.002 PHE N 100 HIS 0.017 0.004 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.32 ( 9575) covalent geometry : angle 0.94628 / 0.57 (13895) hydrogen bonds : bond 0.11182 / 11.72 ( 469) hydrogen bonds : angle 5.21532 / 6.92 ( 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 128 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.335 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: N 27 GLN cc_start: 0.8415 (mt0) cc_final: 0.7744 (tt0) REVERT: Q 72 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7957 (mtt180) REVERT: R 67 ARG cc_start: 0.7459 (mmt90) cc_final: 0.6122 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2253 time to fit residues: 36.9572 Evaluate side-chains 117 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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: 2.9990 chunk 44 optimal weight: 10.0000 chunk 27 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.139718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.123295 restraints weight = 70786.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.128925 restraints weight = 49817.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.130845 restraints weight = 17334.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.132361 restraints weight = 12374.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.132696 restraints weight = 8246.489| |-----------------------------------------------------------------------------| r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6548 moved from start: 0.5311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9575 Z= 0.201 Angle : 0.817 11.386 13895 Z= 0.502 Chirality : 0.051 0.305 1582 Planarity : 0.007 0.088 976 Dihedral : 32.068 174.754 3078 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.57 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: -1.30 (0.34), residues: 532 helix: -0.35 (0.25), residues: 350 sheet: None (None), residues: 0 loop : -1.72 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Q 129 TYR 0.016 0.002 TYR R 72 PHE 0.014 0.002 PHE S 25 HIS 0.012 0.003 HIS M 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.20 ( 9575) covalent geometry : angle 0.81687 / 0.50 (13895) hydrogen bonds : bond 0.08676 / 8.83 ( 469) hydrogen bonds : angle 4.53495 / 5.97 ( 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 129 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.216 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: N 27 GLN cc_start: 0.8462 (mt0) cc_final: 0.7766 (tt0) REVERT: N 100 PHE cc_start: 0.8048 (m-80) cc_final: 0.7254 (m-80) REVERT: R 67 ARG cc_start: 0.7447 (mmt90) cc_final: 0.5928 (tmm-80) REVERT: S 94 ASN cc_start: 0.7834 (t0) cc_final: 0.7633 (t0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1865 time to fit residues: 31.8588 Evaluate side-chains 119 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.316 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.4020 r_free = 0.4020 target = 0.140584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.121663 restraints weight = 72035.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.128247 restraints weight = 52502.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130814 restraints weight = 19227.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.132342 restraints weight = 13698.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132689 restraints weight = 9636.825| |-----------------------------------------------------------------------------| r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9575 Z= 0.197 Angle : 0.794 11.591 13895 Z= 0.488 Chirality : 0.049 0.311 1582 Planarity : 0.007 0.115 976 Dihedral : 32.053 174.597 3078 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.20 % Favored : 96.24 % 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: -1.06 (0.34), residues: 532 helix: -0.13 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -1.70 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG N 39 TYR 0.015 0.002 TYR R 72 PHE 0.009 0.002 PHE S 25 HIS 0.008 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.20 ( 9575) covalent geometry : angle 0.79376 / 0.49 (13895) hydrogen bonds : bond 0.08153 / 8.27 ( 469) hydrogen bonds : angle 4.39276 / 5.85 ( 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 134 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.234 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: 0.8354 (mt0) cc_final: 0.7686 (tt0) REVERT: N 100 PHE cc_start: 0.7986 (m-80) cc_final: 0.7201 (m-80) REVERT: R 67 ARG cc_start: 0.7400 (mmt90) cc_final: 0.5894 (tmm-80) REVERT: S 94 ASN cc_start: 0.7890 (t0) cc_final: 0.7685 (t0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1922 time to fit residues: 33.9808 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 : 0.190 ------------------------------------------------------------------------------- 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: 20.0000 chunk 36 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.4012 r_free = 0.4012 target = 0.139700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120640 restraints weight = 72199.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127125 restraints weight = 51784.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.130040 restraints weight = 19223.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131328 restraints weight = 13306.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.131886 restraints weight = 9688.832| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9575 Z= 0.215 Angle : 0.798 11.714 13895 Z= 0.489 Chirality : 0.049 0.303 1582 Planarity : 0.006 0.068 976 Dihedral : 32.049 174.526 3078 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.34), residues: 532 helix: -0.12 (0.26), residues: 349 sheet: None (None), residues: 0 loop : -1.82 (0.45), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG S 29 TYR 0.018 0.002 TYR R 72 PHE 0.010 0.002 PHE Q 104 HIS 0.009 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.22 ( 9575) covalent geometry : angle 0.79777 / 0.49 (13895) hydrogen bonds : bond 0.08353 / 8.52 ( 469) hydrogen bonds : angle 4.43451 / 5.90 ( 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 136 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.320 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: M 59 GLU cc_start: 0.8320 (mp0) cc_final: 0.8069 (mp0) REVERT: N 27 GLN cc_start: 0.8306 (mt0) cc_final: 0.7684 (tt0) REVERT: N 100 PHE cc_start: 0.7989 (m-80) cc_final: 0.7163 (m-80) REVERT: R 67 ARG cc_start: 0.7476 (mmt90) cc_final: 0.5911 (tmm-80) REVERT: S 91 GLU cc_start: 0.8937 (pm20) cc_final: 0.8387 (pm20) REVERT: T 96 THR cc_start: 0.9423 (m) cc_final: 0.9105 (m) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1740 time to fit residues: 31.8354 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 : 0.311 ------------------------------------------------------------------------------- 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: 7.9990 chunk 66 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 52 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.4059 r_free = 0.4059 target = 0.143593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.124737 restraints weight = 72437.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131920 restraints weight = 52760.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134082 restraints weight = 19025.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.135288 restraints weight = 14547.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.135480 restraints weight = 10450.830| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.5818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9575 Z= 0.175 Angle : 0.753 11.883 13895 Z= 0.464 Chirality : 0.048 0.316 1582 Planarity : 0.006 0.050 976 Dihedral : 32.020 174.126 3078 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.56 % Allowed : 1.88 % Favored : 97.56 % 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: -0.75 (0.35), residues: 532 helix: 0.20 (0.26), residues: 355 sheet: None (None), residues: 0 loop : -1.84 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 128 TYR 0.024 0.002 TYR T 37 PHE 0.022 0.002 PHE S 25 HIS 0.009 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.18 ( 9575) covalent geometry : angle 0.75268 / 0.46 (13895) hydrogen bonds : bond 0.07213 / 7.14 ( 469) hydrogen bonds : angle 4.03765 / 5.38 ( 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 141 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.220 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: N 27 GLN cc_start: 0.8243 (mt0) cc_final: 0.7614 (tt0) REVERT: N 100 PHE cc_start: 0.7891 (m-80) cc_final: 0.7481 (m-80) REVERT: Q 120 MET cc_start: 0.9013 (mtp) cc_final: 0.8766 (mtp) REVERT: R 67 ARG cc_start: 0.7366 (mmt90) cc_final: 0.5845 (tmm-80) REVERT: S 91 GLU cc_start: 0.8914 (pm20) cc_final: 0.8345 (pm20) REVERT: S 94 ASN cc_start: 0.7834 (t0) cc_final: 0.7609 (t0) REVERT: T 96 THR cc_start: 0.9359 (m) cc_final: 0.8964 (p) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.1924 time to fit residues: 36.1435 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 : 0.271 ------------------------------------------------------------------------------- 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: 10.0000 chunk 60 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 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 = 0.4033 r_free = 0.4033 target = 0.141527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.122746 restraints weight = 72057.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.129356 restraints weight = 52724.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131579 restraints weight = 19292.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.133330 restraints weight = 14275.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133510 restraints weight = 9811.255| |-----------------------------------------------------------------------------| r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9575 Z= 0.197 Angle : 0.765 11.564 13895 Z= 0.471 Chirality : 0.047 0.309 1582 Planarity : 0.006 0.061 976 Dihedral : 31.993 174.177 3078 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.01 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.88 (0.35), residues: 532 helix: 0.11 (0.26), residues: 355 sheet: None (None), residues: 0 loop : -1.90 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 128 TYR 0.017 0.002 TYR R 72 PHE 0.040 0.003 PHE S 25 HIS 0.007 0.002 HIS S 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.20 ( 9575) covalent geometry : angle 0.76471 / 0.47 (13895) hydrogen bonds : bond 0.07635 / 7.69 ( 469) hydrogen bonds : angle 4.17042 / 5.56 ( 1171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2355.91 seconds wall clock time: 40 minutes 53.65 seconds (2453.65 seconds total)