Starting phenix.real_space_refine on Thu Feb 5 08:50:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gel_51294/02_2026/9gel_51294.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gel_51294/02_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_51294/02_2026/9gel_51294.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gel_51294/02_2026/9gel_51294.map" model { file = "/net/cci-nas-00/data/ceres_data/9gel_51294/02_2026/9gel_51294.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gel_51294/02_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-2.0-5952/lib/python3.9/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: 2.39, per 1000 atoms: 0.15 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: 0.88 Conformation dependent library (CDL) restraints added in 303.0 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: 2.58 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: 3.37 Time building geometry restraints manager: 1.35 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: 25604 2.67 - 5.33: 3935 5.33 - 8.00: 671 8.00 - 10.66: 27 10.66 - 13.33: 3 Bond angle restraints: 30240 Sorted by residual: angle pdb=" C4' DG L 25 " pdb=" C3' DG L 25 " pdb=" O3' DG L 25 " ideal model delta sigma weight residual 110.00 120.58 -10.58 1.50e+00 4.44e-01 4.97e+01 angle pdb=" O4' DC K -32 " pdb=" C1' DC K -32 " pdb=" N1 DC K -32 " ideal model delta sigma weight residual 108.40 118.96 -10.56 1.50e+00 4.44e-01 4.96e+01 angle pdb=" O5' DT K 57 " pdb=" C5' DT K 57 " pdb=" C4' DT K 57 " ideal model delta sigma weight residual 110.80 120.46 -9.66 1.50e+00 4.44e-01 4.15e+01 angle pdb=" C5' DT K 57 " pdb=" C4' DT K 57 " pdb=" O4' DT K 57 " ideal model delta sigma weight residual 109.40 118.60 -9.20 1.50e+00 4.44e-01 3.76e+01 angle pdb=" O3' DC K 11 " pdb=" C3' DC K 11 " pdb=" C2' DC K 11 " ideal model delta sigma weight residual 111.50 120.63 -9.13 1.50e+00 4.44e-01 3.71e+01 ... (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 - 0.092: 1151 0.092 - 0.185: 360 0.185 - 0.277: 58 0.277 - 0.369: 10 0.369 - 0.462: 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 -0.46 2.00e-01 2.50e+01 5.33e+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 -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.91e+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 -2.66 -2.28 -0.38 2.00e-01 2.50e+01 3.53e+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: 4.160 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: 0.070 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.530 Find NCS groups from input model: 0.100 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 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 : 0.013 0.051 9575 Z= 0.736 Angle : 2.009 10.579 13895 Z= 1.322 Chirality : 0.090 0.462 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 covalent geometry : bond 0.01338 ( 9575) covalent geometry : angle 2.00869 (13895) hydrogen bonds : bond 0.13762 ( 469) hydrogen bonds : angle 7.37831 ( 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 : 0.328 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2536 time to fit residues: 64.6156 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 : 0.302 ------------------------------------------------------------------------------- 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: 0.9990 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: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.138792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.121469 restraints weight = 68765.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.127075 restraints weight = 47825.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.130208 restraints weight = 16733.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131094 restraints weight = 10608.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.131477 restraints weight = 7758.388| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9575 Z= 0.292 Angle : 0.843 7.564 13895 Z= 0.512 Chirality : 0.048 0.203 1582 Planarity : 0.007 0.064 976 Dihedral : 31.739 172.165 3078 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 19.98 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.01 % Favored : 96.62 % Rotamer: Outliers : 0.44 % Allowed : 2.65 % 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: -1.27 (0.33), residues: 532 helix: -0.39 (0.25), residues: 356 sheet: None (None), residues: 0 loop : -1.56 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 39 TYR 0.019 0.002 TYR R 72 PHE 0.018 0.003 PHE S 25 HIS 0.007 0.002 HIS S 31 Details of bonding type rmsd covalent geometry : bond 0.00630 ( 9575) covalent geometry : angle 0.84328 (13895) hydrogen bonds : bond 0.09030 ( 469) hydrogen bonds : angle 4.72859 ( 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 : 0.324 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 94 GLU cc_start: 0.8708 (tp30) cc_final: 0.8395 (tp30) REVERT: N 27 GLN cc_start: 0.8337 (mt0) cc_final: 0.7557 (tt0) REVERT: N 84 MET cc_start: 0.8531 (mmm) cc_final: 0.7492 (tmm) REVERT: N 100 PHE cc_start: 0.8167 (m-80) cc_final: 0.7713 (m-80) REVERT: Q 94 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8062 (tp30) REVERT: Q 120 MET cc_start: 0.8842 (mtp) cc_final: 0.8286 (mtp) REVERT: R 45 ARG cc_start: 0.7820 (mmm-85) cc_final: 0.7544 (mtp85) REVERT: R 67 ARG cc_start: 0.6743 (mmt90) cc_final: 0.6108 (tmm-80) REVERT: R 78 ARG cc_start: 0.7978 (mtm-85) cc_final: 0.7732 (mtm180) REVERT: S 23 LEU cc_start: 0.9120 (mt) cc_final: 0.8690 (mt) REVERT: S 56 GLU cc_start: 0.9236 (OUTLIER) cc_final: 0.8325 (mt-10) REVERT: T 105 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7888 (pm20) outliers start: 2 outliers final: 0 residues processed: 174 average time/residue: 0.2610 time to fit residues: 57.2938 Evaluate side-chains 140 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 0.0670 chunk 64 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 113 HIS ** 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 = 0.3972 r_free = 0.3972 target = 0.136228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.119418 restraints weight = 72782.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.124631 restraints weight = 51366.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.127240 restraints weight = 18052.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.129294 restraints weight = 10634.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.129397 restraints weight = 6855.914| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 9575 Z= 0.305 Angle : 0.830 6.629 13895 Z= 0.509 Chirality : 0.047 0.211 1582 Planarity : 0.007 0.078 976 Dihedral : 31.916 172.725 3078 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.51 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % 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: -1.43 (0.33), residues: 532 helix: -0.41 (0.24), residues: 356 sheet: None (None), residues: 0 loop : -1.88 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 53 TYR 0.019 0.002 TYR R 72 PHE 0.023 0.002 PHE S 25 HIS 0.009 0.002 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 9575) covalent geometry : angle 0.82997 (13895) hydrogen bonds : bond 0.08936 ( 469) hydrogen bonds : angle 4.77024 ( 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 148 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.340 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: 0.7991 (p) cc_final: 0.7717 (p) REVERT: M 59 GLU cc_start: 0.8503 (pm20) cc_final: 0.8258 (mp0) REVERT: M 92 LEU cc_start: 0.8698 (mm) cc_final: 0.8451 (mm) REVERT: N 27 GLN cc_start: 0.8413 (mt0) cc_final: 0.7713 (tt0) REVERT: N 100 PHE cc_start: 0.7862 (m-80) cc_final: 0.7147 (m-80) REVERT: Q 94 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8106 (tp30) REVERT: Q 120 MET cc_start: 0.8903 (mtp) cc_final: 0.8509 (mtp) REVERT: R 45 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7684 (mtp85) REVERT: R 67 ARG cc_start: 0.7262 (mmt90) cc_final: 0.6026 (tmm-80) REVERT: S 25 PHE cc_start: 0.7490 (m-10) cc_final: 0.6889 (m-10) REVERT: S 56 GLU cc_start: 0.9143 (mt-10) cc_final: 0.7301 (tp30) REVERT: S 89 ASN cc_start: 0.8798 (m-40) cc_final: 0.8589 (m110) REVERT: T 80 LEU cc_start: 0.9400 (mt) cc_final: 0.9188 (mt) REVERT: T 105 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8016 (pm20) REVERT: T 115 THR cc_start: 0.8109 (t) cc_final: 0.7889 (t) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2529 time to fit residues: 48.3923 Evaluate side-chains 132 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 9.9990 chunk 23 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 113 HIS ** 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 = 0.4055 r_free = 0.4055 target = 0.143151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.124626 restraints weight = 71891.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.131225 restraints weight = 51616.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.133598 restraints weight = 18632.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135142 restraints weight = 13560.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.135550 restraints weight = 9308.624| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9575 Z= 0.207 Angle : 0.716 6.576 13895 Z= 0.442 Chirality : 0.041 0.192 1582 Planarity : 0.005 0.048 976 Dihedral : 31.807 172.314 3078 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.44 % Favored : 97.18 % 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: -0.37 (0.35), residues: 532 helix: 0.44 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -1.56 (0.45), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG Q 72 TYR 0.016 0.001 TYR R 72 PHE 0.017 0.002 PHE Q 84 HIS 0.012 0.002 HIS S 31 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 9575) covalent geometry : angle 0.71590 (13895) hydrogen bonds : bond 0.06671 ( 469) hydrogen bonds : angle 3.95796 ( 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 146 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 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: N 27 GLN cc_start: 0.8250 (mt0) cc_final: 0.7521 (tt0) REVERT: N 100 PHE cc_start: 0.8071 (m-80) cc_final: 0.7381 (m-80) REVERT: Q 94 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8145 (tp30) REVERT: Q 120 MET cc_start: 0.9057 (mtp) cc_final: 0.8697 (mtp) REVERT: R 67 ARG cc_start: 0.7175 (mmt90) cc_final: 0.5915 (tmm-80) REVERT: S 25 PHE cc_start: 0.6955 (m-10) cc_final: 0.5700 (m-10) REVERT: S 56 GLU cc_start: 0.9076 (mt-10) cc_final: 0.7402 (tp30) REVERT: S 91 GLU cc_start: 0.8886 (pm20) cc_final: 0.8287 (pm20) REVERT: S 94 ASN cc_start: 0.7778 (t0) cc_final: 0.7523 (t0) REVERT: T 33 ARG cc_start: 0.7292 (mtm180) cc_final: 0.6924 (ptp-170) REVERT: T 80 LEU cc_start: 0.9325 (mt) cc_final: 0.8616 (mt) REVERT: T 105 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7758 (pm20) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.2499 time to fit residues: 47.0962 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 : 0.337 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.136718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.119456 restraints weight = 68757.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.125202 restraints weight = 47806.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.127988 restraints weight = 16777.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.129144 restraints weight = 10973.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.129549 restraints weight = 7840.033| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.124 9575 Z= 0.327 Angle : 0.803 7.082 13895 Z= 0.493 Chirality : 0.048 0.211 1582 Planarity : 0.006 0.082 976 Dihedral : 31.824 171.944 3078 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.89 % Favored : 94.55 % 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: -1.03 (0.34), residues: 532 helix: -0.07 (0.25), residues: 354 sheet: None (None), residues: 0 loop : -1.81 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 29 TYR 0.016 0.002 TYR T 40 PHE 0.015 0.002 PHE M 104 HIS 0.007 0.002 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.00702 ( 9575) covalent geometry : angle 0.80337 (13895) hydrogen bonds : bond 0.08746 ( 469) hydrogen bonds : angle 4.57735 ( 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 : 0.340 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: 0.8273 (mt0) cc_final: 0.7545 (tt0) REVERT: N 100 PHE cc_start: 0.7981 (m-80) cc_final: 0.7435 (m-80) REVERT: Q 94 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8199 (tp30) REVERT: Q 120 MET cc_start: 0.8988 (mtp) cc_final: 0.8748 (mtp) REVERT: R 45 ARG cc_start: 0.7228 (mtp85) cc_final: 0.7027 (mtp85) REVERT: R 57 VAL cc_start: 0.8570 (t) cc_final: 0.8268 (p) REVERT: R 67 ARG cc_start: 0.7553 (mmt90) cc_final: 0.5976 (tmm-80) REVERT: S 91 GLU cc_start: 0.8933 (pm20) cc_final: 0.8369 (pm20) REVERT: S 92 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8317 (mm-30) REVERT: S 94 ASN cc_start: 0.7973 (t0) cc_final: 0.7757 (t0) REVERT: T 33 ARG cc_start: 0.7329 (mtm180) cc_final: 0.6952 (ptp-170) REVERT: T 80 LEU cc_start: 0.9397 (mt) cc_final: 0.8714 (mt) REVERT: T 105 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7962 (pm20) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2459 time to fit residues: 44.6326 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 : 0.339 ------------------------------------------------------------------------------- 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: 6.9990 chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 109 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.137524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.121756 restraints weight = 74334.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.127019 restraints weight = 54030.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.129019 restraints weight = 19266.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.129851 restraints weight = 13660.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.130280 restraints weight = 10056.914| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 9575 Z= 0.303 Angle : 0.782 6.600 13895 Z= 0.483 Chirality : 0.047 0.215 1582 Planarity : 0.006 0.085 976 Dihedral : 31.921 171.988 3078 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 23.03 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.32 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -0.27 (0.25), residues: 354 sheet: None (None), residues: 0 loop : -1.94 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 29 TYR 0.015 0.002 TYR R 72 PHE 0.013 0.002 PHE Q 84 HIS 0.008 0.002 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00660 ( 9575) covalent geometry : angle 0.78190 (13895) hydrogen bonds : bond 0.08371 ( 469) hydrogen bonds : angle 4.58969 ( 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 137 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.278 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: M 97 GLU cc_start: 0.9295 (tp30) cc_final: 0.9058 (tp30) REVERT: M 108 ASN cc_start: 0.8772 (t0) cc_final: 0.8235 (t0) REVERT: N 27 GLN cc_start: 0.8279 (mt0) cc_final: 0.7572 (tt0) REVERT: N 44 LYS cc_start: 0.7957 (tptt) cc_final: 0.7598 (tppt) REVERT: N 100 PHE cc_start: 0.8130 (m-80) cc_final: 0.7532 (m-80) REVERT: Q 94 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8180 (tp30) REVERT: R 57 VAL cc_start: 0.8496 (t) cc_final: 0.8171 (p) REVERT: R 67 ARG cc_start: 0.7773 (mmt90) cc_final: 0.5807 (tmm-80) REVERT: S 91 GLU cc_start: 0.8975 (pm20) cc_final: 0.8399 (pm20) REVERT: S 94 ASN cc_start: 0.7919 (t0) cc_final: 0.7677 (t0) REVERT: T 33 ARG cc_start: 0.7269 (mtm180) cc_final: 0.6854 (ptp-170) REVERT: T 80 LEU cc_start: 0.9470 (mt) cc_final: 0.8599 (mt) REVERT: T 105 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7797 (pm20) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2558 time to fit residues: 45.1605 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 : 0.327 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.141067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122184 restraints weight = 72585.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.128964 restraints weight = 52032.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.131296 restraints weight = 19404.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.132509 restraints weight = 14277.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132703 restraints weight = 10115.760| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 9575 Z= 0.226 Angle : 0.714 4.996 13895 Z= 0.443 Chirality : 0.042 0.203 1582 Planarity : 0.005 0.063 976 Dihedral : 31.877 172.274 3078 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.01 % Favored : 96.43 % 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: -0.89 (0.34), residues: 532 helix: 0.04 (0.26), residues: 356 sheet: None (None), residues: 0 loop : -1.78 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 45 TYR 0.014 0.001 TYR R 72 PHE 0.013 0.001 PHE S 25 HIS 0.006 0.001 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00495 ( 9575) covalent geometry : angle 0.71422 (13895) hydrogen bonds : bond 0.06977 ( 469) hydrogen bonds : angle 4.09417 ( 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 140 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.366 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: M 105 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7932 (mm-30) REVERT: N 27 GLN cc_start: 0.8189 (mt0) cc_final: 0.7465 (tt0) REVERT: N 100 PHE cc_start: 0.7908 (m-80) cc_final: 0.7459 (m-80) REVERT: Q 94 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8193 (tp30) REVERT: Q 120 MET cc_start: 0.9116 (mtp) cc_final: 0.8840 (mtp) REVERT: R 57 VAL cc_start: 0.8481 (t) cc_final: 0.8235 (p) REVERT: R 67 ARG cc_start: 0.7629 (mmt90) cc_final: 0.5678 (tmm-80) REVERT: S 91 GLU cc_start: 0.8853 (pm20) cc_final: 0.8345 (pm20) REVERT: S 92 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8390 (mm-30) REVERT: T 33 ARG cc_start: 0.7354 (mtm180) cc_final: 0.6918 (ptp-170) REVERT: T 80 LEU cc_start: 0.9366 (mt) cc_final: 0.8913 (mt) REVERT: T 105 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7773 (pm20) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2727 time to fit residues: 48.5364 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 : 0.347 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.139126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.122453 restraints weight = 73947.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.128175 restraints weight = 51460.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130406 restraints weight = 17853.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131205 restraints weight = 12560.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.131621 restraints weight = 9417.777| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9575 Z= 0.264 Angle : 0.742 5.894 13895 Z= 0.459 Chirality : 0.045 0.207 1582 Planarity : 0.006 0.073 976 Dihedral : 31.861 171.411 3078 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.51 % Favored : 94.92 % 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: -0.01 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -1.92 (0.45), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 45 TYR 0.013 0.002 TYR R 72 PHE 0.013 0.002 PHE Q 84 HIS 0.011 0.002 HIS M 113 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 9575) covalent geometry : angle 0.74234 (13895) hydrogen bonds : bond 0.07915 ( 469) hydrogen bonds : angle 4.23618 ( 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 138 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.254 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: M 59 GLU cc_start: 0.8205 (mp0) cc_final: 0.7614 (tm-30) REVERT: M 97 GLU cc_start: 0.9298 (tp30) cc_final: 0.9004 (tp30) REVERT: M 108 ASN cc_start: 0.8780 (t0) cc_final: 0.8323 (t0) REVERT: N 27 GLN cc_start: 0.8189 (mt0) cc_final: 0.7472 (tt0) REVERT: Q 94 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8208 (tp30) REVERT: R 57 VAL cc_start: 0.8482 (t) cc_final: 0.8170 (p) REVERT: R 67 ARG cc_start: 0.7729 (mmt90) cc_final: 0.5770 (tmm-80) REVERT: S 91 GLU cc_start: 0.8882 (pm20) cc_final: 0.8331 (pm20) REVERT: S 92 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8384 (mm-30) REVERT: S 94 ASN cc_start: 0.8011 (t0) cc_final: 0.7772 (t0) REVERT: T 33 ARG cc_start: 0.7389 (mtm180) cc_final: 0.6988 (ptp-170) REVERT: T 105 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7829 (pm20) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2663 time to fit residues: 46.8750 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 : 0.352 ------------------------------------------------------------------------------- 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: 6.9990 chunk 15 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 49 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.138584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120864 restraints weight = 71998.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.126753 restraints weight = 52104.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129273 restraints weight = 18499.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.130599 restraints weight = 12743.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131131 restraints weight = 9003.783| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 9575 Z= 0.292 Angle : 0.767 6.481 13895 Z= 0.473 Chirality : 0.046 0.208 1582 Planarity : 0.006 0.084 976 Dihedral : 31.920 171.316 3078 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.56 % Allowed : 5.08 % Favored : 94.36 % 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: -1.06 (0.35), residues: 532 helix: -0.13 (0.26), residues: 352 sheet: None (None), residues: 0 loop : -1.72 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 45 TYR 0.015 0.002 TYR T 40 PHE 0.020 0.002 PHE S 25 HIS 0.005 0.001 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.00627 ( 9575) covalent geometry : angle 0.76706 (13895) hydrogen bonds : bond 0.08251 ( 469) hydrogen bonds : angle 4.42549 ( 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 : 0.343 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: M 59 GLU cc_start: 0.8411 (mp0) cc_final: 0.7744 (tm-30) REVERT: M 97 GLU cc_start: 0.9434 (tp30) cc_final: 0.9012 (tp30) REVERT: N 27 GLN cc_start: 0.8173 (mt0) cc_final: 0.7474 (tt0) REVERT: N 88 TYR cc_start: 0.9074 (m-80) cc_final: 0.8310 (t80) REVERT: Q 76 GLN cc_start: 0.7381 (pt0) cc_final: 0.7117 (pt0) REVERT: Q 94 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8238 (tp30) REVERT: Q 120 MET cc_start: 0.9129 (mtp) cc_final: 0.8866 (mtp) REVERT: R 57 VAL cc_start: 0.8454 (t) cc_final: 0.8145 (p) REVERT: R 67 ARG cc_start: 0.8061 (mmt90) cc_final: 0.5742 (tmm-80) REVERT: S 91 GLU cc_start: 0.8872 (pm20) cc_final: 0.8299 (pm20) REVERT: S 94 ASN cc_start: 0.8051 (t0) cc_final: 0.7819 (t0) REVERT: T 33 ARG cc_start: 0.7510 (mtm180) cc_final: 0.7059 (ptp-170) REVERT: T 105 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7896 (pm20) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.2493 time to fit residues: 44.1933 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 : 0.349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 66 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.122753 restraints weight = 71386.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.129725 restraints weight = 51803.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.131704 restraints weight = 18727.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.133422 restraints weight = 14166.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.133805 restraints weight = 9767.850| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 9575 Z= 0.223 Angle : 0.705 5.119 13895 Z= 0.438 Chirality : 0.042 0.195 1582 Planarity : 0.005 0.067 976 Dihedral : 31.825 171.791 3078 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.56 % Allowed : 3.95 % Favored : 95.49 % 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: -0.58 (0.35), residues: 532 helix: 0.30 (0.27), residues: 351 sheet: None (None), residues: 0 loop : -1.64 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 39 TYR 0.013 0.001 TYR R 72 PHE 0.017 0.002 PHE S 25 HIS 0.003 0.001 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.00488 ( 9575) covalent geometry : angle 0.70513 (13895) hydrogen bonds : bond 0.06946 ( 469) hydrogen bonds : angle 4.02480 ( 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 136 residues out of total 453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.370 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: M 58 THR cc_start: 0.8298 (p) cc_final: 0.7829 (t) REVERT: M 59 GLU cc_start: 0.8372 (mp0) cc_final: 0.7712 (tm-30) REVERT: N 27 GLN cc_start: 0.8113 (mt0) cc_final: 0.7332 (tt0) REVERT: N 88 TYR cc_start: 0.9062 (m-80) cc_final: 0.8349 (t80) REVERT: Q 76 GLN cc_start: 0.7326 (pt0) cc_final: 0.7077 (pt0) REVERT: Q 94 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8197 (tp30) REVERT: R 57 VAL cc_start: 0.8467 (t) cc_final: 0.8151 (p) REVERT: R 67 ARG cc_start: 0.7962 (mmt90) cc_final: 0.5689 (tmm-80) REVERT: S 91 GLU cc_start: 0.8881 (pm20) cc_final: 0.8347 (pm20) REVERT: S 92 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8334 (mm-30) REVERT: S 94 ASN cc_start: 0.7944 (t0) cc_final: 0.7699 (t0) REVERT: T 33 ARG cc_start: 0.7382 (mtm180) cc_final: 0.6940 (ptp-170) REVERT: T 105 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7794 (pm20) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2488 time to fit residues: 44.0413 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 : 0.364 ------------------------------------------------------------------------------- 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: 0.9990 chunk 49 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 113 HIS ** 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 = 0.4021 r_free = 0.4021 target = 0.140524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.122269 restraints weight = 69434.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.128596 restraints weight = 49628.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131198 restraints weight = 18450.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.132546 restraints weight = 12938.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133124 restraints weight = 9122.079| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 9575 Z= 0.250 Angle : 0.723 5.752 13895 Z= 0.448 Chirality : 0.044 0.200 1582 Planarity : 0.005 0.072 976 Dihedral : 31.778 170.678 3078 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.56 % Allowed : 4.14 % Favored : 95.30 % 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: -0.58 (0.35), residues: 532 helix: 0.30 (0.27), residues: 350 sheet: None (None), residues: 0 loop : -1.67 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 45 TYR 0.011 0.001 TYR T 40 PHE 0.016 0.002 PHE S 25 HIS 0.004 0.001 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.00542 ( 9575) covalent geometry : angle 0.72259 (13895) hydrogen bonds : bond 0.07497 ( 469) hydrogen bonds : angle 4.10297 ( 1171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2768.70 seconds wall clock time: 48 minutes 12.59 seconds (2892.59 seconds total)