Starting phenix.real_space_refine on Wed Feb 4 17:17:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.map" model { file = "/net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf6_51310/02_2026/9gf6_51310.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 270 5.49 5 S 14 5.16 5 C 6599 2.51 5 N 2229 2.21 5 O 2753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 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: 11865 Number of models: 1 Model: "" Number of chains: 11 Chain: "K" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2787 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "L" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2748 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "M" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 761 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "N" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "O" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "R" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "S" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "T" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "H" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 368 Classifications: {'peptide': 46} Link IDs: {'TRANS': 45} Chain breaks: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 11865 At special positions: 0 Unit cell: (117.488, 134.272, 110.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 270 15.00 O 2753 8.00 N 2229 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 393.2 milliseconds 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1482 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 72.9% alpha, 1.8% beta 132 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.563A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.569A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.550A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 removed outlier: 3.539A pdb=" N GLY N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.505A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.471A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.717A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 Processing helix chain 'P' and resid 37 through 49 Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.553A pdb=" N ILE P 94 " --> pdb=" O THR P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 125 removed outlier: 3.917A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 57 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.195A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.985A pdb=" N MET Q 90 " --> pdb=" O SER Q 86 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 132 removed outlier: 3.759A pdb=" N LEU Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 removed outlier: 4.021A pdb=" N GLY R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 76 removed outlier: 4.269A pdb=" N TYR R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.304A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 removed outlier: 3.682A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 83 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.815A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 Processing helix chain 'H' and resid 172 through 176 Processing helix chain 'H' and resid 177 through 189 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.921A 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 98 Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.817A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'S' and resid 77 through 78 414 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 337 hydrogen bonds 674 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3000 1.34 - 1.46: 3541 1.46 - 1.58: 5512 1.58 - 1.70: 538 1.70 - 1.82: 24 Bond restraints: 12615 Sorted by residual: bond pdb=" CZ ARG H 179 " pdb=" NH2 ARG H 179 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 bond pdb=" CZ ARG O 81 " pdb=" NH2 ARG O 81 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.17e+00 bond pdb=" CZ ARG S 29 " pdb=" NH2 ARG S 29 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.09e+00 bond pdb=" CZ ARG M 131 " pdb=" NH2 ARG M 131 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.08e+00 bond pdb=" CZ ARG R 40 " pdb=" NH2 ARG R 40 " ideal model delta sigma weight residual 1.330 1.293 0.037 1.30e-02 5.92e+03 8.06e+00 ... (remaining 12610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 11940 1.70 - 3.40: 4815 3.40 - 5.10: 1232 5.10 - 6.80: 162 6.80 - 8.50: 31 Bond angle restraints: 18180 Sorted by residual: angle pdb=" O5' DC L -40 " pdb=" C5' DC L -40 " pdb=" C4' DC L -40 " ideal model delta sigma weight residual 110.80 119.23 -8.43 1.50e+00 4.44e-01 3.16e+01 angle pdb=" C4' DC L 20 " pdb=" C3' DC L 20 " pdb=" O3' DC L 20 " ideal model delta sigma weight residual 110.00 118.33 -8.33 1.50e+00 4.44e-01 3.08e+01 angle pdb=" C4' DG L -46 " pdb=" C3' DG L -46 " pdb=" O3' DG L -46 " ideal model delta sigma weight residual 110.00 118.04 -8.04 1.50e+00 4.44e-01 2.88e+01 angle pdb=" CA ARG M 42 " pdb=" C ARG M 42 " pdb=" N PRO M 43 " ideal model delta sigma weight residual 116.90 124.92 -8.02 1.50e+00 4.44e-01 2.86e+01 angle pdb=" O5' DT L -7 " pdb=" C5' DT L -7 " pdb=" C4' DT L -7 " ideal model delta sigma weight residual 110.80 118.63 -7.83 1.50e+00 4.44e-01 2.72e+01 ... (remaining 18175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 5720 34.05 - 68.11: 1156 68.11 - 102.16: 42 102.16 - 136.21: 0 136.21 - 170.27: 1 Dihedral angle restraints: 6919 sinusoidal: 4620 harmonic: 2299 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 180.00 151.04 28.96 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASP N 24 " pdb=" C ASP N 24 " pdb=" N ASN N 25 " pdb=" CA ASN N 25 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA PRO P 103 " pdb=" C PRO P 103 " pdb=" N GLY P 104 " pdb=" CA GLY P 104 " ideal model delta harmonic sigma weight residual 180.00 153.35 26.65 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 6916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1546 0.090 - 0.180: 425 0.180 - 0.270: 63 0.270 - 0.360: 22 0.360 - 0.450: 7 Chirality restraints: 2063 Sorted by residual: 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 -2.21 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" CA LYS O 74 " pdb=" N LYS O 74 " pdb=" C LYS O 74 " pdb=" CB LYS O 74 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" CA LYS T 85 " pdb=" N LYS T 85 " pdb=" C LYS T 85 " pdb=" CB LYS T 85 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.06e+00 ... (remaining 2060 not shown) Planarity restraints: 1375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 47 " -0.383 2.00e-02 2.50e+03 1.95e-01 9.51e+02 pdb=" N1 DT K 47 " 0.014 2.00e-02 2.50e+03 pdb=" C2 DT K 47 " 0.065 2.00e-02 2.50e+03 pdb=" O2 DT K 47 " 0.300 2.00e-02 2.50e+03 pdb=" N3 DT K 47 " -0.014 2.00e-02 2.50e+03 pdb=" C4 DT K 47 " -0.082 2.00e-02 2.50e+03 pdb=" O4 DT K 47 " -0.282 2.00e-02 2.50e+03 pdb=" C5 DT K 47 " 0.083 2.00e-02 2.50e+03 pdb=" C7 DT K 47 " 0.181 2.00e-02 2.50e+03 pdb=" C6 DT K 47 " 0.118 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 26 " 0.425 2.00e-02 2.50e+03 1.69e-01 8.56e+02 pdb=" N9 DG K 26 " -0.060 2.00e-02 2.50e+03 pdb=" C8 DG K 26 " -0.179 2.00e-02 2.50e+03 pdb=" N7 DG K 26 " -0.130 2.00e-02 2.50e+03 pdb=" C5 DG K 26 " -0.059 2.00e-02 2.50e+03 pdb=" C6 DG K 26 " 0.073 2.00e-02 2.50e+03 pdb=" O6 DG K 26 " 0.223 2.00e-02 2.50e+03 pdb=" N1 DG K 26 " 0.090 2.00e-02 2.50e+03 pdb=" C2 DG K 26 " -0.050 2.00e-02 2.50e+03 pdb=" N2 DG K 26 " -0.066 2.00e-02 2.50e+03 pdb=" N3 DG K 26 " -0.143 2.00e-02 2.50e+03 pdb=" C4 DG K 26 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 6 " 0.298 2.00e-02 2.50e+03 1.71e-01 7.29e+02 pdb=" N1 DT K 6 " 0.031 2.00e-02 2.50e+03 pdb=" C2 DT K 6 " -0.053 2.00e-02 2.50e+03 pdb=" O2 DT K 6 " -0.298 2.00e-02 2.50e+03 pdb=" N3 DT K 6 " 0.033 2.00e-02 2.50e+03 pdb=" C4 DT K 6 " 0.090 2.00e-02 2.50e+03 pdb=" O4 DT K 6 " 0.229 2.00e-02 2.50e+03 pdb=" C5 DT K 6 " -0.060 2.00e-02 2.50e+03 pdb=" C7 DT K 6 " -0.202 2.00e-02 2.50e+03 pdb=" C6 DT K 6 " -0.068 2.00e-02 2.50e+03 ... (remaining 1372 not shown) Histogram of nonbonded interaction distances: 2.53 - 3.00: 5358 3.00 - 3.48: 12995 3.48 - 3.95: 22926 3.95 - 4.43: 25577 4.43 - 4.90: 34226 Nonbonded interactions: 101082 Sorted by model distance: nonbonded pdb=" OH TYR M 99 " pdb=" OE1 GLU M 133 " model vdw 2.531 3.040 nonbonded pdb=" OG SER O 40 " pdb=" O SER P 87 " model vdw 2.559 3.040 nonbonded pdb=" O GLY N 102 " pdb=" OG SER T 64 " model vdw 2.561 3.040 nonbonded pdb=" OP1 DC L 48 " pdb=" OH TYR P 40 " model vdw 2.563 3.040 nonbonded pdb=" OG1 THR R 82 " pdb=" OD2 ASP R 85 " model vdw 2.569 3.040 ... (remaining 101077 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 42 through 134) } ncs_group { reference = (chain 'N' and resid 24 through 102) selection = chain 'R' } ncs_group { reference = chain 'O' selection = (chain 'S' and resid 13 through 118) } ncs_group { reference = (chain 'P' and resid 32 through 123) selection = (chain 'T' and resid 32 through 123) } 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: 5.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 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 0.043 12615 Z= 0.699 Angle : 1.901 8.503 18180 Z= 1.257 Chirality : 0.087 0.450 2063 Planarity : 0.034 0.200 1375 Dihedral : 26.724 170.268 5437 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 0.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.11 % Favored : 95.50 % Rotamer: Outliers : 1.06 % Allowed : 5.29 % Favored : 93.66 % Cbeta Deviations : 0.81 % 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 (0.27), residues: 778 helix: -0.63 (0.19), residues: 562 sheet: None (None), residues: 0 loop : -0.42 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 71 TYR 0.162 0.020 TYR S 57 PHE 0.061 0.014 PHE M 78 TRP 0.031 0.012 TRP H 152 HIS 0.018 0.005 HIS S 82 Details of bonding type rmsd covalent geometry : bond 0.01254 (12615) covalent geometry : angle 1.90070 (18180) hydrogen bonds : bond 0.12983 ( 751) hydrogen bonds : angle 6.65496 ( 1898) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 343 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: M 50 GLU cc_start: 0.9317 (tt0) cc_final: 0.9115 (tt0) REVERT: M 60 LEU cc_start: 0.9482 (mt) cc_final: 0.9276 (mm) REVERT: M 61 LEU cc_start: 0.9559 (mt) cc_final: 0.9169 (mm) REVERT: N 80 THR cc_start: 0.8997 (m) cc_final: 0.8789 (t) REVERT: N 84 MET cc_start: 0.9106 (mmm) cc_final: 0.8722 (mmm) REVERT: N 92 ARG cc_start: 0.9015 (tpt90) cc_final: 0.8715 (ttp80) REVERT: N 98 TYR cc_start: 0.9650 (m-10) cc_final: 0.8969 (m-80) REVERT: O 24 GLN cc_start: 0.8963 (mm-40) cc_final: 0.8761 (mm-40) REVERT: O 38 ASN cc_start: 0.8897 (m-40) cc_final: 0.8529 (p0) REVERT: P 35 GLU cc_start: 0.9363 (mp0) cc_final: 0.9109 (mp0) REVERT: Q 41 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.4738 (t80) REVERT: Q 68 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8989 (tm-30) REVERT: Q 93 GLN cc_start: 0.9374 (tt0) cc_final: 0.8919 (tt0) REVERT: R 52 GLU cc_start: 0.9022 (tp30) cc_final: 0.8680 (tp30) REVERT: R 55 ARG cc_start: 0.9411 (mtt90) cc_final: 0.9174 (mtm-85) REVERT: R 73 THR cc_start: 0.9543 (m) cc_final: 0.9307 (p) REVERT: R 84 MET cc_start: 0.9491 (mmm) cc_final: 0.8972 (mmm) REVERT: S 24 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8304 (mm-40) REVERT: S 56 GLU cc_start: 0.9168 (tt0) cc_final: 0.8931 (tm-30) REVERT: S 84 GLN cc_start: 0.9339 (tp-100) cc_final: 0.9032 (tp40) REVERT: S 101 THR cc_start: 0.9152 (m) cc_final: 0.8251 (p) REVERT: S 104 GLN cc_start: 0.9436 (mt0) cc_final: 0.9083 (mp10) REVERT: S 112 GLN cc_start: 0.7989 (mm110) cc_final: 0.7731 (mm-40) REVERT: T 34 LYS cc_start: 0.9411 (mmtm) cc_final: 0.9158 (mttt) REVERT: T 71 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9125 (tm-30) REVERT: T 86 ARG cc_start: 0.8934 (mmt-90) cc_final: 0.8517 (tpp80) REVERT: T 102 LEU cc_start: 0.9441 (mt) cc_final: 0.9229 (mp) REVERT: H 145 GLU cc_start: 0.9061 (tt0) cc_final: 0.8817 (mp0) REVERT: H 164 ASN cc_start: 0.7547 (m-40) cc_final: 0.7261 (t0) REVERT: H 176 LEU cc_start: 0.9126 (mt) cc_final: 0.8108 (mp) outliers start: 7 outliers final: 0 residues processed: 346 average time/residue: 0.1435 time to fit residues: 65.0644 Evaluate side-chains 244 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 243 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 41 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN N 25 ASN ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 49 HIS P 95 GLN R 75 HIS ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS T 84 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.089328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063580 restraints weight = 37830.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.065486 restraints weight = 18036.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066743 restraints weight = 12103.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067500 restraints weight = 9725.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067879 restraints weight = 8634.606| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12615 Z= 0.198 Angle : 0.714 9.048 18180 Z= 0.420 Chirality : 0.041 0.213 2063 Planarity : 0.005 0.039 1375 Dihedral : 31.352 171.982 3850 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.70 % Favored : 97.04 % Rotamer: Outliers : 4.08 % Allowed : 18.28 % Favored : 77.64 % 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: 1.24 (0.29), residues: 778 helix: 1.40 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 35 TYR 0.022 0.002 TYR R 88 PHE 0.014 0.001 PHE M 67 TRP 0.011 0.002 TRP H 152 HIS 0.011 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00433 (12615) covalent geometry : angle 0.71405 (18180) hydrogen bonds : bond 0.04816 ( 751) hydrogen bonds : angle 3.41482 ( 1898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.288 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: M 50 GLU cc_start: 0.8792 (tt0) cc_final: 0.8350 (tt0) REVERT: M 73 GLU cc_start: 0.8684 (tp30) cc_final: 0.7555 (tp30) REVERT: M 76 GLN cc_start: 0.8044 (mt0) cc_final: 0.6844 (mt0) REVERT: M 93 GLN cc_start: 0.9096 (tt0) cc_final: 0.8834 (tt0) REVERT: M 120 MET cc_start: 0.8615 (mtp) cc_final: 0.8109 (mtt) REVERT: N 25 ASN cc_start: 0.8853 (m-40) cc_final: 0.8615 (m110) REVERT: N 80 THR cc_start: 0.8897 (m) cc_final: 0.8422 (p) REVERT: N 84 MET cc_start: 0.8706 (mmm) cc_final: 0.8393 (mmm) REVERT: O 24 GLN cc_start: 0.8718 (mm-40) cc_final: 0.8463 (mm110) REVERT: O 56 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8896 (tm-30) REVERT: O 91 GLU cc_start: 0.8910 (pm20) cc_final: 0.8539 (tm-30) REVERT: P 76 GLU cc_start: 0.8464 (tp30) cc_final: 0.8125 (tp30) REVERT: P 79 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.7935 (mtm-85) REVERT: P 105 GLU cc_start: 0.7788 (tp30) cc_final: 0.7577 (tp30) REVERT: P 120 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8645 (ttpp) REVERT: Q 41 TYR cc_start: 0.4960 (OUTLIER) cc_final: 0.4294 (t80) REVERT: Q 56 LYS cc_start: 0.9114 (ttpt) cc_final: 0.8840 (ttmm) REVERT: Q 60 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8543 (mt) REVERT: Q 73 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8098 (mt-10) REVERT: Q 74 ILE cc_start: 0.9569 (mm) cc_final: 0.9335 (mm) REVERT: Q 93 GLN cc_start: 0.8992 (tt0) cc_final: 0.8665 (tt0) REVERT: Q 94 GLU cc_start: 0.8684 (tp30) cc_final: 0.8330 (tp30) REVERT: Q 123 ASP cc_start: 0.8902 (m-30) cc_final: 0.8684 (m-30) REVERT: Q 126 LEU cc_start: 0.9390 (tp) cc_final: 0.9103 (tt) REVERT: R 31 LYS cc_start: 0.9280 (ttpp) cc_final: 0.8900 (tttm) REVERT: R 52 GLU cc_start: 0.8559 (tp30) cc_final: 0.8289 (tp30) REVERT: R 84 MET cc_start: 0.9151 (mmm) cc_final: 0.8641 (mmm) REVERT: S 24 GLN cc_start: 0.8279 (mm-40) cc_final: 0.7849 (mp10) REVERT: S 57 TYR cc_start: 0.8857 (t80) cc_final: 0.8588 (t80) REVERT: S 61 GLU cc_start: 0.8807 (tp30) cc_final: 0.8357 (tp30) REVERT: S 84 GLN cc_start: 0.9554 (tp-100) cc_final: 0.8914 (tp40) REVERT: S 90 ASP cc_start: 0.8309 (t0) cc_final: 0.8003 (t0) REVERT: S 101 THR cc_start: 0.8886 (m) cc_final: 0.8364 (p) REVERT: T 34 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8876 (mmtp) REVERT: T 35 GLU cc_start: 0.8770 (tp30) cc_final: 0.8448 (tt0) REVERT: T 105 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7471 (tp30) REVERT: H 151 ARG cc_start: 0.6070 (mmp80) cc_final: 0.5843 (mmm160) REVERT: H 153 LEU cc_start: 0.8542 (mt) cc_final: 0.7823 (pp) outliers start: 27 outliers final: 13 residues processed: 292 average time/residue: 0.1289 time to fit residues: 50.9288 Evaluate side-chains 248 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 233 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 8 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 94 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 94 ASN T 82 HIS H 150 GLN H 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.062177 restraints weight = 37981.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.064021 restraints weight = 18408.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065227 restraints weight = 12331.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.065969 restraints weight = 9867.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.066368 restraints weight = 8733.841| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12615 Z= 0.188 Angle : 0.655 8.537 18180 Z= 0.385 Chirality : 0.038 0.153 2063 Planarity : 0.004 0.037 1375 Dihedral : 30.875 172.845 3850 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.21 % Favored : 96.53 % Rotamer: Outliers : 3.63 % Allowed : 22.05 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 778 helix: 1.72 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -0.69 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 181 TYR 0.016 0.002 TYR T 40 PHE 0.013 0.001 PHE M 67 TRP 0.010 0.002 TRP H 152 HIS 0.003 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (12615) covalent geometry : angle 0.65482 (18180) hydrogen bonds : bond 0.04126 ( 751) hydrogen bonds : angle 3.08767 ( 1898) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8835 (tt0) cc_final: 0.8492 (tt0) REVERT: N 63 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8252 (mt-10) REVERT: N 77 LYS cc_start: 0.9494 (mttp) cc_final: 0.9183 (mptt) REVERT: N 80 THR cc_start: 0.8775 (m) cc_final: 0.8522 (t) REVERT: N 84 MET cc_start: 0.8656 (mmm) cc_final: 0.8428 (mmm) REVERT: O 24 GLN cc_start: 0.8826 (mm-40) cc_final: 0.8534 (mm110) REVERT: O 56 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8942 (tm-30) REVERT: O 91 GLU cc_start: 0.8950 (pm20) cc_final: 0.8664 (tm-30) REVERT: P 59 MET cc_start: 0.9275 (tpp) cc_final: 0.8995 (tpp) REVERT: P 79 ARG cc_start: 0.8655 (mtm-85) cc_final: 0.8025 (mtm-85) REVERT: P 105 GLU cc_start: 0.7800 (tp30) cc_final: 0.7331 (tp30) REVERT: P 120 LYS cc_start: 0.8951 (ttmm) cc_final: 0.8679 (ttpp) REVERT: Q 41 TYR cc_start: 0.5051 (OUTLIER) cc_final: 0.4207 (t80) REVERT: Q 56 LYS cc_start: 0.9110 (ttpt) cc_final: 0.8734 (ttmm) REVERT: Q 68 GLN cc_start: 0.8739 (tp-100) cc_final: 0.8196 (tp-100) REVERT: Q 120 MET cc_start: 0.8996 (mmm) cc_final: 0.8610 (mmm) REVERT: Q 134 ARG cc_start: 0.7652 (ttp80) cc_final: 0.7382 (ttp80) REVERT: R 79 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9059 (ttmm) REVERT: R 85 ASP cc_start: 0.8746 (m-30) cc_final: 0.8369 (m-30) REVERT: R 88 TYR cc_start: 0.9092 (m-10) cc_final: 0.8340 (m-80) REVERT: S 56 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8027 (tt0) REVERT: S 61 GLU cc_start: 0.8976 (tp30) cc_final: 0.8684 (tp30) REVERT: S 84 GLN cc_start: 0.9543 (tp-100) cc_final: 0.8955 (tp40) REVERT: S 101 THR cc_start: 0.8879 (m) cc_final: 0.8371 (p) REVERT: T 34 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8878 (mmtm) REVERT: T 71 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8703 (tm-30) REVERT: T 105 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7590 (tp30) outliers start: 24 outliers final: 15 residues processed: 262 average time/residue: 0.1254 time to fit residues: 44.7380 Evaluate side-chains 236 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 36 LYS Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 21 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 47 GLN T 82 HIS H 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.088336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.062920 restraints weight = 38027.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.064763 restraints weight = 18731.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.065978 restraints weight = 12618.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.066696 restraints weight = 10114.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.067111 restraints weight = 8963.761| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12615 Z= 0.172 Angle : 0.634 9.116 18180 Z= 0.371 Chirality : 0.036 0.151 2063 Planarity : 0.004 0.037 1375 Dihedral : 30.593 173.976 3850 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.34 % Favored : 96.53 % Rotamer: Outliers : 3.63 % Allowed : 23.41 % Favored : 72.96 % 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 (0.30), residues: 778 helix: 1.89 (0.22), residues: 572 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG T 86 TYR 0.017 0.002 TYR T 40 PHE 0.015 0.001 PHE M 67 TRP 0.002 0.001 TRP H 152 HIS 0.013 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00377 (12615) covalent geometry : angle 0.63420 (18180) hydrogen bonds : bond 0.03854 ( 751) hydrogen bonds : angle 2.98253 ( 1898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.374 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: M 50 GLU cc_start: 0.8789 (tt0) cc_final: 0.8585 (tt0) REVERT: M 113 HIS cc_start: 0.8507 (t70) cc_final: 0.8260 (t-90) REVERT: M 120 MET cc_start: 0.8538 (mtp) cc_final: 0.8061 (mtt) REVERT: N 63 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8235 (mt-10) REVERT: N 80 THR cc_start: 0.8820 (m) cc_final: 0.8517 (t) REVERT: N 84 MET cc_start: 0.8691 (mmm) cc_final: 0.8398 (mmm) REVERT: O 56 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8994 (tm-30) REVERT: O 91 GLU cc_start: 0.8984 (pm20) cc_final: 0.8766 (tm-30) REVERT: P 59 MET cc_start: 0.9230 (tpp) cc_final: 0.9012 (tpp) REVERT: P 76 GLU cc_start: 0.8653 (tp30) cc_final: 0.8361 (tp30) REVERT: P 105 GLU cc_start: 0.7654 (tp30) cc_final: 0.6723 (tp30) REVERT: P 108 LYS cc_start: 0.9029 (mttm) cc_final: 0.8756 (mtmt) REVERT: Q 41 TYR cc_start: 0.4986 (OUTLIER) cc_final: 0.4204 (t80) REVERT: Q 68 GLN cc_start: 0.8743 (tp-100) cc_final: 0.8218 (tp-100) REVERT: Q 90 MET cc_start: 0.8234 (tpp) cc_final: 0.7563 (tpp) REVERT: Q 93 GLN cc_start: 0.8849 (tt0) cc_final: 0.8374 (tt0) REVERT: Q 120 MET cc_start: 0.9014 (mmm) cc_final: 0.8688 (mmm) REVERT: Q 134 ARG cc_start: 0.7731 (ttp80) cc_final: 0.7452 (ttp80) REVERT: R 25 ASN cc_start: 0.8009 (m-40) cc_final: 0.7493 (t0) REVERT: R 84 MET cc_start: 0.8653 (mmm) cc_final: 0.8424 (tpp) REVERT: R 85 ASP cc_start: 0.8715 (m-30) cc_final: 0.8398 (m-30) REVERT: R 88 TYR cc_start: 0.9160 (m-10) cc_final: 0.8824 (m-80) REVERT: S 56 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8428 (tm-30) REVERT: S 84 GLN cc_start: 0.9533 (tp-100) cc_final: 0.8953 (tp40) REVERT: S 101 THR cc_start: 0.8878 (m) cc_final: 0.8372 (p) REVERT: S 104 GLN cc_start: 0.8579 (mp10) cc_final: 0.8330 (mp10) REVERT: T 71 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8707 (tm-30) REVERT: T 105 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7705 (tp30) REVERT: H 153 LEU cc_start: 0.8644 (mt) cc_final: 0.8000 (pp) outliers start: 24 outliers final: 15 residues processed: 245 average time/residue: 0.1166 time to fit residues: 39.2119 Evaluate side-chains 231 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 215 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN M 108 ASN O 73 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.087969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.062439 restraints weight = 37884.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064267 restraints weight = 18684.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.065467 restraints weight = 12615.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.066178 restraints weight = 10142.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.066594 restraints weight = 8999.890| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12615 Z= 0.179 Angle : 0.625 9.266 18180 Z= 0.366 Chirality : 0.035 0.153 2063 Planarity : 0.004 0.043 1375 Dihedral : 30.499 175.108 3850 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 3.63 % Allowed : 24.77 % Favored : 71.60 % 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: 2.05 (0.30), residues: 778 helix: 2.08 (0.22), residues: 566 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 151 TYR 0.013 0.002 TYR S 39 PHE 0.016 0.001 PHE M 67 TRP 0.002 0.001 TRP H 152 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (12615) covalent geometry : angle 0.62477 (18180) hydrogen bonds : bond 0.03879 ( 751) hydrogen bonds : angle 2.95000 ( 1898) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 60 LEU cc_start: 0.9057 (mm) cc_final: 0.8551 (mt) REVERT: M 73 GLU cc_start: 0.8781 (tp30) cc_final: 0.8378 (tp30) REVERT: M 93 GLN cc_start: 0.9089 (tt0) cc_final: 0.8582 (tm-30) REVERT: M 113 HIS cc_start: 0.8461 (t70) cc_final: 0.8213 (t-90) REVERT: M 120 MET cc_start: 0.8607 (mtp) cc_final: 0.8105 (mtt) REVERT: N 63 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8240 (mt-10) REVERT: N 80 THR cc_start: 0.8865 (m) cc_final: 0.8597 (t) REVERT: N 84 MET cc_start: 0.8645 (mmm) cc_final: 0.8353 (mmm) REVERT: O 56 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9003 (tm-30) REVERT: O 91 GLU cc_start: 0.8973 (pm20) cc_final: 0.8757 (tm-30) REVERT: P 59 MET cc_start: 0.9202 (tpp) cc_final: 0.8917 (tpp) REVERT: P 105 GLU cc_start: 0.7688 (tp30) cc_final: 0.7443 (tp30) REVERT: Q 41 TYR cc_start: 0.4895 (OUTLIER) cc_final: 0.4243 (t80) REVERT: Q 68 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8202 (tp-100) REVERT: Q 90 MET cc_start: 0.8258 (tpp) cc_final: 0.7727 (tpp) REVERT: Q 93 GLN cc_start: 0.8784 (tt0) cc_final: 0.8384 (tt0) REVERT: Q 120 MET cc_start: 0.9022 (mmm) cc_final: 0.8819 (mmm) REVERT: Q 134 ARG cc_start: 0.7797 (ttp80) cc_final: 0.7530 (ttp80) REVERT: R 85 ASP cc_start: 0.8776 (m-30) cc_final: 0.8453 (m-30) REVERT: R 88 TYR cc_start: 0.9090 (m-10) cc_final: 0.8752 (m-80) REVERT: S 56 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8456 (tm-30) REVERT: S 76 THR cc_start: 0.9089 (p) cc_final: 0.8859 (p) REVERT: S 84 GLN cc_start: 0.9508 (tp-100) cc_final: 0.8929 (tp40) REVERT: S 94 ASN cc_start: 0.9093 (t0) cc_final: 0.8837 (t0) REVERT: S 101 THR cc_start: 0.8906 (m) cc_final: 0.8450 (p) REVERT: T 34 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8411 (mmtm) REVERT: T 71 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8760 (tm-30) REVERT: T 105 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7775 (tp30) REVERT: H 153 LEU cc_start: 0.8596 (mt) cc_final: 0.7917 (pp) outliers start: 24 outliers final: 17 residues processed: 232 average time/residue: 0.1079 time to fit residues: 34.5718 Evaluate side-chains 232 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 214 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.086069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.060317 restraints weight = 37035.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.062086 restraints weight = 17502.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063245 restraints weight = 11597.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.063886 restraints weight = 9252.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.064302 restraints weight = 8220.480| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12615 Z= 0.186 Angle : 0.628 9.030 18180 Z= 0.366 Chirality : 0.035 0.151 2063 Planarity : 0.004 0.041 1375 Dihedral : 30.485 176.515 3850 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.47 % Favored : 96.40 % Rotamer: Outliers : 4.68 % Allowed : 23.72 % Favored : 71.60 % 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: 2.01 (0.30), residues: 778 helix: 2.08 (0.22), residues: 567 sheet: None (None), residues: 0 loop : -0.77 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 151 TYR 0.027 0.002 TYR T 40 PHE 0.011 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.004 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00410 (12615) covalent geometry : angle 0.62753 (18180) hydrogen bonds : bond 0.03871 ( 751) hydrogen bonds : angle 2.95389 ( 1898) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9060 (tt0) cc_final: 0.8308 (tm-30) REVERT: M 60 LEU cc_start: 0.9106 (mm) cc_final: 0.8714 (mt) REVERT: M 73 GLU cc_start: 0.8885 (tp30) cc_final: 0.8402 (tt0) REVERT: M 76 GLN cc_start: 0.8923 (tp40) cc_final: 0.8722 (pt0) REVERT: M 79 LYS cc_start: 0.8861 (tttt) cc_final: 0.8588 (ttmt) REVERT: M 93 GLN cc_start: 0.9074 (tt0) cc_final: 0.8468 (tm-30) REVERT: M 120 MET cc_start: 0.8622 (mtp) cc_final: 0.8062 (mtt) REVERT: N 63 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8216 (mt-10) REVERT: N 80 THR cc_start: 0.8787 (m) cc_final: 0.8460 (t) REVERT: N 84 MET cc_start: 0.8749 (mmm) cc_final: 0.8408 (mmm) REVERT: O 56 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8992 (tm-30) REVERT: O 91 GLU cc_start: 0.9032 (pm20) cc_final: 0.8740 (tm-30) REVERT: P 59 MET cc_start: 0.9156 (tpp) cc_final: 0.8942 (tpp) REVERT: P 93 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8317 (mm-30) REVERT: P 105 GLU cc_start: 0.7716 (tp30) cc_final: 0.7473 (tp30) REVERT: Q 41 TYR cc_start: 0.5092 (OUTLIER) cc_final: 0.4479 (t80) REVERT: Q 68 GLN cc_start: 0.8783 (tp-100) cc_final: 0.8415 (tp-100) REVERT: Q 90 MET cc_start: 0.8382 (tpp) cc_final: 0.7862 (tpp) REVERT: Q 93 GLN cc_start: 0.8768 (tt0) cc_final: 0.8461 (tt0) REVERT: Q 120 MET cc_start: 0.9051 (mmm) cc_final: 0.8640 (mmm) REVERT: R 85 ASP cc_start: 0.8860 (m-30) cc_final: 0.8486 (m-30) REVERT: S 56 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8515 (tm-30) REVERT: S 76 THR cc_start: 0.9202 (p) cc_final: 0.8977 (p) REVERT: S 84 GLN cc_start: 0.9475 (tp-100) cc_final: 0.8894 (tp40) REVERT: S 90 ASP cc_start: 0.8421 (t0) cc_final: 0.8159 (t0) REVERT: T 34 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8225 (mttt) REVERT: T 71 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8816 (tm-30) REVERT: T 105 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7497 (tp30) REVERT: T 108 LYS cc_start: 0.9216 (mtmm) cc_final: 0.8560 (mtmm) REVERT: H 153 LEU cc_start: 0.8636 (mt) cc_final: 0.7947 (pp) outliers start: 31 outliers final: 21 residues processed: 237 average time/residue: 0.1008 time to fit residues: 33.1285 Evaluate side-chains 234 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 110 CYS Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 0.0670 chunk 5 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN Q 108 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.085065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.059243 restraints weight = 37148.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060998 restraints weight = 17663.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062155 restraints weight = 11791.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062832 restraints weight = 9429.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063192 restraints weight = 8364.900| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12615 Z= 0.212 Angle : 0.641 8.721 18180 Z= 0.373 Chirality : 0.036 0.166 2063 Planarity : 0.004 0.050 1375 Dihedral : 30.483 176.449 3850 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.76 % Rotamer: Outliers : 4.83 % Allowed : 25.83 % Favored : 69.34 % 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: 1.79 (0.30), residues: 778 helix: 1.91 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 151 TYR 0.031 0.002 TYR T 40 PHE 0.014 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.005 0.001 HIS P 82 Details of bonding type rmsd covalent geometry : bond 0.00473 (12615) covalent geometry : angle 0.64118 (18180) hydrogen bonds : bond 0.04224 ( 751) hydrogen bonds : angle 3.12466 ( 1898) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 226 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9074 (tt0) cc_final: 0.8295 (tm-30) REVERT: M 60 LEU cc_start: 0.9125 (mm) cc_final: 0.8831 (mt) REVERT: M 93 GLN cc_start: 0.9110 (tt0) cc_final: 0.8727 (tt0) REVERT: M 97 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7874 (mt-10) REVERT: M 108 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8331 (t160) REVERT: M 120 MET cc_start: 0.8736 (mtp) cc_final: 0.8178 (mtt) REVERT: N 63 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8226 (mt-10) REVERT: N 80 THR cc_start: 0.8876 (m) cc_final: 0.8644 (t) REVERT: N 98 TYR cc_start: 0.9393 (m-10) cc_final: 0.9170 (m-10) REVERT: O 56 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8988 (tm-30) REVERT: O 91 GLU cc_start: 0.9028 (pm20) cc_final: 0.8706 (tm-30) REVERT: P 105 GLU cc_start: 0.7755 (tp30) cc_final: 0.7534 (tp30) REVERT: Q 41 TYR cc_start: 0.5120 (OUTLIER) cc_final: 0.4631 (t80) REVERT: Q 68 GLN cc_start: 0.8816 (tp-100) cc_final: 0.8481 (tp-100) REVERT: Q 90 MET cc_start: 0.8415 (tpp) cc_final: 0.7924 (tpp) REVERT: Q 93 GLN cc_start: 0.8752 (tt0) cc_final: 0.8526 (tt0) REVERT: Q 120 MET cc_start: 0.9002 (mmm) cc_final: 0.8710 (mmm) REVERT: R 85 ASP cc_start: 0.8846 (m-30) cc_final: 0.8511 (m-30) REVERT: R 88 TYR cc_start: 0.8760 (m-80) cc_final: 0.8510 (m-80) REVERT: S 76 THR cc_start: 0.9225 (p) cc_final: 0.9024 (p) REVERT: S 84 GLN cc_start: 0.9471 (tp-100) cc_final: 0.8873 (tp40) REVERT: S 90 ASP cc_start: 0.8462 (t0) cc_final: 0.8188 (t0) REVERT: S 92 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8707 (tp30) REVERT: T 34 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8237 (mttt) REVERT: T 71 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8824 (tm-30) REVERT: T 105 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7915 (tp30) REVERT: T 108 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8628 (mtmm) REVERT: H 153 LEU cc_start: 0.8663 (mt) cc_final: 0.7906 (pp) outliers start: 32 outliers final: 20 residues processed: 242 average time/residue: 0.1110 time to fit residues: 36.9366 Evaluate side-chains 230 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 94 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.086321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060696 restraints weight = 37025.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.062455 restraints weight = 17381.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.063602 restraints weight = 11534.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.064238 restraints weight = 9238.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.064647 restraints weight = 8238.464| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12615 Z= 0.175 Angle : 0.637 8.841 18180 Z= 0.368 Chirality : 0.035 0.161 2063 Planarity : 0.004 0.044 1375 Dihedral : 30.353 178.572 3850 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 4.08 % Allowed : 26.59 % Favored : 69.34 % 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: 1.72 (0.30), residues: 778 helix: 1.85 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.86 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 151 TYR 0.026 0.002 TYR R 88 PHE 0.010 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.005 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00386 (12615) covalent geometry : angle 0.63664 (18180) hydrogen bonds : bond 0.03811 ( 751) hydrogen bonds : angle 2.99511 ( 1898) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9064 (tt0) cc_final: 0.8334 (tm-30) REVERT: M 60 LEU cc_start: 0.9035 (mm) cc_final: 0.8695 (mt) REVERT: M 79 LYS cc_start: 0.8871 (tttt) cc_final: 0.8650 (ttmt) REVERT: M 93 GLN cc_start: 0.9008 (tt0) cc_final: 0.8653 (tt0) REVERT: M 120 MET cc_start: 0.8584 (mtp) cc_final: 0.8000 (mtt) REVERT: N 63 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8236 (mt-10) REVERT: N 80 THR cc_start: 0.8878 (m) cc_final: 0.8646 (t) REVERT: O 56 GLU cc_start: 0.9254 (tm-30) cc_final: 0.8987 (tm-30) REVERT: O 91 GLU cc_start: 0.8998 (pm20) cc_final: 0.8733 (tm-30) REVERT: P 93 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8385 (mm-30) REVERT: P 105 GLU cc_start: 0.7685 (tp30) cc_final: 0.7350 (tp30) REVERT: Q 41 TYR cc_start: 0.5178 (OUTLIER) cc_final: 0.4617 (t80) REVERT: Q 57 SER cc_start: 0.8642 (t) cc_final: 0.8428 (p) REVERT: Q 68 GLN cc_start: 0.8764 (tp-100) cc_final: 0.8461 (tp-100) REVERT: Q 90 MET cc_start: 0.8353 (tpp) cc_final: 0.7843 (tpp) REVERT: Q 93 GLN cc_start: 0.8736 (tt0) cc_final: 0.8408 (tt0) REVERT: Q 120 MET cc_start: 0.9009 (mmm) cc_final: 0.8605 (mmm) REVERT: R 85 ASP cc_start: 0.8849 (m-30) cc_final: 0.8556 (m-30) REVERT: R 88 TYR cc_start: 0.8700 (m-80) cc_final: 0.8474 (m-80) REVERT: S 75 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8510 (mppt) REVERT: S 84 GLN cc_start: 0.9462 (tp-100) cc_final: 0.8878 (tp40) REVERT: S 90 ASP cc_start: 0.8350 (t0) cc_final: 0.8083 (t0) REVERT: S 92 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8609 (tp30) REVERT: T 34 LYS cc_start: 0.8980 (mmtp) cc_final: 0.8257 (mttt) REVERT: T 71 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8814 (tm-30) REVERT: T 105 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7864 (tp30) REVERT: T 108 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8636 (mtmm) REVERT: H 150 GLN cc_start: 0.6184 (tm-30) cc_final: 0.5801 (tm-30) outliers start: 27 outliers final: 16 residues processed: 240 average time/residue: 0.1055 time to fit residues: 35.2180 Evaluate side-chains 235 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 75 LYS Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** Q 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060956 restraints weight = 36906.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.062757 restraints weight = 17524.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.063925 restraints weight = 11622.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.064622 restraints weight = 9268.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064982 restraints weight = 8192.252| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12615 Z= 0.180 Angle : 0.637 8.682 18180 Z= 0.367 Chirality : 0.035 0.166 2063 Planarity : 0.004 0.040 1375 Dihedral : 30.266 178.423 3850 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.50 % Favored : 95.37 % Rotamer: Outliers : 3.47 % Allowed : 28.85 % Favored : 67.67 % 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: 1.66 (0.30), residues: 778 helix: 1.81 (0.21), residues: 575 sheet: None (None), residues: 0 loop : -0.94 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 79 TYR 0.037 0.003 TYR T 40 PHE 0.010 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.004 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00405 (12615) covalent geometry : angle 0.63697 (18180) hydrogen bonds : bond 0.03907 ( 751) hydrogen bonds : angle 3.04549 ( 1898) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 227 time to evaluate : 0.338 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: M 50 GLU cc_start: 0.9064 (tt0) cc_final: 0.8283 (tm-30) REVERT: M 60 LEU cc_start: 0.9068 (mm) cc_final: 0.8715 (mt) REVERT: M 79 LYS cc_start: 0.8879 (tttt) cc_final: 0.8667 (ttmt) REVERT: M 93 GLN cc_start: 0.8974 (tt0) cc_final: 0.8581 (tt0) REVERT: M 120 MET cc_start: 0.8596 (mtp) cc_final: 0.8064 (mtt) REVERT: N 63 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8291 (mt-10) REVERT: N 80 THR cc_start: 0.8906 (m) cc_final: 0.8701 (t) REVERT: N 81 VAL cc_start: 0.9276 (t) cc_final: 0.9020 (p) REVERT: O 56 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8991 (tm-30) REVERT: O 91 GLU cc_start: 0.8990 (pm20) cc_final: 0.8731 (tm-30) REVERT: P 93 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8459 (mm-30) REVERT: P 105 GLU cc_start: 0.7668 (tp30) cc_final: 0.7418 (tp30) REVERT: Q 41 TYR cc_start: 0.5399 (OUTLIER) cc_final: 0.4851 (t80) REVERT: Q 68 GLN cc_start: 0.8771 (tp-100) cc_final: 0.8485 (tp-100) REVERT: Q 90 MET cc_start: 0.8296 (tpp) cc_final: 0.7758 (tpp) REVERT: Q 93 GLN cc_start: 0.8748 (tt0) cc_final: 0.8432 (tt0) REVERT: Q 120 MET cc_start: 0.9007 (mmm) cc_final: 0.8803 (mmm) REVERT: R 31 LYS cc_start: 0.9291 (ttpp) cc_final: 0.8875 (tttm) REVERT: R 85 ASP cc_start: 0.8816 (m-30) cc_final: 0.8528 (m-30) REVERT: R 88 TYR cc_start: 0.8703 (m-80) cc_final: 0.8488 (m-80) REVERT: S 82 HIS cc_start: 0.8665 (m170) cc_final: 0.8377 (m90) REVERT: S 84 GLN cc_start: 0.9465 (tp-100) cc_final: 0.8907 (tp40) REVERT: S 90 ASP cc_start: 0.8331 (t0) cc_final: 0.8073 (t0) REVERT: S 92 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8674 (tp30) REVERT: T 34 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8300 (mmtp) REVERT: T 71 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8807 (tm-30) REVERT: T 105 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7860 (tp30) REVERT: T 108 LYS cc_start: 0.9197 (mtmm) cc_final: 0.8632 (mtmm) REVERT: H 150 GLN cc_start: 0.6189 (tm-30) cc_final: 0.5828 (tm-30) outliers start: 23 outliers final: 18 residues processed: 237 average time/residue: 0.1211 time to fit residues: 39.7428 Evaluate side-chains 234 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 215 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 113 HIS Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 71 optimal weight: 0.0570 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.085961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.059690 restraints weight = 37322.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.061448 restraints weight = 17896.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.062603 restraints weight = 11974.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063272 restraints weight = 9606.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.063679 restraints weight = 8532.866| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 12615 Z= 0.206 Angle : 0.657 10.389 18180 Z= 0.377 Chirality : 0.035 0.168 2063 Planarity : 0.004 0.039 1375 Dihedral : 30.262 178.097 3850 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.63 % Favored : 95.24 % Rotamer: Outliers : 3.47 % Allowed : 30.36 % Favored : 66.16 % 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: 1.55 (0.30), residues: 778 helix: 1.74 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.99 (0.42), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 86 TYR 0.039 0.003 TYR T 40 PHE 0.012 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.005 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00467 (12615) covalent geometry : angle 0.65702 (18180) hydrogen bonds : bond 0.04107 ( 751) hydrogen bonds : angle 3.17950 ( 1898) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9061 (tt0) cc_final: 0.8294 (tm-30) REVERT: M 60 LEU cc_start: 0.9042 (mm) cc_final: 0.8768 (mt) REVERT: M 79 LYS cc_start: 0.8850 (tttt) cc_final: 0.8630 (ttmt) REVERT: M 93 GLN cc_start: 0.9018 (tt0) cc_final: 0.8604 (tt0) REVERT: M 120 MET cc_start: 0.8736 (mtp) cc_final: 0.8184 (mtt) REVERT: N 63 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8275 (mt-10) REVERT: N 80 THR cc_start: 0.8984 (m) cc_final: 0.8761 (t) REVERT: O 56 GLU cc_start: 0.9275 (tm-30) cc_final: 0.8993 (tm-30) REVERT: O 91 GLU cc_start: 0.9028 (pm20) cc_final: 0.8739 (tm-30) REVERT: P 59 MET cc_start: 0.9108 (tpp) cc_final: 0.8470 (tpp) REVERT: P 93 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8549 (mm-30) REVERT: P 105 GLU cc_start: 0.7737 (tp30) cc_final: 0.7514 (tp30) REVERT: Q 41 TYR cc_start: 0.5631 (OUTLIER) cc_final: 0.5146 (t80) REVERT: Q 68 GLN cc_start: 0.8785 (tp-100) cc_final: 0.8451 (tp-100) REVERT: Q 90 MET cc_start: 0.8365 (tpp) cc_final: 0.7870 (tpp) REVERT: Q 93 GLN cc_start: 0.8729 (tt0) cc_final: 0.8430 (tt0) REVERT: Q 120 MET cc_start: 0.9005 (mmm) cc_final: 0.8772 (mmm) REVERT: R 31 LYS cc_start: 0.9254 (ttpp) cc_final: 0.8844 (tttm) REVERT: R 85 ASP cc_start: 0.8791 (m-30) cc_final: 0.8485 (m-30) REVERT: R 88 TYR cc_start: 0.8741 (m-80) cc_final: 0.7697 (m-80) REVERT: S 84 GLN cc_start: 0.9479 (tp-100) cc_final: 0.8909 (tp40) REVERT: S 90 ASP cc_start: 0.8398 (t0) cc_final: 0.8110 (t0) REVERT: S 92 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8673 (tp30) REVERT: T 34 LYS cc_start: 0.9020 (mmtp) cc_final: 0.8318 (mmtp) REVERT: T 71 GLU cc_start: 0.9128 (tm-30) cc_final: 0.8831 (tm-30) REVERT: H 150 GLN cc_start: 0.6207 (tm-30) cc_final: 0.5845 (tm-30) outliers start: 23 outliers final: 16 residues processed: 228 average time/residue: 0.1220 time to fit residues: 38.4967 Evaluate side-chains 226 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 23 LEU Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 46 LYS Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain R residue 86 VAL Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 75 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.085715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059810 restraints weight = 36927.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061569 restraints weight = 17621.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062708 restraints weight = 11726.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063385 restraints weight = 9369.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.063766 restraints weight = 8308.838| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 12615 Z= 0.218 Angle : 0.675 10.074 18180 Z= 0.384 Chirality : 0.036 0.165 2063 Planarity : 0.005 0.038 1375 Dihedral : 30.289 178.492 3850 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 3.02 % Allowed : 31.12 % Favored : 65.86 % 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: 1.53 (0.30), residues: 778 helix: 1.74 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.07 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG T 31 TYR 0.041 0.003 TYR T 40 PHE 0.011 0.001 PHE M 67 TRP 0.001 0.000 TRP H 152 HIS 0.007 0.001 HIS T 109 Details of bonding type rmsd covalent geometry : bond 0.00492 (12615) covalent geometry : angle 0.67524 (18180) hydrogen bonds : bond 0.04204 ( 751) hydrogen bonds : angle 3.26102 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1950.24 seconds wall clock time: 34 minutes 18.28 seconds (2058.28 seconds total)