Starting phenix.real_space_refine on Fri Jul 3 04:21:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf6_51310/07_2026/9gf6_51310.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf6_51310/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9gf6_51310/07_2026/9gf6_51310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf6_51310/07_2026/9gf6_51310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gf6_51310/07_2026/9gf6_51310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf6_51310/07_2026/9gf6_51310.map" } 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-dev-6108/lib/python3.11/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: 1.79, per 1000 atoms: 0.15 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: 0.86 Conformation dependent library (CDL) restraints added in 177.8 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: 1.66 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: 1.79 Time building geometry restraints manager: 1.20 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=" C5' DG L -29 " pdb=" C4' DG L -29 " ideal model delta sigma weight residual 1.512 1.546 -0.034 7.00e-03 2.04e+04 2.35e+01 bond pdb=" C5' DC L -18 " pdb=" C4' DC L -18 " ideal model delta sigma weight residual 1.512 1.545 -0.033 7.00e-03 2.04e+04 2.27e+01 bond pdb=" C5' DG L -25 " pdb=" C4' DG L -25 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.13e+01 bond pdb=" C5' DC L 11 " pdb=" C4' DC L 11 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.10e+01 bond pdb=" C5' DT K 55 " pdb=" C4' DT K 55 " ideal model delta sigma weight residual 1.512 1.544 -0.032 7.00e-03 2.04e+04 2.03e+01 ... (remaining 12610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 13268 1.97 - 3.93: 4088 3.93 - 5.90: 702 5.90 - 7.87: 94 7.87 - 9.83: 28 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 109.40 119.23 -9.83 8.00e-01 1.56e+00 1.51e+02 angle pdb=" O5' DT L -7 " pdb=" C5' DT L -7 " pdb=" C4' DT L -7 " ideal model delta sigma weight residual 109.40 118.63 -9.23 8.00e-01 1.56e+00 1.33e+02 angle pdb=" O5' DA L -36 " pdb=" C5' DA L -36 " pdb=" C4' DA L -36 " ideal model delta sigma weight residual 109.40 118.61 -9.21 8.00e-01 1.56e+00 1.33e+02 angle pdb=" O5' DA L -31 " pdb=" C5' DA L -31 " pdb=" C4' DA L -31 " ideal model delta sigma weight residual 109.40 118.35 -8.95 8.00e-01 1.56e+00 1.25e+02 angle pdb=" O5' DA L 10 " pdb=" C5' DA L 10 " pdb=" C4' DA L 10 " ideal model delta sigma weight residual 109.40 118.28 -8.88 8.00e-01 1.56e+00 1.23e+02 ... (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 - 0.104: 1592 0.104 - 0.208: 414 0.208 - 0.312: 43 0.312 - 0.416: 13 0.416 - 0.520: 1 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 -2.73 -2.21 -0.52 2.00e-01 2.50e+01 6.77e+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: 3.870 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.450 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.600 ------------------------------------------------------------------------------- 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= 1.233 Angle : 1.916 9.834 18180 Z= 1.922 Chirality : 0.091 0.520 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/Z covalent geometry : bond 0.01285 / 1.23 (12615) covalent geometry : angle 1.91645 / 1.92 (18180) hydrogen bonds : bond 0.12983 / 14.53 ( 751) hydrogen bonds : angle 6.65496 / 8.75 ( 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 : 0.267 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: 0.1211 time to fit residues: 55.4611 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 : 0.295 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.8980 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: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 76 GLN N 25 ASN ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 84 ASN ** 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 = 0.3740 r_free = 0.3740 target = 0.090712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.064095 restraints weight = 38102.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.066112 restraints weight = 18998.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.067425 restraints weight = 12917.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068185 restraints weight = 10441.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.068575 restraints weight = 9337.012| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12615 Z= 0.200 Angle : 0.920 9.955 18180 Z= 0.513 Chirality : 0.060 0.270 2063 Planarity : 0.006 0.042 1375 Dihedral : 31.724 170.718 3850 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.08 % Favored : 96.66 % Rotamer: Outliers : 4.53 % Allowed : 18.43 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 778 helix: 0.93 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 35 TYR 0.029 0.003 TYR R 88 PHE 0.017 0.002 PHE M 67 TRP 0.008 0.002 TRP H 152 HIS 0.008 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.20 (12615) covalent geometry : angle 0.91997 / 0.51 (18180) hydrogen bonds : bond 0.06015 / 6.69 ( 751) hydrogen bonds : angle 3.81462 / 4.99 ( 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 304 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 274 time to evaluate : 0.331 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: 0.8759 (tt0) cc_final: 0.8303 (tt0) REVERT: M 73 GLU cc_start: 0.8746 (tp30) cc_final: 0.8386 (tp30) REVERT: M 97 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7740 (mt-10) REVERT: M 108 ASN cc_start: 0.8878 (t0) cc_final: 0.8635 (t0) REVERT: M 113 HIS cc_start: 0.8774 (t70) cc_final: 0.8477 (t-90) REVERT: M 120 MET cc_start: 0.8823 (mtp) cc_final: 0.8217 (mtt) REVERT: N 25 ASN cc_start: 0.8779 (m-40) cc_final: 0.8565 (m110) REVERT: N 73 THR cc_start: 0.9289 (m) cc_final: 0.8885 (t) REVERT: N 80 THR cc_start: 0.8870 (m) cc_final: 0.8621 (t) REVERT: N 84 MET cc_start: 0.8748 (mmm) cc_final: 0.8422 (mmm) REVERT: O 91 GLU cc_start: 0.8858 (pm20) cc_final: 0.8556 (tm-30) REVERT: P 76 GLU cc_start: 0.8287 (tp30) cc_final: 0.7968 (tp30) REVERT: P 82 HIS cc_start: 0.8804 (t-170) cc_final: 0.8558 (t70) REVERT: P 100 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9089 (tp) REVERT: P 105 GLU cc_start: 0.7768 (tp30) cc_final: 0.7530 (tp30) REVERT: P 120 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8634 (ttpp) REVERT: Q 41 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.4575 (t80) REVERT: Q 56 LYS cc_start: 0.9083 (ttpt) cc_final: 0.8718 (ttmm) REVERT: Q 58 THR cc_start: 0.8790 (p) cc_final: 0.8535 (t) REVERT: Q 60 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8063 (mt) REVERT: Q 68 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8298 (tp-100) REVERT: Q 73 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: Q 93 GLN cc_start: 0.8834 (tt0) cc_final: 0.7982 (tt0) REVERT: Q 97 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7467 (mt-10) REVERT: Q 126 LEU cc_start: 0.9376 (tp) cc_final: 0.9167 (tt) REVERT: R 31 LYS cc_start: 0.9254 (ttpp) cc_final: 0.8883 (tttm) REVERT: R 52 GLU cc_start: 0.8463 (tp30) cc_final: 0.8203 (tp30) REVERT: R 79 LYS cc_start: 0.9159 (mttm) cc_final: 0.8890 (ttmm) REVERT: R 84 MET cc_start: 0.9205 (mmm) cc_final: 0.8587 (mmm) REVERT: R 88 TYR cc_start: 0.9168 (m-80) cc_final: 0.8548 (m-80) REVERT: S 24 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7546 (mm-40) REVERT: S 56 GLU cc_start: 0.8534 (tt0) cc_final: 0.8284 (tm-30) REVERT: S 57 TYR cc_start: 0.8913 (t80) cc_final: 0.8700 (t80) REVERT: S 90 ASP cc_start: 0.8437 (t0) cc_final: 0.8100 (t0) REVERT: S 101 THR cc_start: 0.8936 (m) cc_final: 0.8534 (p) REVERT: T 34 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8584 (mttt) REVERT: T 105 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7552 (tp30) REVERT: H 151 ARG cc_start: 0.6176 (mmp80) cc_final: 0.5937 (mmm160) REVERT: H 153 LEU cc_start: 0.8508 (mt) cc_final: 0.7711 (pp) outliers start: 30 outliers final: 15 residues processed: 287 average time/residue: 0.1071 time to fit residues: 42.2593 Evaluate side-chains 256 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 237 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain P residue 69 ILE Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 73 GLU Chi-restraints excluded: chain Q residue 87 SER 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 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: 10.0000 chunk 97 optimal weight: 6.9990 chunk 14 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 94 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 75 HIS P 49 HIS ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 84 GLN S 94 ASN T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.089432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062833 restraints weight = 38348.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064819 restraints weight = 18670.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066084 restraints weight = 12582.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066818 restraints weight = 10173.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.067123 restraints weight = 9097.711| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12615 Z= 0.181 Angle : 0.801 9.101 18180 Z= 0.456 Chirality : 0.052 0.255 2063 Planarity : 0.005 0.040 1375 Dihedral : 31.626 175.004 3850 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.39 % Allowed : 3.08 % Favored : 96.53 % Rotamer: Outliers : 4.08 % Allowed : 21.90 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.29), residues: 778 helix: 1.27 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.82 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Q 134 TYR 0.017 0.002 TYR N 98 PHE 0.018 0.002 PHE M 67 TRP 0.006 0.002 TRP H 152 HIS 0.010 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (12615) covalent geometry : angle 0.80088 / 0.46 (18180) hydrogen bonds : bond 0.05160 / 5.81 ( 751) hydrogen bonds : angle 3.47298 / 4.51 ( 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 271 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8787 (tt0) cc_final: 0.8331 (tt0) REVERT: M 60 LEU cc_start: 0.9354 (mm) cc_final: 0.9115 (mm) REVERT: M 120 MET cc_start: 0.8716 (mtp) cc_final: 0.8143 (mtt) REVERT: N 63 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8221 (mt-10) REVERT: N 84 MET cc_start: 0.8678 (mmm) cc_final: 0.8389 (mmm) REVERT: O 56 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8735 (tm-30) REVERT: O 91 GLU cc_start: 0.8895 (pm20) cc_final: 0.8584 (tm-30) REVERT: P 46 LYS cc_start: 0.9246 (mmmt) cc_final: 0.8848 (tptp) REVERT: P 76 GLU cc_start: 0.8388 (tp30) cc_final: 0.8083 (tp30) REVERT: P 82 HIS cc_start: 0.8807 (t-170) cc_final: 0.8575 (t-170) REVERT: P 105 GLU cc_start: 0.7807 (tp30) cc_final: 0.6534 (tp30) REVERT: P 108 LYS cc_start: 0.9049 (mttp) cc_final: 0.8462 (mtmm) REVERT: P 120 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8711 (ttpp) REVERT: Q 41 TYR cc_start: 0.5064 (OUTLIER) cc_final: 0.4299 (t80) REVERT: Q 56 LYS cc_start: 0.9062 (ttpt) cc_final: 0.8729 (ttmm) REVERT: Q 57 SER cc_start: 0.8232 (t) cc_final: 0.7612 (p) REVERT: Q 59 GLU cc_start: 0.8076 (pm20) cc_final: 0.7778 (pm20) REVERT: Q 60 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8097 (mt) REVERT: Q 68 GLN cc_start: 0.8713 (tp-100) cc_final: 0.8250 (tp40) REVERT: Q 73 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7945 (mt-10) REVERT: Q 93 GLN cc_start: 0.8843 (tt0) cc_final: 0.8364 (tt0) REVERT: Q 97 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7463 (mt-10) REVERT: R 31 LYS cc_start: 0.9230 (ttpp) cc_final: 0.8905 (tttm) REVERT: R 79 LYS cc_start: 0.9195 (mttm) cc_final: 0.8993 (ttmm) REVERT: R 84 MET cc_start: 0.9139 (mmm) cc_final: 0.8551 (mmm) REVERT: R 88 TYR cc_start: 0.9211 (m-80) cc_final: 0.8557 (m-80) REVERT: S 24 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7844 (mp10) REVERT: S 61 GLU cc_start: 0.8808 (tp30) cc_final: 0.8481 (tp30) REVERT: S 90 ASP cc_start: 0.8355 (t0) cc_final: 0.7855 (t0) REVERT: S 94 ASN cc_start: 0.9017 (t0) cc_final: 0.8696 (t0) REVERT: S 101 THR cc_start: 0.9018 (m) cc_final: 0.8653 (p) REVERT: T 34 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8571 (mttt) REVERT: T 35 GLU cc_start: 0.8761 (tp30) cc_final: 0.8534 (tt0) REVERT: T 105 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7819 (tp30) REVERT: H 147 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8555 (tm-30) REVERT: H 151 ARG cc_start: 0.5880 (mmp80) cc_final: 0.5626 (mmm160) REVERT: H 153 LEU cc_start: 0.8556 (mt) cc_final: 0.7803 (pp) outliers start: 27 outliers final: 18 residues processed: 261 average time/residue: 0.0981 time to fit residues: 35.2093 Evaluate side-chains 242 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 222 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 74 ILE 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 101 THR Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 41 VAL 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: 0.9980 chunk 54 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 93 GLN ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.089226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063367 restraints weight = 38074.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065304 restraints weight = 18128.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066558 restraints weight = 12064.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067325 restraints weight = 9666.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.067662 restraints weight = 8567.774| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12615 Z= 0.175 Angle : 0.753 9.041 18180 Z= 0.432 Chirality : 0.050 0.246 2063 Planarity : 0.005 0.035 1375 Dihedral : 31.617 175.316 3850 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.34 % Favored : 96.40 % Rotamer: Outliers : 4.23 % Allowed : 23.72 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.29), residues: 778 helix: 1.50 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 92 TYR 0.029 0.002 TYR S 50 PHE 0.015 0.001 PHE M 67 TRP 0.003 0.001 TRP H 152 HIS 0.016 0.002 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.18 (12615) covalent geometry : angle 0.75251 / 0.43 (18180) hydrogen bonds : bond 0.04814 / 5.42 ( 751) hydrogen bonds : angle 3.28320 / 4.22 ( 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 262 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8818 (tt0) cc_final: 0.8384 (tt0) REVERT: M 73 GLU cc_start: 0.8643 (tp30) cc_final: 0.8256 (tp30) REVERT: M 120 MET cc_start: 0.8655 (mtp) cc_final: 0.8052 (mtt) REVERT: N 63 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8222 (mt-10) REVERT: N 77 LYS cc_start: 0.9552 (mttp) cc_final: 0.9280 (mptt) REVERT: N 84 MET cc_start: 0.8682 (mmm) cc_final: 0.8422 (mmm) REVERT: O 91 GLU cc_start: 0.8904 (pm20) cc_final: 0.8639 (tm-30) REVERT: P 76 GLU cc_start: 0.8497 (tp30) cc_final: 0.8288 (tp30) REVERT: P 79 ARG cc_start: 0.8722 (mtm-85) cc_final: 0.8003 (mtm-85) REVERT: P 86 ARG cc_start: 0.8569 (tpp80) cc_final: 0.8268 (ttm-80) REVERT: P 105 GLU cc_start: 0.7852 (tp30) cc_final: 0.5963 (tp30) REVERT: P 108 LYS cc_start: 0.9045 (mttp) cc_final: 0.8425 (mtmm) REVERT: P 120 LYS cc_start: 0.8997 (ttmm) cc_final: 0.8716 (ttpp) REVERT: Q 41 TYR cc_start: 0.5058 (OUTLIER) cc_final: 0.4284 (t80) REVERT: Q 56 LYS cc_start: 0.9099 (ttpt) cc_final: 0.8754 (ttmm) REVERT: Q 57 SER cc_start: 0.8472 (t) cc_final: 0.7640 (p) REVERT: Q 60 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8201 (mt) REVERT: Q 68 GLN cc_start: 0.8729 (tp-100) cc_final: 0.8381 (tp-100) REVERT: Q 93 GLN cc_start: 0.8882 (tt0) cc_final: 0.8515 (tt0) REVERT: Q 97 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7513 (mt-10) REVERT: Q 120 MET cc_start: 0.8913 (mmm) cc_final: 0.8675 (mmm) REVERT: R 31 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8844 (tttm) REVERT: R 77 LYS cc_start: 0.9473 (mttp) cc_final: 0.9273 (mmtm) REVERT: R 84 MET cc_start: 0.9109 (mmm) cc_final: 0.8751 (mmm) REVERT: R 85 ASP cc_start: 0.8762 (m-30) cc_final: 0.8348 (m-30) REVERT: R 88 TYR cc_start: 0.9228 (m-10) cc_final: 0.8694 (m-80) REVERT: S 56 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8389 (tm-30) REVERT: S 90 ASP cc_start: 0.8349 (t0) cc_final: 0.7834 (t0) REVERT: S 94 ASN cc_start: 0.9083 (t0) cc_final: 0.8847 (t0) REVERT: S 101 THR cc_start: 0.9019 (m) cc_final: 0.8669 (p) REVERT: T 34 LYS cc_start: 0.9126 (mmtm) cc_final: 0.8544 (mttt) REVERT: H 153 LEU cc_start: 0.8623 (mt) cc_final: 0.7909 (pp) outliers start: 28 outliers final: 17 residues processed: 249 average time/residue: 0.1086 time to fit residues: 36.8377 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 : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 74 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 54 VAL 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 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 S residue 87 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 THR 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: 0.7980 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 30.0000 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 113 HIS ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.081403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.055159 restraints weight = 37052.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.056841 restraints weight = 18112.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057921 restraints weight = 12218.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.058567 restraints weight = 9860.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.058913 restraints weight = 8771.723| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 12615 Z= 0.342 Angle : 0.880 8.825 18180 Z= 0.485 Chirality : 0.053 0.291 2063 Planarity : 0.006 0.075 1375 Dihedral : 31.754 173.729 3850 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.37 % Favored : 95.24 % Rotamer: Outliers : 7.25 % Allowed : 23.56 % Favored : 69.18 % 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: 1.08 (0.29), residues: 778 helix: 1.35 (0.21), residues: 559 sheet: None (None), residues: 0 loop : -0.87 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 67 TYR 0.036 0.003 TYR S 50 PHE 0.023 0.003 PHE M 67 TRP 0.003 0.001 TRP H 152 HIS 0.012 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.34 (12615) covalent geometry : angle 0.88027 / 0.49 (18180) hydrogen bonds : bond 0.06940 / 7.84 ( 751) hydrogen bonds : angle 3.77957 / 4.80 ( 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 260 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8959 (tt0) cc_final: 0.8608 (tt0) REVERT: N 63 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8215 (mt-10) REVERT: N 84 MET cc_start: 0.8822 (mmm) cc_final: 0.8360 (mmm) REVERT: O 56 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8871 (tm-30) REVERT: O 91 GLU cc_start: 0.9024 (pm20) cc_final: 0.8634 (tm-30) REVERT: P 59 MET cc_start: 0.9227 (tpp) cc_final: 0.8758 (tpp) REVERT: P 86 ARG cc_start: 0.8865 (tpp80) cc_final: 0.8559 (ttm-80) REVERT: P 120 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8508 (ttpp) REVERT: Q 41 TYR cc_start: 0.5375 (OUTLIER) cc_final: 0.4710 (t80) REVERT: Q 50 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8718 (tt0) REVERT: Q 68 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8488 (tp-100) REVERT: Q 123 ASP cc_start: 0.9217 (m-30) cc_final: 0.9010 (m-30) REVERT: R 31 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8775 (tttm) REVERT: R 84 MET cc_start: 0.9191 (mmm) cc_final: 0.8939 (tpp) REVERT: R 85 ASP cc_start: 0.8835 (m-30) cc_final: 0.8444 (m-30) REVERT: R 88 TYR cc_start: 0.9287 (m-10) cc_final: 0.9039 (m-80) REVERT: S 75 LYS cc_start: 0.8832 (mmtm) cc_final: 0.8583 (mmtp) REVERT: S 101 THR cc_start: 0.9096 (m) cc_final: 0.8653 (p) REVERT: T 105 GLU cc_start: 0.8246 (tp30) cc_final: 0.7766 (tp30) REVERT: H 150 GLN cc_start: 0.6104 (tp-100) cc_final: 0.5859 (tm-30) REVERT: H 151 ARG cc_start: 0.5830 (mmm160) cc_final: 0.5579 (mmm160) REVERT: H 153 LEU cc_start: 0.8617 (mt) cc_final: 0.7993 (pp) outliers start: 48 outliers final: 37 residues processed: 244 average time/residue: 0.0995 time to fit residues: 33.7409 Evaluate side-chains 238 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 200 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 74 ILE 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 43 VAL Chi-restraints excluded: chain N residue 54 THR Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 82 THR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 59 THR Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 109 LEU 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 54 VAL Chi-restraints excluded: chain S residue 63 LEU Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 80 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: 0.5980 chunk 29 optimal weight: 0.0370 chunk 15 optimal weight: 9.9990 chunk 13 optimal weight: 40.0000 chunk 27 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 60 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 75 HIS ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.084372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.057946 restraints weight = 36777.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059704 restraints weight = 17493.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.060847 restraints weight = 11695.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.061516 restraints weight = 9401.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.061877 restraints weight = 8366.978| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12615 Z= 0.162 Angle : 0.737 9.099 18180 Z= 0.423 Chirality : 0.048 0.252 2063 Planarity : 0.005 0.059 1375 Dihedral : 31.563 174.022 3850 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.21 % Favored : 96.53 % Rotamer: Outliers : 3.78 % Allowed : 27.64 % Favored : 68.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.29), residues: 778 helix: 1.62 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.02 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 53 TYR 0.030 0.002 TYR N 98 PHE 0.017 0.001 PHE M 67 TRP 0.016 0.006 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.16 (12615) covalent geometry : angle 0.73677 / 0.42 (18180) hydrogen bonds : bond 0.04665 / 5.17 ( 751) hydrogen bonds : angle 3.25377 / 4.19 ( 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 259 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 234 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 50 GLU cc_start: 0.8854 (tt0) cc_final: 0.8391 (tt0) REVERT: M 60 LEU cc_start: 0.9206 (mm) cc_final: 0.8990 (mt) REVERT: M 97 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7738 (mt-10) REVERT: M 123 ASP cc_start: 0.9378 (m-30) cc_final: 0.8915 (t0) REVERT: N 63 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8170 (mt-10) REVERT: N 84 MET cc_start: 0.8716 (mmm) cc_final: 0.8330 (mmm) REVERT: O 56 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8846 (tm-30) REVERT: O 91 GLU cc_start: 0.9004 (pm20) cc_final: 0.8656 (tm-30) REVERT: P 59 MET cc_start: 0.9216 (tpp) cc_final: 0.8869 (tpp) REVERT: P 76 GLU cc_start: 0.8629 (tp30) cc_final: 0.8423 (tp30) REVERT: P 79 ARG cc_start: 0.8672 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: P 86 ARG cc_start: 0.8732 (tpp80) cc_final: 0.8363 (ttm-80) REVERT: P 108 LYS cc_start: 0.9051 (mttp) cc_final: 0.8467 (mtmm) REVERT: P 120 LYS cc_start: 0.8866 (ttmm) cc_final: 0.8589 (ttpp) REVERT: Q 41 TYR cc_start: 0.5227 (OUTLIER) cc_final: 0.4340 (t80) REVERT: Q 60 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8808 (mt) REVERT: Q 68 GLN cc_start: 0.8799 (tp-100) cc_final: 0.8436 (tp-100) REVERT: Q 73 GLU cc_start: 0.8868 (tt0) cc_final: 0.8565 (tt0) REVERT: Q 97 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7464 (mt-10) REVERT: Q 120 MET cc_start: 0.8976 (mmm) cc_final: 0.8734 (mmm) REVERT: Q 123 ASP cc_start: 0.9079 (m-30) cc_final: 0.8817 (m-30) REVERT: R 31 LYS cc_start: 0.9142 (ttpp) cc_final: 0.8766 (tttm) REVERT: R 84 MET cc_start: 0.9023 (mmm) cc_final: 0.8763 (tpp) REVERT: R 85 ASP cc_start: 0.8781 (m-30) cc_final: 0.8434 (m-30) REVERT: R 88 TYR cc_start: 0.9215 (m-10) cc_final: 0.8964 (m-80) REVERT: S 76 THR cc_start: 0.9162 (p) cc_final: 0.8958 (p) REVERT: S 90 ASP cc_start: 0.8401 (t0) cc_final: 0.8078 (t0) REVERT: S 101 THR cc_start: 0.8979 (m) cc_final: 0.8591 (p) REVERT: T 105 GLU cc_start: 0.8255 (tp30) cc_final: 0.7784 (tp30) REVERT: H 147 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8244 (tm-30) REVERT: H 150 GLN cc_start: 0.6167 (tp-100) cc_final: 0.5850 (tm-30) REVERT: H 151 ARG cc_start: 0.5746 (mmm160) cc_final: 0.5373 (mmm160) REVERT: H 153 LEU cc_start: 0.8670 (mt) cc_final: 0.8130 (pp) outliers start: 25 outliers final: 17 residues processed: 249 average time/residue: 0.1034 time to fit residues: 35.5215 Evaluate side-chains 239 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 74 ILE 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 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain S residue 16 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 87 ILE Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 THR 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: 0.5980 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 92 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** 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 = 0.3545 r_free = 0.3545 target = 0.084180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058550 restraints weight = 36606.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060311 restraints weight = 17084.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.061450 restraints weight = 11258.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.062121 restraints weight = 8985.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.062456 restraints weight = 7953.234| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 12615 Z= 0.169 Angle : 0.724 9.058 18180 Z= 0.416 Chirality : 0.047 0.308 2063 Planarity : 0.005 0.072 1375 Dihedral : 31.423 175.275 3850 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.98 % Favored : 95.89 % Rotamer: Outliers : 4.53 % Allowed : 27.95 % Favored : 67.52 % 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: 1.48 (0.29), residues: 778 helix: 1.69 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -0.99 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 52 TYR 0.033 0.002 TYR P 83 PHE 0.016 0.001 PHE M 67 TRP 0.022 0.008 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (12615) covalent geometry : angle 0.72436 / 0.42 (18180) hydrogen bonds : bond 0.04585 / 5.15 ( 751) hydrogen bonds : angle 3.22688 / 4.12 ( 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 253 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8927 (tt0) cc_final: 0.8576 (tt0) REVERT: M 97 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7678 (mt-10) REVERT: N 63 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8167 (mt-10) REVERT: O 91 GLU cc_start: 0.9023 (pm20) cc_final: 0.8649 (tm-30) REVERT: P 59 MET cc_start: 0.9184 (tpp) cc_final: 0.8905 (tpp) REVERT: P 86 ARG cc_start: 0.8724 (tpp80) cc_final: 0.8359 (ttm-80) REVERT: P 93 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8208 (mm-30) REVERT: P 108 LYS cc_start: 0.9037 (mttp) cc_final: 0.8454 (mtmm) REVERT: P 120 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8573 (ttpp) REVERT: Q 41 TYR cc_start: 0.5270 (OUTLIER) cc_final: 0.4476 (t80) REVERT: Q 60 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8564 (mt) REVERT: Q 68 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8449 (tp-100) REVERT: Q 93 GLN cc_start: 0.8820 (tt0) cc_final: 0.8286 (tt0) REVERT: Q 94 GLU cc_start: 0.8497 (tp30) cc_final: 0.8241 (tp30) REVERT: Q 120 MET cc_start: 0.8982 (mmm) cc_final: 0.8725 (mmm) REVERT: Q 123 ASP cc_start: 0.9073 (m-30) cc_final: 0.8804 (m-30) REVERT: R 85 ASP cc_start: 0.8811 (m-30) cc_final: 0.8468 (m-30) REVERT: R 88 TYR cc_start: 0.9194 (m-10) cc_final: 0.8962 (m-80) REVERT: S 76 THR cc_start: 0.9155 (p) cc_final: 0.8948 (p) REVERT: S 90 ASP cc_start: 0.8371 (t0) cc_final: 0.8032 (t0) REVERT: S 101 THR cc_start: 0.9015 (m) cc_final: 0.8648 (p) REVERT: T 105 GLU cc_start: 0.8259 (tp30) cc_final: 0.7768 (tp30) REVERT: H 147 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8377 (tm-30) REVERT: H 150 GLN cc_start: 0.6123 (tp-100) cc_final: 0.5908 (tm-30) REVERT: H 151 ARG cc_start: 0.5900 (mmm160) cc_final: 0.5569 (mmm160) REVERT: H 153 LEU cc_start: 0.8564 (mt) cc_final: 0.7977 (pp) outliers start: 30 outliers final: 23 residues processed: 240 average time/residue: 0.0975 time to fit residues: 32.6081 Evaluate side-chains 241 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 216 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 74 ILE 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 101 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 25 ASN 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 S residue 87 ILE Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 41 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 71 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.082640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.056950 restraints weight = 36779.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.058656 restraints weight = 17394.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059776 restraints weight = 11547.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060418 restraints weight = 9220.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060763 restraints weight = 8181.350| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12615 Z= 0.261 Angle : 0.769 8.922 18180 Z= 0.436 Chirality : 0.048 0.245 2063 Planarity : 0.005 0.046 1375 Dihedral : 31.424 174.058 3850 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.37 % Favored : 95.50 % Rotamer: Outliers : 4.83 % Allowed : 28.55 % Favored : 66.62 % 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: 1.34 (0.29), residues: 778 helix: 1.60 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -1.10 (0.40), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 67 TYR 0.070 0.003 TYR P 83 PHE 0.019 0.002 PHE M 67 TRP 0.014 0.005 TRP H 152 HIS 0.010 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 (12615) covalent geometry : angle 0.76916 / 0.44 (18180) hydrogen bonds : bond 0.05338 / 6.04 ( 751) hydrogen bonds : angle 3.43545 / 4.36 ( 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 244 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9058 (tt0) cc_final: 0.8636 (tt0) REVERT: M 60 LEU cc_start: 0.9079 (mt) cc_final: 0.8857 (tp) REVERT: M 97 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7800 (mt-10) REVERT: N 63 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8206 (mt-10) REVERT: N 77 LYS cc_start: 0.9602 (mptt) cc_final: 0.9224 (mptt) REVERT: N 84 MET cc_start: 0.8651 (tpp) cc_final: 0.8445 (tpp) REVERT: O 56 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8882 (tm-30) REVERT: O 91 GLU cc_start: 0.9024 (pm20) cc_final: 0.8638 (tm-30) REVERT: P 59 MET cc_start: 0.9221 (tpp) cc_final: 0.8699 (tpp) REVERT: P 86 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8464 (ttm-80) REVERT: P 93 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8399 (mm-30) REVERT: P 108 LYS cc_start: 0.9077 (mttp) cc_final: 0.8470 (mtmm) REVERT: P 120 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8607 (ttpp) REVERT: Q 41 TYR cc_start: 0.5255 (OUTLIER) cc_final: 0.4548 (t80) REVERT: Q 68 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8486 (tp-100) REVERT: Q 94 GLU cc_start: 0.8557 (tp30) cc_final: 0.8286 (tp30) REVERT: Q 123 ASP cc_start: 0.9109 (m-30) cc_final: 0.8883 (m-30) REVERT: R 37 LEU cc_start: 0.9410 (tp) cc_final: 0.9170 (tp) REVERT: R 84 MET cc_start: 0.9085 (tpp) cc_final: 0.8753 (tpp) REVERT: R 85 ASP cc_start: 0.8820 (m-30) cc_final: 0.8493 (m-30) REVERT: R 88 TYR cc_start: 0.9154 (m-10) cc_final: 0.8814 (m-80) REVERT: S 50 TYR cc_start: 0.8577 (t80) cc_final: 0.8286 (t80) REVERT: S 56 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8610 (tm-30) REVERT: S 76 THR cc_start: 0.9176 (p) cc_final: 0.8970 (p) REVERT: T 93 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8347 (mp0) REVERT: T 105 GLU cc_start: 0.8322 (tp30) cc_final: 0.7862 (tp30) REVERT: H 147 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8385 (tm-30) REVERT: H 150 GLN cc_start: 0.6197 (tp-100) cc_final: 0.5930 (tm-30) REVERT: H 151 ARG cc_start: 0.5935 (mmm160) cc_final: 0.5658 (mmm160) REVERT: H 153 LEU cc_start: 0.8611 (mt) cc_final: 0.7998 (pp) outliers start: 32 outliers final: 26 residues processed: 232 average time/residue: 0.0987 time to fit residues: 32.1596 Evaluate side-chains 234 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 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 74 ILE 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 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 107 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 25 ASN 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 S residue 87 ILE Chi-restraints excluded: chain S residue 102 ILE Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 41 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.084348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.058310 restraints weight = 36546.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.060043 restraints weight = 17327.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061186 restraints weight = 11558.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.061828 restraints weight = 9270.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.062200 restraints weight = 8247.722| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12615 Z= 0.170 Angle : 0.722 9.068 18180 Z= 0.415 Chirality : 0.046 0.247 2063 Planarity : 0.004 0.050 1375 Dihedral : 31.303 174.377 3850 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.24 % Favored : 95.63 % Rotamer: Outliers : 4.83 % Allowed : 29.31 % 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: 1.31 (0.30), residues: 778 helix: 1.59 (0.21), residues: 573 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 79 TYR 0.064 0.003 TYR P 83 PHE 0.014 0.001 PHE M 67 TRP 0.012 0.003 TRP H 152 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (12615) covalent geometry : angle 0.72168 / 0.42 (18180) hydrogen bonds : bond 0.04417 / 4.96 ( 751) hydrogen bonds : angle 3.22445 / 4.13 ( 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 259 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 227 time to evaluate : 0.212 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: 0.9021 (tt0) cc_final: 0.8218 (tm-30) REVERT: M 60 LEU cc_start: 0.9031 (mt) cc_final: 0.8772 (tp) REVERT: M 97 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7797 (mt-10) REVERT: M 120 MET cc_start: 0.8757 (mtp) cc_final: 0.8182 (mtt) REVERT: M 123 ASP cc_start: 0.9405 (m-30) cc_final: 0.8863 (t0) REVERT: N 63 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8171 (mt-10) REVERT: N 98 TYR cc_start: 0.9255 (m-10) cc_final: 0.9053 (m-80) REVERT: O 56 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8700 (tm-30) REVERT: O 73 ASN cc_start: 0.9514 (t0) cc_final: 0.9306 (t0) REVERT: O 91 GLU cc_start: 0.9010 (pm20) cc_final: 0.8601 (tm-30) REVERT: P 59 MET cc_start: 0.9155 (tpp) cc_final: 0.8670 (tpp) REVERT: P 86 ARG cc_start: 0.8752 (tpp80) cc_final: 0.8395 (ttm-80) REVERT: P 93 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8350 (mm-30) REVERT: P 108 LYS cc_start: 0.9079 (mttp) cc_final: 0.8492 (mtmm) REVERT: Q 41 TYR cc_start: 0.5196 (OUTLIER) cc_final: 0.4418 (t80) REVERT: Q 68 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8390 (tp-100) REVERT: Q 123 ASP cc_start: 0.9082 (m-30) cc_final: 0.8806 (m-30) REVERT: Q 134 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7508 (ttp80) REVERT: R 84 MET cc_start: 0.9049 (tpp) cc_final: 0.8735 (tpp) REVERT: R 85 ASP cc_start: 0.8811 (m-30) cc_final: 0.8473 (m-30) REVERT: R 88 TYR cc_start: 0.9115 (m-10) cc_final: 0.8774 (m-80) REVERT: S 24 GLN cc_start: 0.8346 (mm-40) cc_final: 0.8120 (tp40) REVERT: S 90 ASP cc_start: 0.8304 (t0) cc_final: 0.8017 (t0) REVERT: T 105 GLU cc_start: 0.8347 (tp30) cc_final: 0.7647 (tp30) REVERT: T 108 LYS cc_start: 0.9181 (mtmm) cc_final: 0.8550 (mtmm) REVERT: H 147 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8458 (tm-30) REVERT: H 150 GLN cc_start: 0.6175 (tp-100) cc_final: 0.5931 (tm-30) REVERT: H 151 ARG cc_start: 0.6060 (mmm160) cc_final: 0.5827 (mmm160) REVERT: H 153 LEU cc_start: 0.8582 (mt) cc_final: 0.7965 (pp) outliers start: 32 outliers final: 25 residues processed: 244 average time/residue: 0.1009 time to fit residues: 34.5027 Evaluate side-chains 241 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 215 time to evaluate : 0.200 ------------------------------------------------------------------------------- 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 74 ILE 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 93 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 25 ASN 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 S residue 87 ILE Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 41 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 0.0470 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 71 optimal weight: 0.0470 chunk 72 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.082800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.057338 restraints weight = 37141.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059043 restraints weight = 17496.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.060147 restraints weight = 11587.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.060791 restraints weight = 9245.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.061135 restraints weight = 8187.948| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12615 Z= 0.259 Angle : 0.765 8.900 18180 Z= 0.433 Chirality : 0.047 0.244 2063 Planarity : 0.005 0.049 1375 Dihedral : 31.306 174.421 3850 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.76 % Favored : 95.12 % Rotamer: Outliers : 3.93 % Allowed : 30.51 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.30), residues: 778 helix: 1.46 (0.21), residues: 577 sheet: None (None), residues: 0 loop : -1.24 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 92 TYR 0.024 0.003 TYR P 83 PHE 0.015 0.002 PHE M 67 TRP 0.015 0.004 TRP H 152 HIS 0.010 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.26 (12615) covalent geometry : angle 0.76529 / 0.43 (18180) hydrogen bonds : bond 0.05136 / 5.85 ( 751) hydrogen bonds : angle 3.42884 / 4.34 ( 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 237 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9063 (tt0) cc_final: 0.8638 (tt0) REVERT: M 60 LEU cc_start: 0.8988 (mt) cc_final: 0.8718 (tp) REVERT: M 97 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7805 (mt-10) REVERT: M 123 ASP cc_start: 0.9443 (m-30) cc_final: 0.8841 (t0) REVERT: N 63 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8187 (mt-10) REVERT: N 77 LYS cc_start: 0.9594 (mptt) cc_final: 0.9121 (mptt) REVERT: N 98 TYR cc_start: 0.9338 (m-10) cc_final: 0.9083 (m-80) REVERT: O 56 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8885 (tm-30) REVERT: O 73 ASN cc_start: 0.9504 (t0) cc_final: 0.9294 (t0) REVERT: O 91 GLU cc_start: 0.9025 (pm20) cc_final: 0.8600 (tm-30) REVERT: P 59 MET cc_start: 0.9161 (tpp) cc_final: 0.8918 (tpp) REVERT: P 86 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8475 (ttm-80) REVERT: P 93 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8377 (mm-30) REVERT: P 108 LYS cc_start: 0.9085 (mttp) cc_final: 0.8485 (mtmm) REVERT: Q 41 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.4620 (t80) REVERT: Q 68 GLN cc_start: 0.8909 (tp-100) cc_final: 0.8461 (tp-100) REVERT: Q 93 GLN cc_start: 0.8915 (tt0) cc_final: 0.8521 (tp-100) REVERT: Q 123 ASP cc_start: 0.9102 (m-30) cc_final: 0.8833 (m-30) REVERT: Q 134 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7529 (ttp80) REVERT: R 84 MET cc_start: 0.9103 (tpp) cc_final: 0.8683 (tpp) REVERT: R 85 ASP cc_start: 0.8809 (m-30) cc_final: 0.8482 (m-30) REVERT: R 88 TYR cc_start: 0.9170 (m-10) cc_final: 0.8766 (m-80) REVERT: S 90 ASP cc_start: 0.8332 (t0) cc_final: 0.8052 (t0) REVERT: T 105 GLU cc_start: 0.8400 (tp30) cc_final: 0.7738 (tp30) REVERT: T 108 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8585 (mtmm) REVERT: H 147 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8341 (tm-30) REVERT: H 150 GLN cc_start: 0.6182 (tp-100) cc_final: 0.5907 (tm-30) REVERT: H 151 ARG cc_start: 0.6152 (mmm160) cc_final: 0.5943 (mmm160) REVERT: H 153 LEU cc_start: 0.8616 (mt) cc_final: 0.7984 (pp) outliers start: 26 outliers final: 23 residues processed: 229 average time/residue: 0.1025 time to fit residues: 32.4979 Evaluate side-chains 230 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 74 ILE 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 54 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 93 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 39 ILE Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain Q residue 41 TYR Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 109 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 S residue 87 ILE Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 THR 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: 0.6980 chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 0.0980 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 25 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 84 ASN ** H 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.084644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.058818 restraints weight = 36769.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060560 restraints weight = 17281.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.061701 restraints weight = 11437.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.062367 restraints weight = 9134.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.062719 restraints weight = 8093.959| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 12615 Z= 0.163 Angle : 0.716 9.093 18180 Z= 0.411 Chirality : 0.045 0.247 2063 Planarity : 0.004 0.050 1375 Dihedral : 31.187 175.173 3850 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.88 % Favored : 94.99 % Rotamer: Outliers : 4.08 % Allowed : 30.82 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.30), residues: 778 helix: 1.57 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 92 TYR 0.021 0.002 TYR O 39 PHE 0.013 0.001 PHE M 67 TRP 0.012 0.003 TRP H 152 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (12615) covalent geometry : angle 0.71618 / 0.41 (18180) hydrogen bonds : bond 0.04345 / 4.92 ( 751) hydrogen bonds : angle 3.24611 / 4.12 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1766.81 seconds wall clock time: 31 minutes 10.64 seconds (1870.64 seconds total)