Starting phenix.real_space_refine on Wed Aug 5 22:24:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gf6_51310/08_2026/9gf6_51310.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gf6_51310/08_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_51310/08_2026/9gf6_51310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gf6_51310/08_2026/9gf6_51310.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gf6_51310/08_2026/9gf6_51310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gf6_51310/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.74, 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: 0.68 Conformation dependent library (CDL) restraints added in 171.0 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: 1.85 Creating SS restraints... Processing helix chain 'M' and resid 44 through 57 removed outlier: 3.563A pdb=" N ARG M 52 " --> pdb=" O LEU M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.569A pdb=" N LEU M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 131 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.550A pdb=" N ILE N 29 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 removed outlier: 3.539A pdb=" N GLY N 41 " --> pdb=" O LEU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.505A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 Processing helix chain 'O' and resid 16 through 22 Processing helix chain 'O' and resid 26 through 37 Processing helix chain 'O' and resid 45 through 73 removed outlier: 4.471A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.717A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 98 Processing helix chain 'P' and resid 37 through 49 Processing helix chain 'P' and resid 55 through 84 Processing helix chain 'P' and resid 90 through 102 removed outlier: 3.553A pdb=" N ILE P 94 " --> pdb=" O THR P 90 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 125 removed outlier: 3.917A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 57 Processing helix chain 'Q' and resid 63 through 77 removed outlier: 4.195A pdb=" N ARG Q 72 " --> pdb=" O GLN Q 68 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Q 73 " --> pdb=" O ARG Q 69 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP Q 77 " --> pdb=" O GLU Q 73 " (cutoff:3.500A) Processing helix chain 'Q' and resid 85 through 114 removed outlier: 3.985A pdb=" N MET Q 90 " --> pdb=" O SER Q 86 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP Q 106 " --> pdb=" O GLY Q 102 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU Q 109 " --> pdb=" O GLU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 120 through 132 removed outlier: 3.759A pdb=" N LEU Q 126 " --> pdb=" O LYS Q 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 removed outlier: 4.021A pdb=" N GLY R 41 " --> pdb=" O LEU R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 76 removed outlier: 4.269A pdb=" N TYR R 51 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU R 52 " --> pdb=" O GLY R 48 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG R 55 " --> pdb=" O TYR R 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL R 57 " --> pdb=" O GLU R 53 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 93 Processing helix chain 'S' and resid 16 through 22 Processing helix chain 'S' and resid 26 through 37 Processing helix chain 'S' and resid 45 through 73 removed outlier: 4.304A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 89 removed outlier: 3.682A pdb=" N ASN S 89 " --> pdb=" O LEU S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 83 Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 122 removed outlier: 3.815A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 Processing helix chain 'H' and resid 172 through 176 Processing helix chain 'H' and resid 177 through 189 Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.921A pdb=" N ARG M 83 " --> pdb=" O VAL N 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'N' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'Q' and resid 83 through 84 removed outlier: 6.817A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'S' and resid 77 through 78 414 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 337 hydrogen bonds 674 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 0.91 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: 13231 1.97 - 3.93: 4105 3.93 - 5.90: 722 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: 5.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.900 ------------------------------------------------------------------------------- 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 : 1.926 9.834 18180 Z= 1.933 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 1.92640 / 1.93 (18180) hydrogen bonds : bond 0.12983 / 14.61 ( 751) hydrogen bonds : angle 6.65496 / 8.76 ( 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 : 0.210 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: 0.9116 (tt0) REVERT: M 60 LEU cc_start: 0.9482 (mt) cc_final: 0.9277 (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: 0.8762 (mm-40) REVERT: O 38 ASN cc_start: 0.8897 (m-40) cc_final: 0.8530 (p0) REVERT: P 35 GLU cc_start: 0.9363 (mp0) cc_final: 0.9110 (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: 0.9309 (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: 0.8932 (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 71 GLU cc_start: 0.9358 (mt-10) cc_final: 0.9124 (tm-30) 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: 0.8107 (mp) outliers start: 7 outliers final: 0 residues processed: 346 average time/residue: 0.1138 time to fit residues: 52.4233 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 : 0.192 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 25 ASN ** N 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.089743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.062981 restraints weight = 38135.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064955 restraints weight = 18855.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.066213 restraints weight = 12817.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.066964 restraints weight = 10403.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067385 restraints weight = 9296.952| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12615 Z= 0.211 Angle : 0.951 9.955 18180 Z= 0.522 Chirality : 0.061 0.310 2063 Planarity : 0.006 0.041 1375 Dihedral : 31.734 169.686 3850 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.08 % Favored : 96.79 % Rotamer: Outliers : 4.83 % Allowed : 17.98 % Favored : 77.19 % 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 : -0.79 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 67 TYR 0.030 0.003 TYR R 88 PHE 0.016 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 0.00383 / 0.21 (12615) covalent geometry : angle 0.95051 / 0.52 (18180) hydrogen bonds : bond 0.06094 / 6.82 ( 751) hydrogen bonds : angle 3.78610 / 4.95 ( 1898) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.209 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: 0.8790 (tt0) cc_final: 0.8305 (tt0) REVERT: M 73 GLU cc_start: 0.8813 (tp30) cc_final: 0.8404 (tp30) REVERT: M 97 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7886 (mt-10) REVERT: M 108 ASN cc_start: 0.8870 (t0) cc_final: 0.8638 (t0) REVERT: M 113 HIS cc_start: 0.8775 (t70) cc_final: 0.8504 (t-90) REVERT: M 120 MET cc_start: 0.8819 (mtp) cc_final: 0.8272 (mtt) REVERT: N 25 ASN cc_start: 0.8809 (m-40) cc_final: 0.8574 (m110) REVERT: N 73 THR cc_start: 0.9294 (m) cc_final: 0.8868 (t) REVERT: N 80 THR cc_start: 0.8865 (m) cc_final: 0.8423 (p) REVERT: N 84 MET cc_start: 0.8770 (mmm) cc_final: 0.8369 (mmm) REVERT: O 24 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8652 (mm110) REVERT: O 91 GLU cc_start: 0.8914 (pm20) cc_final: 0.8566 (tm-30) REVERT: P 46 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8937 (tptp) REVERT: P 59 MET cc_start: 0.9113 (tpp) cc_final: 0.8486 (tpp) REVERT: P 82 HIS cc_start: 0.8835 (t-170) cc_final: 0.8550 (t-170) REVERT: P 105 GLU cc_start: 0.7827 (tp30) cc_final: 0.7560 (tp30) REVERT: Q 41 TYR cc_start: 0.5149 (OUTLIER) cc_final: 0.4575 (t80) REVERT: Q 56 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8869 (ttmm) REVERT: Q 58 THR cc_start: 0.8756 (p) cc_final: 0.8490 (t) REVERT: Q 60 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.7989 (mt) REVERT: Q 68 GLN cc_start: 0.8747 (tp-100) cc_final: 0.8351 (tp-100) REVERT: Q 73 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7926 (mt-10) REVERT: Q 93 GLN cc_start: 0.8950 (tt0) cc_final: 0.7922 (tt0) REVERT: Q 97 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7512 (mt-10) REVERT: Q 126 LEU cc_start: 0.9353 (tp) cc_final: 0.9036 (tt) REVERT: R 31 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8879 (tttm) REVERT: R 47 SER cc_start: 0.9132 (p) cc_final: 0.8932 (p) REVERT: R 52 GLU cc_start: 0.8504 (tp30) cc_final: 0.8226 (tp30) REVERT: R 84 MET cc_start: 0.9231 (mmm) cc_final: 0.8626 (mmm) REVERT: R 88 TYR cc_start: 0.9182 (m-80) cc_final: 0.8600 (m-80) REVERT: S 24 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7881 (mp10) REVERT: S 57 TYR cc_start: 0.8934 (t80) cc_final: 0.8724 (t80) REVERT: S 61 GLU cc_start: 0.8902 (tp30) cc_final: 0.8536 (tp30) REVERT: S 90 ASP cc_start: 0.8460 (t0) cc_final: 0.8049 (t0) REVERT: S 101 THR cc_start: 0.8925 (m) cc_final: 0.8517 (p) REVERT: T 35 GLU cc_start: 0.8817 (tp30) cc_final: 0.8594 (tt0) REVERT: T 105 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7562 (tp30) REVERT: H 153 LEU cc_start: 0.8519 (mt) cc_final: 0.7710 (pp) REVERT: H 176 LEU cc_start: 0.8374 (mt) cc_final: 0.8173 (mp) outliers start: 32 outliers final: 16 residues processed: 288 average time/residue: 0.0923 time to fit residues: 36.5291 Evaluate side-chains 260 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 30 THR Chi-restraints excluded: chain N residue 62 LEU Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain O residue 59 THR 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 34 ILE 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: 9.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 93 GLN P 49 HIS P 95 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.088807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062812 restraints weight = 38139.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.064755 restraints weight = 18349.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.066027 restraints weight = 12266.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066793 restraints weight = 9839.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.067219 restraints weight = 8733.620| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12615 Z= 0.188 Angle : 0.809 9.116 18180 Z= 0.458 Chirality : 0.053 0.270 2063 Planarity : 0.005 0.049 1375 Dihedral : 31.528 175.170 3850 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 4.98 % Allowed : 21.00 % 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: 1.11 (0.29), residues: 778 helix: 1.32 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.77 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 134 TYR 0.019 0.002 TYR N 98 PHE 0.018 0.002 PHE M 67 TRP 0.008 0.002 TRP H 152 HIS 0.010 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (12615) covalent geometry : angle 0.80854 / 0.46 (18180) hydrogen bonds : bond 0.05350 / 6.06 ( 751) hydrogen bonds : angle 3.47873 / 4.50 ( 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 279 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 246 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8792 (tt0) cc_final: 0.8348 (tt0) REVERT: M 73 GLU cc_start: 0.8609 (tp30) cc_final: 0.8356 (tp30) REVERT: M 120 MET cc_start: 0.8767 (mtp) cc_final: 0.8041 (mtt) REVERT: M 125 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8651 (mm-40) REVERT: N 25 ASN cc_start: 0.8775 (m-40) cc_final: 0.8563 (m110) REVERT: N 63 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8187 (mt-10) REVERT: N 80 THR cc_start: 0.8870 (m) cc_final: 0.8661 (t) REVERT: N 84 MET cc_start: 0.8685 (mmm) cc_final: 0.8343 (mmm) REVERT: O 56 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8807 (tm-30) REVERT: O 91 GLU cc_start: 0.8906 (pm20) cc_final: 0.8627 (tm-30) REVERT: P 46 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8880 (tptp) REVERT: P 59 MET cc_start: 0.9183 (tpp) cc_final: 0.8796 (tpp) REVERT: P 76 GLU cc_start: 0.8425 (tp30) cc_final: 0.8092 (tp30) REVERT: P 105 GLU cc_start: 0.7857 (tp30) cc_final: 0.6432 (tp30) REVERT: P 108 LYS cc_start: 0.9062 (mttp) cc_final: 0.8483 (mtmm) REVERT: P 120 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8723 (ttpp) REVERT: Q 41 TYR cc_start: 0.5051 (OUTLIER) cc_final: 0.4321 (t80) REVERT: Q 56 LYS cc_start: 0.9072 (ttpt) cc_final: 0.8719 (ttmm) REVERT: Q 57 SER cc_start: 0.8310 (t) cc_final: 0.7769 (p) REVERT: Q 59 GLU cc_start: 0.8046 (pm20) cc_final: 0.7842 (pm20) REVERT: Q 60 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8128 (mt) REVERT: Q 68 GLN cc_start: 0.8701 (tp-100) cc_final: 0.8379 (tp-100) REVERT: Q 73 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7880 (mt-10) REVERT: Q 93 GLN cc_start: 0.8920 (tt0) cc_final: 0.8516 (tt0) REVERT: Q 97 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7434 (mt-10) REVERT: R 31 LYS cc_start: 0.9222 (ttpp) cc_final: 0.8877 (tttm) REVERT: R 84 MET cc_start: 0.9109 (mmm) cc_final: 0.8613 (mmm) REVERT: R 85 ASP cc_start: 0.8747 (m-30) cc_final: 0.8318 (m-30) REVERT: R 88 TYR cc_start: 0.9241 (m-80) cc_final: 0.8664 (m-80) REVERT: S 56 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8404 (tm-30) REVERT: S 90 ASP cc_start: 0.8391 (t0) cc_final: 0.7915 (t0) REVERT: S 94 ASN cc_start: 0.9066 (t0) cc_final: 0.8745 (t0) REVERT: S 101 THR cc_start: 0.9057 (m) cc_final: 0.8684 (p) REVERT: T 105 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7843 (tp30) outliers start: 33 outliers final: 24 residues processed: 263 average time/residue: 0.0970 time to fit residues: 35.2188 Evaluate side-chains 245 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 218 time to evaluate : 0.290 ------------------------------------------------------------------------------- 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 M residue 125 GLN Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 30 THR 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 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 R residue 34 ILE Chi-restraints excluded: chain R residue 79 LYS 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 61 ILE 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: 1.9990 chunk 54 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 164 ASN H 185 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.059944 restraints weight = 37816.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.061748 restraints weight = 18692.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.062930 restraints weight = 12640.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.063630 restraints weight = 10193.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063990 restraints weight = 9064.434| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 12615 Z= 0.196 Angle : 0.775 9.034 18180 Z= 0.438 Chirality : 0.050 0.269 2063 Planarity : 0.005 0.039 1375 Dihedral : 31.525 174.774 3850 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 5.29 % Allowed : 22.96 % Favored : 71.75 % 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: 1.36 (0.30), residues: 778 helix: 1.54 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.80 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 92 TYR 0.033 0.002 TYR S 50 PHE 0.017 0.002 PHE M 67 TRP 0.004 0.001 TRP H 152 HIS 0.010 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.20 (12615) covalent geometry : angle 0.77531 / 0.44 (18180) hydrogen bonds : bond 0.05034 / 5.71 ( 751) hydrogen bonds : angle 3.37457 / 4.33 ( 1898) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.301 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: 0.8869 (tt0) cc_final: 0.8402 (tt0) REVERT: M 73 GLU cc_start: 0.8517 (tp30) cc_final: 0.7566 (tt0) REVERT: M 120 MET cc_start: 0.8677 (mtp) cc_final: 0.8091 (mtt) REVERT: N 63 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8186 (mt-10) REVERT: N 77 LYS cc_start: 0.9557 (mttp) cc_final: 0.9329 (mptt) REVERT: N 80 THR cc_start: 0.8840 (m) cc_final: 0.8601 (t) REVERT: N 84 MET cc_start: 0.8730 (mmm) cc_final: 0.8395 (mmm) REVERT: O 91 GLU cc_start: 0.8946 (pm20) cc_final: 0.8639 (tm-30) REVERT: O 92 GLU cc_start: 0.8298 (mm-30) cc_final: 0.8082 (tp30) REVERT: P 59 MET cc_start: 0.9232 (tpp) cc_final: 0.9028 (tpp) REVERT: P 76 GLU cc_start: 0.8557 (tp30) cc_final: 0.8215 (tp30) REVERT: P 105 GLU cc_start: 0.7940 (tp30) cc_final: 0.6784 (tp30) REVERT: P 108 LYS cc_start: 0.9052 (mttp) cc_final: 0.8614 (mtmt) REVERT: P 120 LYS cc_start: 0.9012 (ttmm) cc_final: 0.8738 (ttpp) REVERT: Q 41 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.4327 (t80) REVERT: Q 56 LYS cc_start: 0.9131 (ttpt) cc_final: 0.8803 (ttmm) REVERT: Q 60 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8498 (mt) REVERT: Q 68 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8428 (tp-100) REVERT: Q 97 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7582 (mt-10) REVERT: Q 120 MET cc_start: 0.8957 (mmm) cc_final: 0.8647 (mmm) REVERT: Q 134 ARG cc_start: 0.7955 (ttt-90) cc_final: 0.7520 (ttp80) REVERT: R 84 MET cc_start: 0.9114 (mmm) cc_final: 0.8643 (mmm) REVERT: R 85 ASP cc_start: 0.8776 (m-30) cc_final: 0.8368 (m-30) REVERT: R 88 TYR cc_start: 0.9239 (m-10) cc_final: 0.8696 (m-80) REVERT: S 56 GLU cc_start: 0.8718 (tm-30) cc_final: 0.8516 (tm-30) REVERT: S 61 GLU cc_start: 0.9047 (tp30) cc_final: 0.8815 (tp30) REVERT: S 90 ASP cc_start: 0.8433 (t0) cc_final: 0.7893 (t0) REVERT: S 94 ASN cc_start: 0.9104 (t0) cc_final: 0.8870 (t0) REVERT: S 101 THR cc_start: 0.9060 (m) cc_final: 0.8714 (p) REVERT: T 105 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7766 (tp30) REVERT: H 153 LEU cc_start: 0.8524 (mt) cc_final: 0.7777 (pp) outliers start: 35 outliers final: 24 residues processed: 242 average time/residue: 0.1057 time to fit residues: 35.1352 Evaluate side-chains 239 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.288 ------------------------------------------------------------------------------- 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 30 THR 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 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 107 THR Chi-restraints excluded: chain Q residue 109 LEU Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 79 LYS 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 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: 0.5980 chunk 4 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 40.0000 chunk 52 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 25 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 185 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060647 restraints weight = 36452.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.062474 restraints weight = 17755.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.063680 restraints weight = 11947.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064398 restraints weight = 9596.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.064801 restraints weight = 8522.330| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12615 Z= 0.172 Angle : 0.737 9.028 18180 Z= 0.422 Chirality : 0.048 0.264 2063 Planarity : 0.005 0.064 1375 Dihedral : 31.392 175.222 3850 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % Rotamer: Outliers : 4.68 % Allowed : 22.96 % Favored : 72.36 % 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: 1.54 (0.30), residues: 778 helix: 1.73 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Q 131 TYR 0.026 0.002 TYR N 98 PHE 0.017 0.002 PHE M 67 TRP 0.002 0.001 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (12615) covalent geometry : angle 0.73748 / 0.42 (18180) hydrogen bonds : bond 0.04620 / 5.20 ( 751) hydrogen bonds : angle 3.21410 / 4.12 ( 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 265 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8833 (tt0) cc_final: 0.8377 (tt0) REVERT: M 60 LEU cc_start: 0.9219 (mm) cc_final: 0.9012 (mt) REVERT: M 73 GLU cc_start: 0.8499 (tp30) cc_final: 0.7875 (tt0) REVERT: M 118 THR cc_start: 0.9403 (m) cc_final: 0.9096 (p) REVERT: M 120 MET cc_start: 0.8655 (mtp) cc_final: 0.8066 (mtt) REVERT: N 44 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8388 (mtpp) REVERT: N 63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8225 (mt-10) REVERT: N 80 THR cc_start: 0.8792 (m) cc_final: 0.8513 (t) REVERT: N 84 MET cc_start: 0.8720 (mmm) cc_final: 0.8397 (mmm) REVERT: O 56 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8871 (tm-30) REVERT: O 91 GLU cc_start: 0.8911 (pm20) cc_final: 0.8651 (tm-30) REVERT: P 46 LYS cc_start: 0.9268 (mmmt) cc_final: 0.8972 (tptp) REVERT: P 59 MET cc_start: 0.9238 (tpp) cc_final: 0.8859 (tpp) REVERT: P 105 GLU cc_start: 0.7902 (tp30) cc_final: 0.7101 (tp30) REVERT: P 108 LYS cc_start: 0.9055 (mttp) cc_final: 0.8618 (mtmt) REVERT: P 120 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8695 (ttpp) REVERT: Q 41 TYR cc_start: 0.5129 (OUTLIER) cc_final: 0.4306 (t80) REVERT: Q 68 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8316 (tp-100) REVERT: Q 73 GLU cc_start: 0.8736 (tt0) cc_final: 0.8378 (tt0) REVERT: R 84 MET cc_start: 0.9030 (mmm) cc_final: 0.8809 (tpp) REVERT: R 85 ASP cc_start: 0.8735 (m-30) cc_final: 0.8404 (m-30) REVERT: R 88 TYR cc_start: 0.9191 (m-10) cc_final: 0.8889 (m-80) REVERT: S 56 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8480 (tm-30) REVERT: S 76 THR cc_start: 0.9098 (p) cc_final: 0.8875 (p) REVERT: S 90 ASP cc_start: 0.8487 (t0) cc_final: 0.7935 (t0) REVERT: S 94 ASN cc_start: 0.9070 (t0) cc_final: 0.8843 (t0) REVERT: S 101 THR cc_start: 0.9037 (m) cc_final: 0.8669 (p) REVERT: T 34 LYS cc_start: 0.8707 (mppt) cc_final: 0.8474 (mttt) REVERT: T 105 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7731 (tp30) REVERT: H 150 GLN cc_start: 0.6223 (tp-100) cc_final: 0.5801 (tm-30) REVERT: H 153 LEU cc_start: 0.8596 (mt) cc_final: 0.7884 (pp) outliers start: 31 outliers final: 25 residues processed: 251 average time/residue: 0.1034 time to fit residues: 35.9706 Evaluate side-chains 247 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 30 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 58 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 80 LEU Chi-restraints excluded: chain P residue 92 ARG Chi-restraints excluded: chain P residue 100 LEU Chi-restraints excluded: chain Q residue 41 TYR 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 30 THR Chi-restraints excluded: chain R residue 79 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 74 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 40.0000 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 60 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN M 113 HIS ** Q 93 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.087268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.060971 restraints weight = 36677.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.062805 restraints weight = 17798.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063998 restraints weight = 11958.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.064723 restraints weight = 9612.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.065137 restraints weight = 8529.835| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12615 Z= 0.162 Angle : 0.719 9.051 18180 Z= 0.411 Chirality : 0.047 0.262 2063 Planarity : 0.004 0.035 1375 Dihedral : 31.241 175.593 3850 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 4.23 % Allowed : 25.83 % Favored : 69.94 % 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: 1.61 (0.30), residues: 778 helix: 1.81 (0.21), residues: 569 sheet: None (None), residues: 0 loop : -1.01 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 69 TYR 0.029 0.002 TYR N 98 PHE 0.015 0.001 PHE M 67 TRP 0.002 0.001 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.16 (12615) covalent geometry : angle 0.71922 / 0.41 (18180) hydrogen bonds : bond 0.04451 / 5.01 ( 751) hydrogen bonds : angle 3.12205 / 3.98 ( 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 256 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8839 (tt0) cc_final: 0.8390 (tt0) REVERT: M 60 LEU cc_start: 0.9179 (mm) cc_final: 0.8959 (mt) REVERT: M 93 GLN cc_start: 0.9099 (tt0) cc_final: 0.8774 (tt0) REVERT: M 118 THR cc_start: 0.9391 (m) cc_final: 0.9111 (p) REVERT: M 120 MET cc_start: 0.8657 (mtp) cc_final: 0.8077 (mtt) REVERT: N 63 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8211 (mt-10) REVERT: N 80 THR cc_start: 0.8810 (m) cc_final: 0.8539 (t) REVERT: N 84 MET cc_start: 0.8669 (mmm) cc_final: 0.8332 (mmm) REVERT: O 56 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8826 (tm-30) REVERT: O 91 GLU cc_start: 0.8916 (pm20) cc_final: 0.8668 (tm-30) REVERT: P 59 MET cc_start: 0.9209 (tpp) cc_final: 0.8930 (tpp) REVERT: P 76 GLU cc_start: 0.8529 (tp30) cc_final: 0.8262 (tp30) REVERT: P 79 ARG cc_start: 0.8686 (mtm-85) cc_final: 0.8052 (mtm-85) REVERT: P 105 GLU cc_start: 0.7834 (tp30) cc_final: 0.6773 (tp30) REVERT: P 108 LYS cc_start: 0.9042 (mttp) cc_final: 0.8601 (mtmt) REVERT: P 120 LYS cc_start: 0.8904 (ttmm) cc_final: 0.8696 (ttpp) REVERT: Q 41 TYR cc_start: 0.5162 (OUTLIER) cc_final: 0.4302 (t80) REVERT: Q 68 GLN cc_start: 0.8808 (tp-100) cc_final: 0.8297 (tp-100) REVERT: R 31 LYS cc_start: 0.9293 (ttpp) cc_final: 0.8908 (tttm) REVERT: R 85 ASP cc_start: 0.8727 (m-30) cc_final: 0.8377 (m-30) REVERT: R 88 TYR cc_start: 0.9168 (m-10) cc_final: 0.8916 (m-80) REVERT: S 76 THR cc_start: 0.9085 (p) cc_final: 0.8865 (p) REVERT: S 90 ASP cc_start: 0.8407 (t0) cc_final: 0.7843 (t0) REVERT: S 101 THR cc_start: 0.9014 (m) cc_final: 0.8677 (p) REVERT: T 105 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7729 (tp30) REVERT: H 150 GLN cc_start: 0.6284 (tp-100) cc_final: 0.6016 (tm-30) REVERT: H 153 LEU cc_start: 0.8656 (mt) cc_final: 0.7969 (pp) outliers start: 28 outliers final: 24 residues processed: 241 average time/residue: 0.1081 time to fit residues: 35.7504 Evaluate side-chains 244 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 219 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 N residue 30 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 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 46 VAL 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 R residue 34 ILE Chi-restraints excluded: chain R residue 79 LYS 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: 0.8980 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 92 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 93 GLN R 25 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.059239 restraints weight = 36759.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.061030 restraints weight = 17356.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.062201 restraints weight = 11520.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.062876 restraints weight = 9214.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.063233 restraints weight = 8172.773| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12615 Z= 0.159 Angle : 0.709 9.044 18180 Z= 0.406 Chirality : 0.045 0.261 2063 Planarity : 0.004 0.040 1375 Dihedral : 31.149 175.730 3850 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 4.38 % Allowed : 25.98 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 778 helix: 1.87 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 174 TYR 0.017 0.002 TYR S 50 PHE 0.015 0.001 PHE M 67 TRP 0.002 0.001 TRP H 152 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (12615) covalent geometry : angle 0.70932 / 0.41 (18180) hydrogen bonds : bond 0.04308 / 4.84 ( 751) hydrogen bonds : angle 3.08082 / 3.94 ( 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 250 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8894 (tt0) cc_final: 0.8664 (tt0) REVERT: M 60 LEU cc_start: 0.9238 (mm) cc_final: 0.8865 (mt) REVERT: M 93 GLN cc_start: 0.9114 (tt0) cc_final: 0.8791 (tt0) REVERT: M 120 MET cc_start: 0.8611 (mtp) cc_final: 0.7993 (mtt) REVERT: N 25 ASN cc_start: 0.8714 (m-40) cc_final: 0.7717 (t0) REVERT: N 63 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8195 (mt-10) REVERT: N 80 THR cc_start: 0.8747 (m) cc_final: 0.8479 (t) REVERT: N 84 MET cc_start: 0.8727 (mmm) cc_final: 0.8379 (mmm) REVERT: O 91 GLU cc_start: 0.8996 (pm20) cc_final: 0.8717 (tm-30) REVERT: P 59 MET cc_start: 0.9193 (tpp) cc_final: 0.8685 (tpp) REVERT: P 79 ARG cc_start: 0.8664 (mtm-85) cc_final: 0.8061 (mtm-85) REVERT: P 105 GLU cc_start: 0.7667 (tp30) cc_final: 0.7127 (tp30) REVERT: P 108 LYS cc_start: 0.9030 (mttp) cc_final: 0.8581 (mtmt) REVERT: P 120 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8693 (ttpp) REVERT: Q 41 TYR cc_start: 0.5176 (OUTLIER) cc_final: 0.4339 (t80) REVERT: Q 68 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8449 (tp-100) REVERT: Q 94 GLU cc_start: 0.8406 (tp30) cc_final: 0.6675 (tp30) REVERT: R 31 LYS cc_start: 0.9236 (ttpp) cc_final: 0.8818 (tttm) REVERT: R 84 MET cc_start: 0.9027 (tpp) cc_final: 0.8655 (tpp) REVERT: R 85 ASP cc_start: 0.8816 (m-30) cc_final: 0.8453 (m-30) REVERT: R 88 TYR cc_start: 0.9076 (m-10) cc_final: 0.8688 (m-80) REVERT: S 76 THR cc_start: 0.9150 (p) cc_final: 0.8940 (p) REVERT: S 90 ASP cc_start: 0.8372 (t0) cc_final: 0.7749 (t0) REVERT: S 101 THR cc_start: 0.9024 (m) cc_final: 0.8632 (p) REVERT: T 105 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7756 (tp30) REVERT: H 153 LEU cc_start: 0.8670 (mt) cc_final: 0.8039 (pp) outliers start: 29 outliers final: 22 residues processed: 232 average time/residue: 0.1016 time to fit residues: 33.0460 Evaluate side-chains 238 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 215 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 30 THR 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 46 VAL 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 R residue 79 LYS 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 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN M 113 HIS ** N 25 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 25 ASN ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.084934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058935 restraints weight = 36739.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.060719 restraints weight = 17363.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.061874 restraints weight = 11532.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.062546 restraints weight = 9221.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.062928 restraints weight = 8181.041| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12615 Z= 0.180 Angle : 0.723 9.005 18180 Z= 0.414 Chirality : 0.046 0.262 2063 Planarity : 0.004 0.041 1375 Dihedral : 31.109 175.601 3850 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.73 % Favored : 96.14 % Rotamer: Outliers : 4.23 % Allowed : 26.44 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.69 (0.30), residues: 778 helix: 1.85 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.91 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 52 TYR 0.019 0.002 TYR S 50 PHE 0.013 0.001 PHE M 67 TRP 0.025 0.006 TRP H 152 HIS 0.009 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (12615) covalent geometry : angle 0.72298 / 0.41 (18180) hydrogen bonds : bond 0.04432 / 5.01 ( 751) hydrogen bonds : angle 3.14431 / 3.99 ( 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 246 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.8984 (tt0) cc_final: 0.8624 (tt0) REVERT: M 60 LEU cc_start: 0.9249 (mm) cc_final: 0.8796 (mt) REVERT: M 93 GLN cc_start: 0.9098 (tt0) cc_final: 0.8734 (tt0) REVERT: M 120 MET cc_start: 0.8656 (mtp) cc_final: 0.8009 (mtt) REVERT: N 25 ASN cc_start: 0.8646 (m-40) cc_final: 0.7735 (t0) REVERT: N 63 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8203 (mt-10) REVERT: N 80 THR cc_start: 0.8754 (m) cc_final: 0.8476 (t) REVERT: N 84 MET cc_start: 0.8738 (mmm) cc_final: 0.8340 (mmm) REVERT: O 56 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8860 (tm-30) REVERT: O 73 ASN cc_start: 0.9506 (t0) cc_final: 0.9293 (t0) REVERT: O 91 GLU cc_start: 0.9030 (pm20) cc_final: 0.8729 (tm-30) REVERT: P 59 MET cc_start: 0.9201 (tpp) cc_final: 0.8677 (tpp) REVERT: P 79 ARG cc_start: 0.8673 (mtm-85) cc_final: 0.8169 (mtm-85) REVERT: P 105 GLU cc_start: 0.7861 (tp30) cc_final: 0.6433 (tp30) REVERT: P 108 LYS cc_start: 0.9031 (mttp) cc_final: 0.8416 (mtmm) REVERT: P 120 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8708 (ttpp) REVERT: Q 41 TYR cc_start: 0.5210 (OUTLIER) cc_final: 0.4440 (t80) REVERT: Q 68 GLN cc_start: 0.8811 (tp-100) cc_final: 0.8425 (tp-100) REVERT: Q 94 GLU cc_start: 0.8581 (tp30) cc_final: 0.8081 (tp30) REVERT: Q 97 GLU cc_start: 0.7778 (pp20) cc_final: 0.7565 (pp20) REVERT: R 31 LYS cc_start: 0.9228 (ttpp) cc_final: 0.8782 (tttm) REVERT: R 84 MET cc_start: 0.9068 (tpp) cc_final: 0.8567 (tpp) REVERT: R 85 ASP cc_start: 0.8831 (m-30) cc_final: 0.8478 (m-30) REVERT: R 88 TYR cc_start: 0.9111 (m-10) cc_final: 0.8637 (m-80) REVERT: S 76 THR cc_start: 0.9149 (p) cc_final: 0.8942 (p) REVERT: S 101 THR cc_start: 0.8974 (m) cc_final: 0.8599 (p) REVERT: T 105 GLU cc_start: 0.8275 (mm-30) cc_final: 0.7551 (tp30) REVERT: T 108 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8540 (mtmm) outliers start: 28 outliers final: 24 residues processed: 228 average time/residue: 0.0989 time to fit residues: 31.7691 Evaluate side-chains 239 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 214 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 30 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 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 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 R residue 79 LYS 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 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 44 optimal weight: 0.0970 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN ** N 25 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.085578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.059706 restraints weight = 36470.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.061476 restraints weight = 17099.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.062641 restraints weight = 11344.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.063323 restraints weight = 9069.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.063664 restraints weight = 8039.385| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12615 Z= 0.159 Angle : 0.713 9.039 18180 Z= 0.409 Chirality : 0.045 0.262 2063 Planarity : 0.004 0.048 1375 Dihedral : 31.054 175.874 3850 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 4.98 % Allowed : 26.28 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.30), residues: 778 helix: 1.80 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.89 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 151 TYR 0.037 0.002 TYR P 83 PHE 0.013 0.001 PHE M 67 TRP 0.022 0.005 TRP H 152 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (12615) covalent geometry : angle 0.71281 / 0.41 (18180) hydrogen bonds : bond 0.04245 / 4.77 ( 751) hydrogen bonds : angle 3.09832 / 3.95 ( 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 258 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9013 (tt0) cc_final: 0.8605 (tt0) REVERT: M 60 LEU cc_start: 0.9204 (mm) cc_final: 0.8734 (mt) REVERT: M 93 GLN cc_start: 0.9090 (tt0) cc_final: 0.8775 (tt0) REVERT: M 120 MET cc_start: 0.8642 (mtp) cc_final: 0.7955 (mtt) REVERT: N 25 ASN cc_start: 0.8602 (m-40) cc_final: 0.7857 (t0) REVERT: N 63 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8199 (mt-10) REVERT: N 80 THR cc_start: 0.8723 (m) cc_final: 0.8413 (t) REVERT: N 98 TYR cc_start: 0.9293 (m-10) cc_final: 0.9061 (m-80) REVERT: O 56 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8865 (tm-30) REVERT: O 91 GLU cc_start: 0.9043 (pm20) cc_final: 0.8727 (tm-30) REVERT: P 59 MET cc_start: 0.9185 (tpp) cc_final: 0.8657 (tpp) REVERT: P 79 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8134 (mtm-85) REVERT: P 105 GLU cc_start: 0.7721 (tp30) cc_final: 0.6999 (tp30) REVERT: P 108 LYS cc_start: 0.9037 (mttp) cc_final: 0.8585 (mtmt) REVERT: Q 41 TYR cc_start: 0.5107 (OUTLIER) cc_final: 0.4266 (t80) REVERT: Q 68 GLN cc_start: 0.8782 (tp-100) cc_final: 0.8374 (tp-100) REVERT: Q 90 MET cc_start: 0.8438 (tpp) cc_final: 0.7808 (tpp) REVERT: Q 94 GLU cc_start: 0.8631 (tp30) cc_final: 0.8027 (tp30) REVERT: Q 123 ASP cc_start: 0.9081 (m-30) cc_final: 0.8855 (m-30) REVERT: R 31 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8785 (tttm) REVERT: R 84 MET cc_start: 0.9052 (tpp) cc_final: 0.8587 (tpp) REVERT: R 85 ASP cc_start: 0.8818 (m-30) cc_final: 0.8476 (m-30) REVERT: R 88 TYR cc_start: 0.9080 (m-10) cc_final: 0.8611 (m-80) REVERT: S 76 THR cc_start: 0.9145 (p) cc_final: 0.8944 (p) REVERT: S 90 ASP cc_start: 0.8235 (t0) cc_final: 0.7814 (t0) REVERT: S 94 ASN cc_start: 0.9116 (t0) cc_final: 0.8565 (m110) REVERT: T 105 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7526 (tp30) REVERT: T 108 LYS cc_start: 0.9119 (mtmm) cc_final: 0.8522 (mtmm) REVERT: H 152 TRP cc_start: 0.7574 (t60) cc_final: 0.7125 (t60) outliers start: 33 outliers final: 27 residues processed: 238 average time/residue: 0.1147 time to fit residues: 38.2034 Evaluate side-chains 244 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 216 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain N residue 30 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 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 61 LEU Chi-restraints excluded: chain Q residue 93 GLN 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 R residue 60 VAL Chi-restraints excluded: chain R residue 79 LYS 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 94 ILE Chi-restraints excluded: chain T residue 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 67 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 43 optimal weight: 0.0040 chunk 98 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN N 25 ASN O 73 ASN 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.085287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059447 restraints weight = 37062.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.061212 restraints weight = 17381.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.062379 restraints weight = 11491.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.063042 restraints weight = 9170.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063438 restraints weight = 8132.950| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 12615 Z= 0.171 Angle : 0.723 9.009 18180 Z= 0.414 Chirality : 0.045 0.263 2063 Planarity : 0.004 0.049 1375 Dihedral : 31.027 176.208 3850 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.86 % Favored : 96.02 % Rotamer: Outliers : 4.98 % Allowed : 27.49 % 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: 1.54 (0.30), residues: 778 helix: 1.77 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 151 TYR 0.026 0.002 TYR P 83 PHE 0.010 0.001 PHE M 67 TRP 0.023 0.006 TRP H 152 HIS 0.009 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (12615) covalent geometry : angle 0.72323 / 0.41 (18180) hydrogen bonds : bond 0.04320 / 4.88 ( 751) hydrogen bonds : angle 3.16050 / 4.02 ( 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 253 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 220 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 50 GLU cc_start: 0.9021 (tt0) cc_final: 0.8214 (tm-30) REVERT: M 60 LEU cc_start: 0.9202 (mm) cc_final: 0.8683 (mt) REVERT: M 120 MET cc_start: 0.8633 (mtp) cc_final: 0.7981 (mtt) REVERT: N 25 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.7851 (t0) REVERT: N 63 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8206 (mt-10) REVERT: N 80 THR cc_start: 0.8626 (m) cc_final: 0.8345 (t) REVERT: N 98 TYR cc_start: 0.9308 (m-10) cc_final: 0.9052 (m-80) REVERT: O 56 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8887 (tm-30) REVERT: O 91 GLU cc_start: 0.9037 (pm20) cc_final: 0.8722 (tm-30) REVERT: P 59 MET cc_start: 0.9186 (tpp) cc_final: 0.8953 (tpp) REVERT: P 79 ARG cc_start: 0.8549 (mtm-85) cc_final: 0.8309 (mtm-85) REVERT: P 93 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8139 (mm-30) REVERT: P 105 GLU cc_start: 0.7736 (tp30) cc_final: 0.6999 (tp30) REVERT: P 108 LYS cc_start: 0.9040 (mttp) cc_final: 0.8584 (mtmt) REVERT: Q 41 TYR cc_start: 0.5100 (OUTLIER) cc_final: 0.4382 (t80) REVERT: Q 68 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8425 (tp-100) REVERT: Q 90 MET cc_start: 0.8415 (tpp) cc_final: 0.7824 (tpp) REVERT: Q 93 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.7585 (tm-30) REVERT: Q 123 ASP cc_start: 0.9093 (m-30) cc_final: 0.8864 (m-30) REVERT: R 31 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8790 (tttm) REVERT: R 84 MET cc_start: 0.9075 (tpp) cc_final: 0.8644 (tpp) REVERT: R 85 ASP cc_start: 0.8808 (m-30) cc_final: 0.8472 (m-30) REVERT: R 88 TYR cc_start: 0.9089 (m-10) cc_final: 0.8652 (m-80) REVERT: S 75 LYS cc_start: 0.8750 (mppt) cc_final: 0.8501 (mppt) REVERT: S 76 THR cc_start: 0.9179 (p) cc_final: 0.8960 (p) REVERT: S 90 ASP cc_start: 0.8273 (t0) cc_final: 0.7849 (t0) REVERT: S 94 ASN cc_start: 0.9126 (t0) cc_final: 0.8586 (m110) REVERT: T 105 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7558 (tp30) REVERT: T 108 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8507 (mtmm) REVERT: H 151 ARG cc_start: 0.6062 (mmm160) cc_final: 0.5811 (mmm160) REVERT: H 152 TRP cc_start: 0.7593 (t60) cc_final: 0.7212 (t60) outliers start: 33 outliers final: 27 residues processed: 233 average time/residue: 0.1020 time to fit residues: 33.5822 Evaluate side-chains 246 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 46 VAL Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 130 ILE Chi-restraints excluded: chain N residue 25 ASN Chi-restraints excluded: chain N residue 30 THR 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 61 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 93 GLN 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 R residue 60 VAL Chi-restraints excluded: chain R residue 79 LYS 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 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 75 optimal weight: 0.9990 chunk 4 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 ASN ** N 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 73 ASN Q 93 GLN ** Q 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 24 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.085697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.059774 restraints weight = 36862.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.061563 restraints weight = 17297.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.062736 restraints weight = 11454.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.063416 restraints weight = 9142.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.063768 restraints weight = 8102.183| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12615 Z= 0.163 Angle : 0.727 9.022 18180 Z= 0.415 Chirality : 0.045 0.262 2063 Planarity : 0.005 0.049 1375 Dihedral : 30.996 176.517 3850 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.11 % Favored : 95.76 % Rotamer: Outliers : 4.38 % Allowed : 28.70 % Favored : 66.92 % 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 (0.30), residues: 778 helix: 1.72 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -0.98 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 92 TYR 0.036 0.003 TYR P 83 PHE 0.012 0.001 PHE M 67 TRP 0.022 0.005 TRP H 152 HIS 0.008 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.16 (12615) covalent geometry : angle 0.72666 / 0.42 (18180) hydrogen bonds : bond 0.04256 / 4.82 ( 751) hydrogen bonds : angle 3.17441 / 4.05 ( 1898) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1796.03 seconds wall clock time: 31 minutes 37.64 seconds (1897.64 seconds total)