Starting phenix.real_space_refine on Wed Feb 4 18:20:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gfm_51313/02_2026/9gfm_51313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gfm_51313/02_2026/9gfm_51313.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/9gfm_51313/02_2026/9gfm_51313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gfm_51313/02_2026/9gfm_51313.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gfm_51313/02_2026/9gfm_51313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gfm_51313/02_2026/9gfm_51313.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= 0.046 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 278 5.49 5 S 14 5.16 5 C 6736 2.51 5 N 2277 2.21 5 O 2820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12125 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'TRANS': 49} Chain: "K" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2868 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "L" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 2831 Classifications: {'DNA': 139} Link IDs: {'rna3p': 138} Chain: "M" Number of atoms: 756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 756 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "N" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "O" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "P" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "Q" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} 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: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 854 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "T" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Time building chain proxies: 2.95, per 1000 atoms: 0.24 Number of scatterers: 12125 At special positions: 0 Unit cell: (116.439, 134.272, 112.243, 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 278 15.00 O 2820 8.00 N 2277 7.00 C 6736 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: 0.94 Conformation dependent library (CDL) restraints added in 477.7 milliseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 10 sheets defined 72.3% alpha, 3.0% beta 135 base pairs and 223 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'H' and resid 141 through 159 removed outlier: 4.038A pdb=" N GLU H 145 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU H 148 " --> pdb=" O GLN H 144 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU H 149 " --> pdb=" O GLU H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 176 Processing helix chain 'H' and resid 177 through 188 Processing helix chain 'M' and resid 44 through 57 removed outlier: 4.257A pdb=" N LEU M 48 " --> pdb=" O GLY M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 76 Processing helix chain 'M' and resid 85 through 114 removed outlier: 3.554A pdb=" N VAL M 89 " --> pdb=" O GLN M 85 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP M 106 " --> pdb=" O GLY M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'N' and resid 24 through 29 removed outlier: 3.884A pdb=" N GLN N 27 " --> pdb=" O ASP N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 41 Processing helix chain 'N' and resid 49 through 76 removed outlier: 3.722A pdb=" N GLU N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY N 56 " --> pdb=" O GLU N 52 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP N 68 " --> pdb=" O ASN N 64 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 93 removed outlier: 3.593A pdb=" N VAL N 86 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA N 89 " --> pdb=" O ASP N 85 " (cutoff:3.500A) 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: 4.489A pdb=" N VAL O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 90 removed outlier: 3.638A pdb=" N LEU O 83 " --> pdb=" O ILE O 79 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP O 90 " --> pdb=" O ALA O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 97 Processing helix chain 'O' and resid 112 through 116 Processing helix chain 'P' and resid 37 through 46 Processing helix chain 'P' and resid 55 through 84 removed outlier: 3.703A pdb=" N ARG P 79 " --> pdb=" O GLY P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 90 through 102 removed outlier: 4.720A pdb=" N THR P 96 " --> pdb=" O ARG P 92 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG P 99 " --> pdb=" O GLN P 95 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU P 102 " --> pdb=" O VAL P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 125 removed outlier: 3.509A pdb=" N LYS P 108 " --> pdb=" O GLY P 104 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 57 Processing helix chain 'Q' and resid 63 through 76 Processing helix chain 'Q' and resid 87 through 114 Processing helix chain 'Q' and resid 120 through 131 removed outlier: 3.564A pdb=" N ILE Q 124 " --> pdb=" O MET Q 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 29 Processing helix chain 'R' and resid 30 through 41 Processing helix chain 'R' and resid 49 through 76 removed outlier: 3.573A pdb=" N GLU R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY R 56 " --> pdb=" O GLU R 52 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP R 68 " --> pdb=" O ASN R 64 " (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: 4.309A pdb=" N VAL S 49 " --> pdb=" O ALA S 45 " (cutoff:3.500A) Processing helix chain 'S' and resid 79 through 90 Processing helix chain 'S' and resid 90 through 97 removed outlier: 3.795A pdb=" N LYS S 95 " --> pdb=" O GLU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 116 Processing helix chain 'T' and resid 37 through 49 Processing helix chain 'T' and resid 55 through 83 removed outlier: 4.035A pdb=" N ASN T 67 " --> pdb=" O ASN T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 90 through 102 Processing helix chain 'T' and resid 104 through 123 removed outlier: 3.929A pdb=" N LYS T 108 " --> pdb=" O GLY T 104 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER T 123 " --> pdb=" O THR T 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84 removed outlier: 6.895A 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 removed outlier: 6.712A pdb=" N THR N 96 " --> pdb=" O THR S 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 42 through 43 removed outlier: 7.071A pdb=" N ARG O 42 " --> pdb=" O ILE P 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'O' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'O' and resid 100 through 102 removed outlier: 6.743A pdb=" N THR O 101 " --> pdb=" O TYR R 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'Q' and resid 83 through 84 removed outlier: 7.065A pdb=" N ARG Q 83 " --> pdb=" O VAL R 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'S' and resid 42 through 43 removed outlier: 6.996A pdb=" N ARG S 42 " --> pdb=" O ILE T 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'S' and resid 77 through 78 409 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 223 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.33 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: 3039 1.34 - 1.46: 3607 1.46 - 1.58: 5671 1.58 - 1.70: 555 1.70 - 1.82: 24 Bond restraints: 12896 Sorted by residual: bond pdb=" CA ARG P 92 " pdb=" C ARG P 92 " ideal model delta sigma weight residual 1.522 1.644 -0.122 1.45e-02 4.76e+03 7.09e+01 bond pdb=" N GLY T 53 " pdb=" CA GLY T 53 " ideal model delta sigma weight residual 1.444 1.482 -0.038 1.02e-02 9.61e+03 1.39e+01 bond pdb=" CZ ARG H 179 " pdb=" NH2 ARG H 179 " ideal model delta sigma weight residual 1.330 1.290 0.040 1.30e-02 5.92e+03 9.66e+00 bond pdb=" CZ ARG M 131 " pdb=" NH2 ARG M 131 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.59e+00 bond pdb=" CZ ARG M 116 " pdb=" NH2 ARG M 116 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.54e+00 ... (remaining 12891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 17415 3.53 - 7.06: 1158 7.06 - 10.58: 18 10.58 - 14.11: 2 14.11 - 17.64: 1 Bond angle restraints: 18594 Sorted by residual: angle pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" CB GLU P 93 " ideal model delta sigma weight residual 110.49 92.85 17.64 1.69e+00 3.50e-01 1.09e+02 angle pdb=" CA ARG P 92 " pdb=" C ARG P 92 " pdb=" O ARG P 92 " ideal model delta sigma weight residual 119.61 130.15 -10.54 1.18e+00 7.18e-01 7.98e+01 angle pdb=" CA ARG P 92 " pdb=" C ARG P 92 " pdb=" N GLU P 93 " ideal model delta sigma weight residual 118.01 107.40 10.61 1.30e+00 5.92e-01 6.66e+01 angle pdb=" CA PRO M 43 " pdb=" N PRO M 43 " pdb=" CD PRO M 43 " ideal model delta sigma weight residual 112.00 101.93 10.07 1.40e+00 5.10e-01 5.17e+01 angle pdb=" N ARG P 92 " pdb=" CA ARG P 92 " pdb=" C ARG P 92 " ideal model delta sigma weight residual 112.34 121.18 -8.84 1.30e+00 5.92e-01 4.63e+01 ... (remaining 18589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.43: 5896 34.43 - 68.86: 1146 68.86 - 103.29: 28 103.29 - 137.72: 0 137.72 - 172.15: 1 Dihedral angle restraints: 7071 sinusoidal: 4737 harmonic: 2334 Sorted by residual: dihedral pdb=" C ARG P 92 " pdb=" N ARG P 92 " pdb=" CA ARG P 92 " pdb=" CB ARG P 92 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.49e+01 dihedral pdb=" CA THR T 88 " pdb=" C THR T 88 " pdb=" N ILE T 89 " pdb=" CA ILE T 89 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA LEU T 100 " pdb=" C LEU T 100 " pdb=" N LEU T 101 " pdb=" CA LEU T 101 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 7068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1672 0.093 - 0.187: 374 0.187 - 0.280: 51 0.280 - 0.374: 8 0.374 - 0.467: 4 Chirality restraints: 2109 Sorted by residual: chirality pdb=" CA ARG P 92 " pdb=" N ARG P 92 " pdb=" C ARG P 92 " pdb=" CB ARG P 92 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.45e+00 chirality pdb=" CA LYS R 79 " pdb=" N LYS R 79 " pdb=" C LYS R 79 " pdb=" CB LYS R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.44 2.00e-01 2.50e+01 4.74e+00 chirality pdb=" C3' DC L 20 " pdb=" C4' DC L 20 " pdb=" O3' DC L 20 " pdb=" C2' DC L 20 " both_signs ideal model delta sigma weight residual False -2.66 -2.24 -0.42 2.00e-01 2.50e+01 4.36e+00 ... (remaining 2106 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 6 " 0.372 2.00e-02 2.50e+03 2.08e-01 1.08e+03 pdb=" N1 DT K 6 " 0.035 2.00e-02 2.50e+03 pdb=" C2 DT K 6 " -0.064 2.00e-02 2.50e+03 pdb=" O2 DT K 6 " -0.351 2.00e-02 2.50e+03 pdb=" N3 DT K 6 " 0.019 2.00e-02 2.50e+03 pdb=" C4 DT K 6 " 0.091 2.00e-02 2.50e+03 pdb=" O4 DT K 6 " 0.301 2.00e-02 2.50e+03 pdb=" C5 DT K 6 " -0.089 2.00e-02 2.50e+03 pdb=" C7 DT K 6 " -0.227 2.00e-02 2.50e+03 pdb=" C6 DT K 6 " -0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG K 26 " 0.439 2.00e-02 2.50e+03 1.76e-01 9.26e+02 pdb=" N9 DG K 26 " -0.070 2.00e-02 2.50e+03 pdb=" C8 DG K 26 " -0.224 2.00e-02 2.50e+03 pdb=" N7 DG K 26 " -0.140 2.00e-02 2.50e+03 pdb=" C5 DG K 26 " -0.040 2.00e-02 2.50e+03 pdb=" C6 DG K 26 " 0.098 2.00e-02 2.50e+03 pdb=" O6 DG K 26 " 0.213 2.00e-02 2.50e+03 pdb=" N1 DG K 26 " 0.094 2.00e-02 2.50e+03 pdb=" C2 DG K 26 " -0.043 2.00e-02 2.50e+03 pdb=" N2 DG K 26 " -0.113 2.00e-02 2.50e+03 pdb=" N3 DG K 26 " -0.115 2.00e-02 2.50e+03 pdb=" C4 DG K 26 " -0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT K 47 " -0.365 2.00e-02 2.50e+03 1.88e-01 8.81e+02 pdb=" N1 DT K 47 " -0.005 2.00e-02 2.50e+03 pdb=" C2 DT K 47 " 0.094 2.00e-02 2.50e+03 pdb=" O2 DT K 47 " 0.282 2.00e-02 2.50e+03 pdb=" N3 DT K 47 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DT K 47 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT K 47 " -0.267 2.00e-02 2.50e+03 pdb=" C5 DT K 47 " 0.081 2.00e-02 2.50e+03 pdb=" C7 DT K 47 " 0.177 2.00e-02 2.50e+03 pdb=" C6 DT K 47 " 0.108 2.00e-02 2.50e+03 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 5825 3.01 - 3.49: 13500 3.49 - 3.96: 23156 3.96 - 4.43: 26209 4.43 - 4.90: 34712 Nonbonded interactions: 103402 Sorted by model distance: nonbonded pdb=" OP2 DC L -54 " pdb=" OG SER T 56 " model vdw 2.543 3.040 nonbonded pdb=" OG1 THR T 90 " pdb=" OE1 GLU T 93 " model vdw 2.550 3.040 nonbonded pdb=" OH TYR Q 99 " pdb=" OE1 GLU Q 133 " model vdw 2.551 3.040 nonbonded pdb=" OP1 DG K -34 " pdb=" OG1 THR P 88 " model vdw 2.574 3.040 nonbonded pdb=" OP1 DC L 48 " pdb=" OH TYR P 40 " model vdw 2.575 3.040 ... (remaining 103397 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'M' selection = (chain 'Q' and resid 43 through 135) } 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 31 through 123) selection = (chain 'T' and (resid 31 through 122 or (resid 123 and (name N or name CA or nam \ e C or name O or name CB or name OG )))) } 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: 5.890 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: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.530 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 0.122 12896 Z= 0.701 Angle : 1.867 17.640 18594 Z= 1.230 Chirality : 0.082 0.467 2109 Planarity : 0.036 0.208 1401 Dihedral : 26.362 172.148 5567 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.51 % Allowed : 3.79 % Favored : 95.71 % Rotamer: Outliers : 1.19 % Allowed : 3.58 % Favored : 95.23 % Cbeta Deviations : 0.53 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.28), residues: 792 helix: -0.52 (0.20), residues: 558 sheet: None (None), residues: 0 loop : -0.31 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 129 TYR 0.136 0.021 TYR Q 54 PHE 0.044 0.010 PHE M 84 TRP 0.054 0.026 TRP H 152 HIS 0.010 0.003 HIS P 82 Details of bonding type rmsd covalent geometry : bond 0.01255 (12896) covalent geometry : angle 1.86652 (18594) hydrogen bonds : bond 0.11870 ( 753) hydrogen bonds : angle 6.45087 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 374 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8872 (mt) cc_final: 0.8307 (mp) REVERT: H 164 ASN cc_start: 0.9081 (m110) cc_final: 0.8694 (p0) REVERT: H 180 GLN cc_start: 0.9495 (mt0) cc_final: 0.9089 (mt0) REVERT: M 58 THR cc_start: 0.9315 (p) cc_final: 0.9081 (t) REVERT: M 81 ASP cc_start: 0.9106 (m-30) cc_final: 0.8808 (p0) REVERT: M 97 GLU cc_start: 0.9265 (mt-10) cc_final: 0.9055 (mt-10) REVERT: M 101 VAL cc_start: 0.9496 (t) cc_final: 0.9290 (m) REVERT: M 118 THR cc_start: 0.9196 (m) cc_final: 0.8905 (p) REVERT: N 84 MET cc_start: 0.9055 (mmm) cc_final: 0.8553 (mmm) REVERT: N 98 TYR cc_start: 0.9649 (m-10) cc_final: 0.9424 (m-80) REVERT: O 35 ARG cc_start: 0.8857 (mtm-85) cc_final: 0.8528 (mtm-85) REVERT: O 50 TYR cc_start: 0.9215 (t80) cc_final: 0.8964 (t80) REVERT: O 90 ASP cc_start: 0.8104 (t70) cc_final: 0.7401 (t0) REVERT: O 91 GLU cc_start: 0.9218 (pm20) cc_final: 0.8718 (tm-30) REVERT: O 111 ILE cc_start: 0.9673 (mm) cc_final: 0.9455 (mp) REVERT: O 118 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8382 (mtmm) REVERT: P 68 ASP cc_start: 0.9457 (t70) cc_final: 0.9251 (t0) REVERT: P 86 ARG cc_start: 0.9005 (mmt-90) cc_final: 0.8766 (ttm-80) REVERT: P 125 LYS cc_start: 0.8710 (mttt) cc_final: 0.8373 (tppt) REVERT: Q 70 LEU cc_start: 0.9245 (tp) cc_final: 0.8994 (tt) REVERT: Q 77 ASP cc_start: 0.9469 (m-30) cc_final: 0.8993 (m-30) REVERT: Q 93 GLN cc_start: 0.9235 (tt0) cc_final: 0.9014 (tt0) REVERT: R 39 ARG cc_start: 0.9091 (mmt90) cc_final: 0.8829 (tpp-160) REVERT: R 93 GLN cc_start: 0.8544 (mt0) cc_final: 0.7992 (mt0) REVERT: R 100 PHE cc_start: 0.9302 (m-80) cc_final: 0.9037 (m-10) REVERT: S 39 TYR cc_start: 0.9446 (m-80) cc_final: 0.9205 (m-80) REVERT: S 90 ASP cc_start: 0.9174 (t0) cc_final: 0.8951 (t0) REVERT: T 51 ASP cc_start: 0.9333 (p0) cc_final: 0.9129 (t0) REVERT: T 54 ILE cc_start: 0.9296 (mm) cc_final: 0.8943 (tt) REVERT: T 57 LYS cc_start: 0.9365 (mppt) cc_final: 0.9156 (tppt) REVERT: T 68 ASP cc_start: 0.9483 (t0) cc_final: 0.9004 (t0) REVERT: T 93 GLU cc_start: 0.9225 (mp0) cc_final: 0.8997 (mm-30) REVERT: T 106 LEU cc_start: 0.9284 (mt) cc_final: 0.8943 (mp) outliers start: 8 outliers final: 2 residues processed: 377 average time/residue: 0.1297 time to fit residues: 65.4301 Evaluate side-chains 281 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 279 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 164 ASN M 93 GLN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.073438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.052546 restraints weight = 46627.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.054194 restraints weight = 22802.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.055319 restraints weight = 15190.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.055986 restraints weight = 11955.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.056398 restraints weight = 10457.469| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12896 Z= 0.216 Angle : 0.727 7.075 18594 Z= 0.427 Chirality : 0.043 0.190 2109 Planarity : 0.005 0.041 1401 Dihedral : 30.124 168.306 3952 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.27 % Favored : 97.60 % Rotamer: Outliers : 3.58 % Allowed : 18.93 % Favored : 77.50 % 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: 0.70 (0.29), residues: 792 helix: 0.87 (0.21), residues: 564 sheet: None (None), residues: 0 loop : -0.33 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG R 35 TYR 0.019 0.002 TYR Q 54 PHE 0.019 0.002 PHE Q 78 TRP 0.020 0.004 TRP H 152 HIS 0.009 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00474 (12896) covalent geometry : angle 0.72684 (18594) hydrogen bonds : bond 0.05304 ( 753) hydrogen bonds : angle 3.40026 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 311 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 GLU cc_start: 0.8937 (pp20) cc_final: 0.8724 (pp20) REVERT: H 148 GLU cc_start: 0.9081 (tt0) cc_final: 0.8838 (tm-30) REVERT: H 151 ARG cc_start: 0.9212 (mtt-85) cc_final: 0.8810 (ptt90) REVERT: H 153 LEU cc_start: 0.8415 (mt) cc_final: 0.7817 (mp) REVERT: H 180 GLN cc_start: 0.9362 (mt0) cc_final: 0.8917 (mt0) REVERT: M 101 VAL cc_start: 0.9378 (t) cc_final: 0.8919 (p) REVERT: M 106 ASP cc_start: 0.8983 (m-30) cc_final: 0.8591 (m-30) REVERT: M 108 ASN cc_start: 0.9323 (t0) cc_final: 0.9108 (m-40) REVERT: M 120 MET cc_start: 0.8221 (mtp) cc_final: 0.7970 (mpp) REVERT: M 122 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8645 (ttpp) REVERT: N 44 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9043 (ttmt) REVERT: N 84 MET cc_start: 0.8866 (mmm) cc_final: 0.8151 (mmm) REVERT: N 92 ARG cc_start: 0.9017 (ptm-80) cc_final: 0.8769 (ttp80) REVERT: N 98 TYR cc_start: 0.9394 (m-10) cc_final: 0.8947 (m-80) REVERT: O 50 TYR cc_start: 0.8505 (t80) cc_final: 0.8303 (t80) REVERT: O 84 GLN cc_start: 0.9335 (tp40) cc_final: 0.8837 (tm-30) REVERT: O 90 ASP cc_start: 0.7714 (t70) cc_final: 0.7208 (t0) REVERT: O 91 GLU cc_start: 0.8744 (pm20) cc_final: 0.8341 (tm-30) REVERT: O 92 GLU cc_start: 0.7895 (mt-10) cc_final: 0.6047 (tt0) REVERT: O 116 LEU cc_start: 0.9405 (mt) cc_final: 0.9057 (pp) REVERT: P 57 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9310 (mmmm) REVERT: P 68 ASP cc_start: 0.9225 (t70) cc_final: 0.8726 (t0) REVERT: P 71 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8824 (tm-30) REVERT: P 93 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8264 (pt0) REVERT: P 106 LEU cc_start: 0.9671 (tp) cc_final: 0.9211 (tp) REVERT: P 125 LYS cc_start: 0.8372 (mttt) cc_final: 0.7889 (tppt) REVERT: Q 50 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8814 (mm-30) REVERT: Q 68 GLN cc_start: 0.8721 (tt0) cc_final: 0.8244 (tp40) REVERT: Q 76 GLN cc_start: 0.8539 (pp30) cc_final: 0.8171 (pp30) REVERT: Q 77 ASP cc_start: 0.7929 (m-30) cc_final: 0.7665 (m-30) REVERT: Q 123 ASP cc_start: 0.9007 (m-30) cc_final: 0.8191 (m-30) REVERT: Q 130 ILE cc_start: 0.9410 (mm) cc_final: 0.9073 (mm) REVERT: R 36 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: R 39 ARG cc_start: 0.8882 (mmt90) cc_final: 0.8402 (tpp-160) REVERT: R 68 ASP cc_start: 0.9025 (m-30) cc_final: 0.8540 (m-30) REVERT: R 84 MET cc_start: 0.8828 (mmm) cc_final: 0.8448 (mmp) REVERT: S 39 TYR cc_start: 0.8752 (m-80) cc_final: 0.8336 (m-80) REVERT: S 57 TYR cc_start: 0.8810 (t80) cc_final: 0.8537 (t80) REVERT: S 59 THR cc_start: 0.9099 (m) cc_final: 0.8724 (p) REVERT: S 61 GLU cc_start: 0.9009 (tp30) cc_final: 0.8612 (tp30) REVERT: S 89 ASN cc_start: 0.9416 (m-40) cc_final: 0.8992 (m-40) REVERT: S 90 ASP cc_start: 0.8763 (t0) cc_final: 0.8196 (t0) REVERT: S 110 ASN cc_start: 0.9182 (t0) cc_final: 0.8896 (t0) REVERT: T 34 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8756 (mmmm) REVERT: T 38 SER cc_start: 0.9444 (t) cc_final: 0.9239 (m) REVERT: T 51 ASP cc_start: 0.8192 (p0) cc_final: 0.7905 (t0) REVERT: T 57 LYS cc_start: 0.9234 (mppt) cc_final: 0.8999 (mmmt) REVERT: T 64 SER cc_start: 0.9213 (m) cc_final: 0.8413 (p) REVERT: T 68 ASP cc_start: 0.8781 (t0) cc_final: 0.8285 (t0) REVERT: T 79 ARG cc_start: 0.8612 (ttp80) cc_final: 0.8035 (mtm-85) outliers start: 24 outliers final: 11 residues processed: 317 average time/residue: 0.1303 time to fit residues: 55.0961 Evaluate side-chains 292 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 280 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 189 SER Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain P residue 93 GLU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 45 optimal weight: 0.0980 chunk 102 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 108 ASN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.073822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.053485 restraints weight = 46843.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055218 restraints weight = 21719.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056378 restraints weight = 13977.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.057141 restraints weight = 10806.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057589 restraints weight = 9282.355| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12896 Z= 0.181 Angle : 0.659 7.755 18594 Z= 0.388 Chirality : 0.039 0.196 2109 Planarity : 0.004 0.037 1401 Dihedral : 29.707 169.035 3950 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.90 % Favored : 96.84 % Rotamer: Outliers : 3.13 % Allowed : 22.65 % Favored : 74.22 % 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: 0.93 (0.29), residues: 792 helix: 1.13 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.56 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 99 TYR 0.026 0.002 TYR T 83 PHE 0.011 0.002 PHE M 67 TRP 0.015 0.003 TRP H 152 HIS 0.007 0.001 HIS R 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (12896) covalent geometry : angle 0.65869 (18594) hydrogen bonds : bond 0.04303 ( 753) hydrogen bonds : angle 3.07370 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 153 LEU cc_start: 0.8404 (mt) cc_final: 0.8035 (mt) REVERT: H 180 GLN cc_start: 0.9326 (mt0) cc_final: 0.9018 (mt0) REVERT: M 105 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8501 (mt-10) REVERT: M 106 ASP cc_start: 0.8807 (m-30) cc_final: 0.8594 (m-30) REVERT: M 120 MET cc_start: 0.8229 (mtp) cc_final: 0.7777 (mtt) REVERT: M 122 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8787 (ttpp) REVERT: N 84 MET cc_start: 0.8891 (mmm) cc_final: 0.7965 (mmm) REVERT: O 19 SER cc_start: 0.9612 (t) cc_final: 0.9314 (p) REVERT: O 75 LYS cc_start: 0.9271 (mttm) cc_final: 0.9008 (mmmm) REVERT: O 81 ARG cc_start: 0.9115 (mmm160) cc_final: 0.8906 (tpt170) REVERT: O 91 GLU cc_start: 0.8723 (pm20) cc_final: 0.8156 (tm-30) REVERT: O 95 LYS cc_start: 0.9328 (tttt) cc_final: 0.8897 (ttmm) REVERT: P 57 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9287 (mmmm) REVERT: P 68 ASP cc_start: 0.9218 (t70) cc_final: 0.8746 (t0) REVERT: P 71 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8777 (tm-30) REVERT: P 125 LYS cc_start: 0.8335 (mttt) cc_final: 0.7905 (tppt) REVERT: Q 50 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8888 (mm-30) REVERT: Q 64 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9204 (mmmm) REVERT: Q 68 GLN cc_start: 0.8818 (tt0) cc_final: 0.8399 (tp40) REVERT: Q 76 GLN cc_start: 0.8781 (pp30) cc_final: 0.8405 (pp30) REVERT: Q 77 ASP cc_start: 0.8037 (m-30) cc_final: 0.7815 (m-30) REVERT: Q 109 LEU cc_start: 0.9437 (mm) cc_final: 0.9190 (mm) REVERT: Q 123 ASP cc_start: 0.9049 (m-30) cc_final: 0.8322 (m-30) REVERT: Q 130 ILE cc_start: 0.9308 (mm) cc_final: 0.9047 (tt) REVERT: R 36 ARG cc_start: 0.8586 (mtm-85) cc_final: 0.8128 (mtm-85) REVERT: R 39 ARG cc_start: 0.8877 (mmt90) cc_final: 0.8378 (tpp-160) REVERT: R 68 ASP cc_start: 0.8962 (m-30) cc_final: 0.8521 (m-30) REVERT: R 84 MET cc_start: 0.8686 (mmm) cc_final: 0.8170 (mmp) REVERT: R 92 ARG cc_start: 0.9004 (tmm-80) cc_final: 0.8703 (tmm-80) REVERT: S 19 SER cc_start: 0.9542 (t) cc_final: 0.9081 (p) REVERT: S 61 GLU cc_start: 0.9013 (tp30) cc_final: 0.8661 (tp30) REVERT: S 90 ASP cc_start: 0.8567 (t0) cc_final: 0.8069 (t0) REVERT: T 51 ASP cc_start: 0.8283 (p0) cc_final: 0.7825 (t0) REVERT: T 57 LYS cc_start: 0.9155 (mppt) cc_final: 0.8927 (mmmt) REVERT: T 64 SER cc_start: 0.9262 (m) cc_final: 0.8789 (p) REVERT: T 68 ASP cc_start: 0.8726 (t0) cc_final: 0.8427 (t0) REVERT: T 71 GLU cc_start: 0.8971 (tp30) cc_final: 0.8714 (tm-30) REVERT: T 105 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8461 (mm-30) REVERT: T 108 LYS cc_start: 0.8926 (ptmt) cc_final: 0.8572 (ptpp) outliers start: 21 outliers final: 11 residues processed: 313 average time/residue: 0.1325 time to fit residues: 55.6689 Evaluate side-chains 282 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 271 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 54 THR Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 38 ASN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS R 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.072185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051759 restraints weight = 45908.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.053462 restraints weight = 20508.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.054588 restraints weight = 13016.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055299 restraints weight = 10004.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.055702 restraints weight = 8596.545| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.4543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12896 Z= 0.198 Angle : 0.658 11.199 18594 Z= 0.383 Chirality : 0.038 0.204 2109 Planarity : 0.004 0.035 1401 Dihedral : 29.776 168.118 3950 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.91 % Favored : 95.83 % Rotamer: Outliers : 4.32 % Allowed : 24.89 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.29), residues: 792 helix: 1.14 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -0.53 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 35 TYR 0.032 0.003 TYR P 40 PHE 0.008 0.001 PHE T 65 TRP 0.008 0.002 TRP H 152 HIS 0.020 0.002 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00441 (12896) covalent geometry : angle 0.65814 (18594) hydrogen bonds : bond 0.04364 ( 753) hydrogen bonds : angle 3.14128 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.291 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: H 148 GLU cc_start: 0.8680 (tm-30) cc_final: 0.7887 (tm-30) REVERT: H 151 ARG cc_start: 0.9221 (mtt-85) cc_final: 0.8893 (ptt90) REVERT: H 164 ASN cc_start: 0.9212 (p0) cc_final: 0.8980 (p0) REVERT: H 180 GLN cc_start: 0.9310 (mt0) cc_final: 0.8971 (mt0) REVERT: M 81 ASP cc_start: 0.8841 (m-30) cc_final: 0.8622 (m-30) REVERT: M 105 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8580 (mt-10) REVERT: M 106 ASP cc_start: 0.8797 (m-30) cc_final: 0.8459 (m-30) REVERT: M 120 MET cc_start: 0.8259 (mtp) cc_final: 0.7864 (mtt) REVERT: M 122 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8795 (ttpp) REVERT: N 44 LYS cc_start: 0.9400 (ttpt) cc_final: 0.8979 (ttmt) REVERT: N 74 GLU cc_start: 0.9139 (mm-30) cc_final: 0.8824 (mm-30) REVERT: N 77 LYS cc_start: 0.9039 (mttp) cc_final: 0.8644 (mtmm) REVERT: N 84 MET cc_start: 0.8900 (mmm) cc_final: 0.7979 (mmm) REVERT: O 19 SER cc_start: 0.9598 (t) cc_final: 0.9297 (p) REVERT: O 27 VAL cc_start: 0.9353 (t) cc_final: 0.9072 (m) REVERT: O 50 TYR cc_start: 0.8279 (t80) cc_final: 0.8051 (t80) REVERT: O 75 LYS cc_start: 0.9251 (mttm) cc_final: 0.9017 (mmmm) REVERT: O 81 ARG cc_start: 0.9079 (mmm160) cc_final: 0.8874 (tpt170) REVERT: O 91 GLU cc_start: 0.8666 (pm20) cc_final: 0.8099 (tm-30) REVERT: P 68 ASP cc_start: 0.9190 (t70) cc_final: 0.8770 (t0) REVERT: P 71 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8783 (tm-30) REVERT: P 93 GLU cc_start: 0.8564 (pt0) cc_final: 0.8277 (pm20) REVERT: P 106 LEU cc_start: 0.9584 (tp) cc_final: 0.9344 (tp) REVERT: P 125 LYS cc_start: 0.8329 (mttt) cc_final: 0.7766 (tppt) REVERT: Q 50 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8868 (mm-30) REVERT: Q 64 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9131 (mmmm) REVERT: Q 68 GLN cc_start: 0.8803 (tt0) cc_final: 0.8368 (tp40) REVERT: Q 76 GLN cc_start: 0.8888 (pp30) cc_final: 0.8447 (pp30) REVERT: Q 77 ASP cc_start: 0.8225 (m-30) cc_final: 0.8023 (m-30) REVERT: Q 123 ASP cc_start: 0.8978 (m-30) cc_final: 0.8513 (m-30) REVERT: Q 130 ILE cc_start: 0.9291 (mm) cc_final: 0.8937 (mm) REVERT: R 39 ARG cc_start: 0.8943 (mmt90) cc_final: 0.8442 (tpp-160) REVERT: S 19 SER cc_start: 0.9534 (t) cc_final: 0.9069 (p) REVERT: S 59 THR cc_start: 0.9211 (m) cc_final: 0.8983 (p) REVERT: S 90 ASP cc_start: 0.8633 (t0) cc_final: 0.8185 (t0) REVERT: T 51 ASP cc_start: 0.8217 (p0) cc_final: 0.7789 (t0) REVERT: T 57 LYS cc_start: 0.9163 (mppt) cc_final: 0.8950 (mmmt) REVERT: T 64 SER cc_start: 0.9215 (m) cc_final: 0.8786 (p) REVERT: T 68 ASP cc_start: 0.8780 (t0) cc_final: 0.8461 (t0) REVERT: T 93 GLU cc_start: 0.8602 (mm-30) cc_final: 0.7787 (mm-30) REVERT: T 105 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8466 (mm-30) REVERT: T 108 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8625 (ptpp) outliers start: 29 outliers final: 18 residues processed: 293 average time/residue: 0.1266 time to fit residues: 50.0799 Evaluate side-chains 276 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 258 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 36 LYS Chi-restraints excluded: chain S residue 49 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 GLN ** Q 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS ** S 38 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 = 0.3505 r_free = 0.3505 target = 0.073359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.052077 restraints weight = 46004.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053744 restraints weight = 21666.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.054857 restraints weight = 14150.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055563 restraints weight = 11085.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055984 restraints weight = 9627.363| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12896 Z= 0.177 Angle : 0.642 11.697 18594 Z= 0.374 Chirality : 0.037 0.194 2109 Planarity : 0.004 0.046 1401 Dihedral : 29.710 169.478 3950 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.54 % Favored : 96.21 % Rotamer: Outliers : 2.83 % Allowed : 29.06 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.29), residues: 792 helix: 1.26 (0.21), residues: 566 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 71 TYR 0.021 0.002 TYR N 88 PHE 0.008 0.001 PHE M 67 TRP 0.006 0.002 TRP H 152 HIS 0.019 0.002 HIS Q 39 Details of bonding type rmsd covalent geometry : bond 0.00393 (12896) covalent geometry : angle 0.64187 (18594) hydrogen bonds : bond 0.03899 ( 753) hydrogen bonds : angle 3.01492 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 280 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 151 ARG cc_start: 0.9227 (mtt-85) cc_final: 0.8884 (ptt90) REVERT: H 164 ASN cc_start: 0.9161 (p0) cc_final: 0.8907 (p0) REVERT: H 180 GLN cc_start: 0.9298 (mt0) cc_final: 0.8908 (mt0) REVERT: M 50 GLU cc_start: 0.9184 (tt0) cc_final: 0.8722 (tt0) REVERT: M 81 ASP cc_start: 0.8804 (m-30) cc_final: 0.8601 (m-30) REVERT: M 105 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8435 (mt-10) REVERT: M 106 ASP cc_start: 0.8746 (m-30) cc_final: 0.8449 (m-30) REVERT: M 120 MET cc_start: 0.8282 (mtp) cc_final: 0.7841 (mtt) REVERT: N 44 LYS cc_start: 0.9422 (ttpt) cc_final: 0.8966 (ttmm) REVERT: N 77 LYS cc_start: 0.9014 (mttp) cc_final: 0.8667 (mtmm) REVERT: N 84 MET cc_start: 0.8913 (mmm) cc_final: 0.8065 (mmm) REVERT: O 19 SER cc_start: 0.9600 (t) cc_final: 0.9321 (p) REVERT: O 27 VAL cc_start: 0.9181 (t) cc_final: 0.8941 (m) REVERT: O 39 TYR cc_start: 0.8883 (m-80) cc_final: 0.8471 (m-80) REVERT: O 75 LYS cc_start: 0.9214 (mttm) cc_final: 0.8981 (mmmm) REVERT: O 84 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8967 (tp-100) REVERT: O 91 GLU cc_start: 0.8659 (pm20) cc_final: 0.8130 (tm-30) REVERT: O 92 GLU cc_start: 0.8961 (tp30) cc_final: 0.8656 (tp30) REVERT: O 95 LYS cc_start: 0.9309 (tttt) cc_final: 0.8906 (ttmm) REVERT: P 68 ASP cc_start: 0.9193 (t70) cc_final: 0.8810 (t0) REVERT: P 71 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8773 (tm-30) REVERT: P 86 ARG cc_start: 0.8892 (mmt-90) cc_final: 0.8587 (mmm-85) REVERT: P 125 LYS cc_start: 0.8310 (mttt) cc_final: 0.7767 (tppt) REVERT: Q 50 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8875 (mm-30) REVERT: Q 68 GLN cc_start: 0.8747 (tt0) cc_final: 0.8371 (tp40) REVERT: Q 76 GLN cc_start: 0.8920 (pp30) cc_final: 0.8439 (pp30) REVERT: Q 90 MET cc_start: 0.8479 (tpp) cc_final: 0.8051 (tpp) REVERT: Q 123 ASP cc_start: 0.8995 (m-30) cc_final: 0.8580 (m-30) REVERT: R 39 ARG cc_start: 0.8929 (mmt90) cc_final: 0.8406 (tpp-160) REVERT: S 19 SER cc_start: 0.9527 (t) cc_final: 0.9049 (p) REVERT: S 59 THR cc_start: 0.9193 (m) cc_final: 0.8990 (p) REVERT: S 61 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8762 (mm-30) REVERT: S 78 ILE cc_start: 0.8907 (mm) cc_final: 0.8673 (mm) REVERT: S 90 ASP cc_start: 0.8622 (t0) cc_final: 0.8197 (t0) REVERT: T 51 ASP cc_start: 0.8186 (p0) cc_final: 0.7817 (t0) REVERT: T 57 LYS cc_start: 0.9127 (mppt) cc_final: 0.8893 (mmmt) REVERT: T 64 SER cc_start: 0.9234 (m) cc_final: 0.8776 (p) REVERT: T 68 ASP cc_start: 0.8750 (t0) cc_final: 0.8438 (t0) REVERT: T 93 GLU cc_start: 0.8615 (mm-30) cc_final: 0.7874 (tm-30) REVERT: T 105 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8531 (mm-30) outliers start: 19 outliers final: 16 residues processed: 286 average time/residue: 0.1195 time to fit residues: 46.8485 Evaluate side-chains 273 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 102 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 85 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.073271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.052415 restraints weight = 45942.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.054158 restraints weight = 20795.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.055313 restraints weight = 13267.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.056044 restraints weight = 10226.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.056448 restraints weight = 8796.242| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12896 Z= 0.180 Angle : 0.648 12.310 18594 Z= 0.373 Chirality : 0.037 0.182 2109 Planarity : 0.004 0.035 1401 Dihedral : 29.738 169.453 3950 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.41 % Favored : 96.34 % Rotamer: Outliers : 3.87 % Allowed : 29.21 % 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: 1.27 (0.29), residues: 792 helix: 1.35 (0.21), residues: 565 sheet: None (None), residues: 0 loop : -0.31 (0.41), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 181 TYR 0.025 0.002 TYR S 39 PHE 0.011 0.001 PHE M 67 TRP 0.005 0.001 TRP H 152 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00401 (12896) covalent geometry : angle 0.64766 (18594) hydrogen bonds : bond 0.03997 ( 753) hydrogen bonds : angle 3.06551 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 148 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8447 (pp20) REVERT: H 164 ASN cc_start: 0.9123 (p0) cc_final: 0.8794 (p0) REVERT: H 180 GLN cc_start: 0.9340 (mt0) cc_final: 0.8822 (mt0) REVERT: M 73 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8231 (mm-30) REVERT: M 81 ASP cc_start: 0.8737 (m-30) cc_final: 0.8462 (m-30) REVERT: M 105 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8425 (mt-10) REVERT: M 106 ASP cc_start: 0.8748 (m-30) cc_final: 0.8462 (m-30) REVERT: M 122 LYS cc_start: 0.9232 (ttmt) cc_final: 0.8920 (ttpp) REVERT: N 44 LYS cc_start: 0.9407 (ttpt) cc_final: 0.9042 (ttmt) REVERT: N 74 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8886 (mm-30) REVERT: N 77 LYS cc_start: 0.9029 (mttp) cc_final: 0.8662 (mtmm) REVERT: N 84 MET cc_start: 0.8914 (mmm) cc_final: 0.7898 (mmm) REVERT: N 88 TYR cc_start: 0.8611 (m-80) cc_final: 0.8193 (m-80) REVERT: O 19 SER cc_start: 0.9589 (t) cc_final: 0.9309 (p) REVERT: O 36 LYS cc_start: 0.9553 (mmmt) cc_final: 0.9342 (mmtt) REVERT: O 39 TYR cc_start: 0.8890 (m-80) cc_final: 0.8440 (m-80) REVERT: O 91 GLU cc_start: 0.8745 (pm20) cc_final: 0.8294 (tm-30) REVERT: O 92 GLU cc_start: 0.9022 (tp30) cc_final: 0.8644 (tp30) REVERT: P 68 ASP cc_start: 0.9207 (t70) cc_final: 0.8874 (t0) REVERT: P 71 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8776 (tm-30) REVERT: P 76 GLU cc_start: 0.8352 (tp30) cc_final: 0.7722 (tp30) REVERT: P 79 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.7880 (mtm-85) REVERT: P 125 LYS cc_start: 0.8285 (mttt) cc_final: 0.7711 (tppt) REVERT: Q 50 GLU cc_start: 0.9235 (OUTLIER) cc_final: 0.8895 (mm-30) REVERT: Q 64 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9211 (mmmm) REVERT: Q 68 GLN cc_start: 0.8764 (tt0) cc_final: 0.8366 (tp40) REVERT: Q 76 GLN cc_start: 0.9022 (pp30) cc_final: 0.8569 (pp30) REVERT: Q 90 MET cc_start: 0.8530 (tpp) cc_final: 0.7423 (tpp) REVERT: Q 94 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7836 (mm-30) REVERT: Q 123 ASP cc_start: 0.9002 (m-30) cc_final: 0.8633 (m-30) REVERT: R 39 ARG cc_start: 0.8895 (mmt90) cc_final: 0.8552 (tpp-160) REVERT: S 19 SER cc_start: 0.9515 (t) cc_final: 0.9039 (p) REVERT: S 59 THR cc_start: 0.9215 (m) cc_final: 0.8972 (p) REVERT: S 61 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8715 (mm-30) REVERT: S 90 ASP cc_start: 0.8656 (t0) cc_final: 0.8147 (t0) REVERT: T 51 ASP cc_start: 0.8188 (p0) cc_final: 0.7800 (t0) REVERT: T 57 LYS cc_start: 0.9132 (mppt) cc_final: 0.8868 (mmmt) REVERT: T 64 SER cc_start: 0.9234 (m) cc_final: 0.8770 (p) REVERT: T 68 ASP cc_start: 0.8793 (t0) cc_final: 0.8491 (t0) REVERT: T 93 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7710 (tm-30) REVERT: T 105 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8595 (mm-30) outliers start: 26 outliers final: 16 residues processed: 276 average time/residue: 0.1141 time to fit residues: 43.3284 Evaluate side-chains 268 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 2 optimal weight: 0.0060 chunk 102 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 31 HIS ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** S 38 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 = 0.3530 r_free = 0.3530 target = 0.074582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053899 restraints weight = 46046.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.055636 restraints weight = 21082.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.056823 restraints weight = 13514.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.057542 restraints weight = 10398.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.057968 restraints weight = 8952.621| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12896 Z= 0.162 Angle : 0.651 12.979 18594 Z= 0.371 Chirality : 0.036 0.197 2109 Planarity : 0.004 0.031 1401 Dihedral : 29.669 171.950 3950 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.90 % Favored : 96.84 % Rotamer: Outliers : 2.98 % Allowed : 30.70 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.30), residues: 792 helix: 1.44 (0.22), residues: 560 sheet: None (None), residues: 0 loop : -0.37 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 181 TYR 0.030 0.002 TYR P 40 PHE 0.008 0.001 PHE O 25 TRP 0.013 0.003 TRP H 152 HIS 0.009 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00360 (12896) covalent geometry : angle 0.65122 (18594) hydrogen bonds : bond 0.03709 ( 753) hydrogen bonds : angle 3.05472 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8776 (mm) cc_final: 0.8472 (tp) REVERT: H 164 ASN cc_start: 0.9056 (p0) cc_final: 0.8823 (p0) REVERT: M 81 ASP cc_start: 0.8798 (m-30) cc_final: 0.8449 (m-30) REVERT: M 94 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8629 (mm-30) REVERT: M 105 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8419 (mt-10) REVERT: M 106 ASP cc_start: 0.8660 (m-30) cc_final: 0.8374 (m-30) REVERT: N 44 LYS cc_start: 0.9383 (ttpt) cc_final: 0.9029 (ttmt) REVERT: N 74 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8801 (mm-30) REVERT: N 77 LYS cc_start: 0.9003 (mttp) cc_final: 0.8711 (mtmm) REVERT: N 84 MET cc_start: 0.8993 (mmm) cc_final: 0.7993 (mmm) REVERT: N 88 TYR cc_start: 0.8517 (m-80) cc_final: 0.8043 (m-80) REVERT: O 19 SER cc_start: 0.9561 (t) cc_final: 0.9281 (p) REVERT: O 39 TYR cc_start: 0.8834 (m-80) cc_final: 0.8279 (m-80) REVERT: O 84 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8923 (tp-100) REVERT: O 91 GLU cc_start: 0.8698 (pm20) cc_final: 0.8247 (tm-30) REVERT: O 92 GLU cc_start: 0.8965 (tp30) cc_final: 0.8685 (tp30) REVERT: P 68 ASP cc_start: 0.9227 (t70) cc_final: 0.8827 (t0) REVERT: P 71 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8764 (tm-30) REVERT: P 76 GLU cc_start: 0.8461 (tp30) cc_final: 0.8252 (tp30) REVERT: P 125 LYS cc_start: 0.8275 (mttt) cc_final: 0.7695 (tppt) REVERT: Q 50 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8924 (mm-30) REVERT: Q 64 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9177 (mmmm) REVERT: Q 68 GLN cc_start: 0.8757 (tt0) cc_final: 0.8389 (tp40) REVERT: Q 76 GLN cc_start: 0.9019 (pp30) cc_final: 0.8574 (pp30) REVERT: Q 90 MET cc_start: 0.8422 (tpp) cc_final: 0.7317 (tpp) REVERT: Q 94 GLU cc_start: 0.8459 (mm-30) cc_final: 0.7859 (mm-30) REVERT: Q 123 ASP cc_start: 0.9010 (m-30) cc_final: 0.8644 (m-30) REVERT: R 39 ARG cc_start: 0.8798 (mmt90) cc_final: 0.8343 (tpp-160) REVERT: S 19 SER cc_start: 0.9499 (t) cc_final: 0.9033 (p) REVERT: S 59 THR cc_start: 0.9177 (m) cc_final: 0.8937 (p) REVERT: S 61 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8709 (mm-30) REVERT: S 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8145 (t0) REVERT: S 104 GLN cc_start: 0.8786 (mt0) cc_final: 0.8437 (mm110) REVERT: T 51 ASP cc_start: 0.8157 (p0) cc_final: 0.7700 (t0) REVERT: T 57 LYS cc_start: 0.9112 (mppt) cc_final: 0.8822 (mmmt) REVERT: T 64 SER cc_start: 0.9205 (m) cc_final: 0.8715 (p) REVERT: T 68 ASP cc_start: 0.8765 (t0) cc_final: 0.8393 (t0) outliers start: 20 outliers final: 17 residues processed: 275 average time/residue: 0.1181 time to fit residues: 44.9413 Evaluate side-chains 272 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 112 GLN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 75 HIS ** S 38 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 = 0.3513 r_free = 0.3513 target = 0.074075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052743 restraints weight = 46338.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.054425 restraints weight = 22011.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055584 restraints weight = 14385.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.056265 restraints weight = 11208.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.056656 restraints weight = 9756.893| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12896 Z= 0.177 Angle : 0.656 14.982 18594 Z= 0.372 Chirality : 0.036 0.179 2109 Planarity : 0.004 0.032 1401 Dihedral : 29.683 173.094 3950 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 3.73 % Allowed : 30.70 % Favored : 65.57 % 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: 1.37 (0.29), residues: 792 helix: 1.49 (0.22), residues: 559 sheet: None (None), residues: 0 loop : -0.41 (0.40), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 79 TYR 0.027 0.002 TYR N 88 PHE 0.011 0.001 PHE M 67 TRP 0.006 0.002 TRP H 152 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd covalent geometry : bond 0.00395 (12896) covalent geometry : angle 0.65625 (18594) hydrogen bonds : bond 0.03878 ( 753) hydrogen bonds : angle 3.08876 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 260 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 161 LEU cc_start: 0.8893 (mm) cc_final: 0.8583 (tp) REVERT: M 50 GLU cc_start: 0.9206 (tt0) cc_final: 0.8730 (tt0) REVERT: M 81 ASP cc_start: 0.8820 (m-30) cc_final: 0.8480 (m-30) REVERT: M 94 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8659 (mm-30) REVERT: M 97 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8622 (mm-30) REVERT: M 105 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8419 (mt-10) REVERT: M 106 ASP cc_start: 0.8696 (m-30) cc_final: 0.8449 (m-30) REVERT: N 44 LYS cc_start: 0.9362 (ttpt) cc_final: 0.8799 (ttmt) REVERT: N 77 LYS cc_start: 0.9048 (mttp) cc_final: 0.8721 (mtmm) REVERT: N 84 MET cc_start: 0.8911 (mmm) cc_final: 0.7924 (mmm) REVERT: N 88 TYR cc_start: 0.8584 (m-80) cc_final: 0.7848 (m-80) REVERT: N 91 LYS cc_start: 0.9198 (ttpp) cc_final: 0.8998 (ttpp) REVERT: O 19 SER cc_start: 0.9585 (t) cc_final: 0.9303 (p) REVERT: O 36 LYS cc_start: 0.9399 (mmtt) cc_final: 0.8912 (mmmt) REVERT: O 39 TYR cc_start: 0.8882 (m-80) cc_final: 0.8157 (m-80) REVERT: O 84 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8995 (tp-100) REVERT: O 91 GLU cc_start: 0.8695 (pm20) cc_final: 0.8249 (tm-30) REVERT: O 92 GLU cc_start: 0.8927 (tp30) cc_final: 0.8628 (tp30) REVERT: P 68 ASP cc_start: 0.9225 (t70) cc_final: 0.8881 (t0) REVERT: P 71 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8782 (tm-30) REVERT: P 76 GLU cc_start: 0.8326 (tp30) cc_final: 0.8124 (tp30) REVERT: P 125 LYS cc_start: 0.8238 (mttt) cc_final: 0.7675 (tppt) REVERT: Q 50 GLU cc_start: 0.9209 (OUTLIER) cc_final: 0.8923 (mm-30) REVERT: Q 64 LYS cc_start: 0.9489 (mmmm) cc_final: 0.9284 (mmmm) REVERT: Q 68 GLN cc_start: 0.8782 (tt0) cc_final: 0.8355 (tp40) REVERT: Q 76 GLN cc_start: 0.9061 (pp30) cc_final: 0.8602 (pp30) REVERT: Q 90 MET cc_start: 0.8459 (tpp) cc_final: 0.7685 (tpp) REVERT: Q 123 ASP cc_start: 0.9042 (m-30) cc_final: 0.8730 (m-30) REVERT: R 39 ARG cc_start: 0.8826 (mmt90) cc_final: 0.8362 (tpp-160) REVERT: S 19 SER cc_start: 0.9512 (t) cc_final: 0.9039 (p) REVERT: S 59 THR cc_start: 0.9194 (m) cc_final: 0.8945 (p) REVERT: S 61 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8703 (mm-30) REVERT: S 90 ASP cc_start: 0.8677 (t0) cc_final: 0.8176 (t0) REVERT: S 104 GLN cc_start: 0.8855 (mt0) cc_final: 0.8481 (mm110) REVERT: T 35 GLU cc_start: 0.8066 (mp0) cc_final: 0.7834 (mp0) REVERT: T 51 ASP cc_start: 0.8209 (p0) cc_final: 0.7750 (t0) REVERT: T 57 LYS cc_start: 0.9112 (mppt) cc_final: 0.8802 (mmmt) REVERT: T 64 SER cc_start: 0.9255 (m) cc_final: 0.8751 (p) REVERT: T 68 ASP cc_start: 0.8766 (t0) cc_final: 0.8484 (t0) REVERT: T 105 GLU cc_start: 0.8870 (mm-30) cc_final: 0.8221 (mm-30) REVERT: T 108 LYS cc_start: 0.9070 (ptmt) cc_final: 0.8752 (ptpp) outliers start: 25 outliers final: 19 residues processed: 269 average time/residue: 0.1142 time to fit residues: 42.4898 Evaluate side-chains 274 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 254 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 36 LYS Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 76 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN T 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.074215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.052969 restraints weight = 45794.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.054656 restraints weight = 21879.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055805 restraints weight = 14332.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.056486 restraints weight = 11175.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.056858 restraints weight = 9729.572| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12896 Z= 0.178 Angle : 0.668 13.725 18594 Z= 0.377 Chirality : 0.037 0.200 2109 Planarity : 0.004 0.037 1401 Dihedral : 29.671 176.393 3950 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 3.43 % Allowed : 31.59 % Favored : 64.98 % 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: 1.33 (0.30), residues: 792 helix: 1.44 (0.22), residues: 561 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 181 TYR 0.023 0.002 TYR N 88 PHE 0.007 0.001 PHE T 65 TRP 0.008 0.002 TRP H 152 HIS 0.015 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00397 (12896) covalent geometry : angle 0.66796 (18594) hydrogen bonds : bond 0.03901 ( 753) hydrogen bonds : angle 3.13684 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 156 LEU cc_start: 0.8269 (tp) cc_final: 0.8044 (mt) REVERT: H 161 LEU cc_start: 0.8912 (mm) cc_final: 0.8625 (tp) REVERT: H 173 GLU cc_start: 0.9044 (mp0) cc_final: 0.8837 (mp0) REVERT: M 50 GLU cc_start: 0.9223 (tt0) cc_final: 0.8757 (tt0) REVERT: M 81 ASP cc_start: 0.8810 (m-30) cc_final: 0.8512 (m-30) REVERT: M 94 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8662 (mm-30) REVERT: M 105 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8425 (mt-10) REVERT: M 106 ASP cc_start: 0.8710 (m-30) cc_final: 0.8456 (m-30) REVERT: N 44 LYS cc_start: 0.9339 (ttpt) cc_final: 0.8788 (ttmt) REVERT: N 47 SER cc_start: 0.9101 (t) cc_final: 0.8761 (m) REVERT: N 77 LYS cc_start: 0.9033 (mttp) cc_final: 0.8677 (mtmm) REVERT: N 84 MET cc_start: 0.8857 (mmm) cc_final: 0.8239 (mmm) REVERT: N 88 TYR cc_start: 0.8572 (m-80) cc_final: 0.7881 (m-80) REVERT: O 19 SER cc_start: 0.9576 (t) cc_final: 0.9294 (p) REVERT: O 35 ARG cc_start: 0.9209 (ttm-80) cc_final: 0.9001 (ttm-80) REVERT: O 36 LYS cc_start: 0.9341 (mmtt) cc_final: 0.8838 (mmmt) REVERT: O 39 TYR cc_start: 0.8842 (m-80) cc_final: 0.8030 (m-80) REVERT: O 91 GLU cc_start: 0.8691 (pm20) cc_final: 0.8245 (tm-30) REVERT: O 92 GLU cc_start: 0.8916 (tp30) cc_final: 0.8633 (tp30) REVERT: P 68 ASP cc_start: 0.9227 (t70) cc_final: 0.8859 (t0) REVERT: P 71 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8795 (tm-30) REVERT: P 125 LYS cc_start: 0.8267 (mttt) cc_final: 0.7679 (tppt) REVERT: Q 50 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.8912 (mm-30) REVERT: Q 64 LYS cc_start: 0.9495 (mmmm) cc_final: 0.9269 (mmmm) REVERT: Q 68 GLN cc_start: 0.8781 (tt0) cc_final: 0.8364 (tp40) REVERT: Q 76 GLN cc_start: 0.9079 (pp30) cc_final: 0.8611 (pp30) REVERT: Q 90 MET cc_start: 0.8431 (tpp) cc_final: 0.7380 (tpp) REVERT: Q 94 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7827 (mm-30) REVERT: Q 123 ASP cc_start: 0.9082 (m-30) cc_final: 0.8785 (m-30) REVERT: R 39 ARG cc_start: 0.8808 (mmt90) cc_final: 0.8350 (tpp-160) REVERT: R 77 LYS cc_start: 0.9432 (mmmm) cc_final: 0.8936 (mmtp) REVERT: S 19 SER cc_start: 0.9502 (t) cc_final: 0.9017 (p) REVERT: S 59 THR cc_start: 0.9152 (m) cc_final: 0.8910 (p) REVERT: S 61 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8686 (mm-30) REVERT: S 90 ASP cc_start: 0.8670 (t0) cc_final: 0.8167 (t0) REVERT: S 104 GLN cc_start: 0.8850 (mt0) cc_final: 0.8489 (mm110) REVERT: T 51 ASP cc_start: 0.8228 (p0) cc_final: 0.7699 (t70) REVERT: T 57 LYS cc_start: 0.9091 (mppt) cc_final: 0.8757 (mmmt) REVERT: T 64 SER cc_start: 0.9241 (m) cc_final: 0.8785 (p) REVERT: T 68 ASP cc_start: 0.8759 (t0) cc_final: 0.8465 (t0) REVERT: T 105 GLU cc_start: 0.8754 (mm-30) cc_final: 0.7980 (mm-30) REVERT: T 108 LYS cc_start: 0.9026 (ptmt) cc_final: 0.8684 (ptpp) outliers start: 23 outliers final: 18 residues processed: 273 average time/residue: 0.1188 time to fit residues: 44.1452 Evaluate side-chains 271 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 252 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 7.9990 chunk 82 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.073991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.052903 restraints weight = 47526.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.054641 restraints weight = 22480.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.055775 restraints weight = 14623.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056504 restraints weight = 11403.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.056927 restraints weight = 9854.804| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12896 Z= 0.203 Angle : 0.683 14.302 18594 Z= 0.385 Chirality : 0.037 0.181 2109 Planarity : 0.004 0.032 1401 Dihedral : 29.735 177.033 3950 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.29 % Favored : 95.45 % Rotamer: Outliers : 3.13 % Allowed : 33.08 % Favored : 63.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.29), residues: 792 helix: 1.40 (0.22), residues: 557 sheet: None (None), residues: 0 loop : -0.40 (0.39), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 52 TYR 0.025 0.002 TYR N 88 PHE 0.010 0.001 PHE T 65 TRP 0.009 0.002 TRP H 152 HIS 0.015 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00459 (12896) covalent geometry : angle 0.68312 (18594) hydrogen bonds : bond 0.04297 ( 753) hydrogen bonds : angle 3.22533 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 251 time to evaluate : 0.211 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: H 147 GLU cc_start: 0.8924 (pp20) cc_final: 0.8194 (pp20) REVERT: H 148 GLU cc_start: 0.8651 (pp20) cc_final: 0.7927 (pp20) REVERT: H 151 ARG cc_start: 0.9234 (mtt-85) cc_final: 0.8872 (ptt-90) REVERT: M 50 GLU cc_start: 0.9246 (tt0) cc_final: 0.8779 (tt0) REVERT: M 81 ASP cc_start: 0.8780 (m-30) cc_final: 0.8490 (m-30) REVERT: M 105 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8134 (mt-10) REVERT: N 44 LYS cc_start: 0.9311 (ttpt) cc_final: 0.8752 (ttmt) REVERT: N 47 SER cc_start: 0.9193 (t) cc_final: 0.8895 (m) REVERT: N 77 LYS cc_start: 0.9039 (mttp) cc_final: 0.8735 (mtmm) REVERT: N 84 MET cc_start: 0.8875 (mmm) cc_final: 0.8596 (mmm) REVERT: N 88 TYR cc_start: 0.8768 (m-80) cc_final: 0.7891 (m-80) REVERT: O 19 SER cc_start: 0.9588 (t) cc_final: 0.9300 (p) REVERT: O 35 ARG cc_start: 0.9237 (ttm-80) cc_final: 0.9012 (ttm110) REVERT: O 36 LYS cc_start: 0.9365 (mmtt) cc_final: 0.8859 (mmmt) REVERT: O 39 TYR cc_start: 0.8942 (m-80) cc_final: 0.8296 (m-80) REVERT: O 84 GLN cc_start: 0.9323 (tp-100) cc_final: 0.9061 (tm-30) REVERT: O 91 GLU cc_start: 0.8713 (pm20) cc_final: 0.8329 (tm-30) REVERT: O 92 GLU cc_start: 0.8939 (tp30) cc_final: 0.8704 (tp30) REVERT: P 68 ASP cc_start: 0.9253 (t70) cc_final: 0.8875 (t0) REVERT: P 71 GLU cc_start: 0.9238 (tm-30) cc_final: 0.8827 (tm-30) REVERT: P 125 LYS cc_start: 0.8333 (mttt) cc_final: 0.7625 (tppt) REVERT: Q 50 GLU cc_start: 0.9210 (OUTLIER) cc_final: 0.8961 (mm-30) REVERT: Q 68 GLN cc_start: 0.8762 (tt0) cc_final: 0.8364 (tp40) REVERT: Q 76 GLN cc_start: 0.9088 (pp30) cc_final: 0.8611 (pp30) REVERT: Q 90 MET cc_start: 0.8468 (tpp) cc_final: 0.7742 (tpp) REVERT: Q 123 ASP cc_start: 0.9028 (m-30) cc_final: 0.8762 (m-30) REVERT: R 77 LYS cc_start: 0.9438 (mmmm) cc_final: 0.8996 (mmtp) REVERT: S 19 SER cc_start: 0.9512 (t) cc_final: 0.9030 (p) REVERT: S 59 THR cc_start: 0.9232 (m) cc_final: 0.8995 (p) REVERT: S 61 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8691 (mm-30) REVERT: S 90 ASP cc_start: 0.8776 (t0) cc_final: 0.8279 (t0) REVERT: T 35 GLU cc_start: 0.8097 (mp0) cc_final: 0.7875 (mp0) REVERT: T 51 ASP cc_start: 0.8188 (p0) cc_final: 0.7638 (t70) REVERT: T 57 LYS cc_start: 0.9141 (mppt) cc_final: 0.8828 (mmmt) REVERT: T 64 SER cc_start: 0.9260 (m) cc_final: 0.8821 (p) REVERT: T 68 ASP cc_start: 0.8749 (t0) cc_final: 0.8353 (t0) REVERT: T 105 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8131 (mm-30) REVERT: T 108 LYS cc_start: 0.9040 (ptmt) cc_final: 0.8708 (ptpp) outliers start: 21 outliers final: 20 residues processed: 259 average time/residue: 0.1190 time to fit residues: 42.2760 Evaluate side-chains 266 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 70 VAL Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 50 GLU Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 30 THR Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain S residue 40 SER Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 36 SER Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 82 HIS Chi-restraints excluded: chain T residue 88 THR Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.1980 chunk 78 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 98 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN ** O 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 110 ASN T 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.074577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053159 restraints weight = 45969.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.054879 restraints weight = 21876.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.056042 restraints weight = 14296.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.056738 restraints weight = 11135.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.057122 restraints weight = 9683.044| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.5795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12896 Z= 0.171 Angle : 0.687 14.091 18594 Z= 0.383 Chirality : 0.037 0.184 2109 Planarity : 0.004 0.033 1401 Dihedral : 29.690 179.596 3950 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.16 % Favored : 96.59 % Rotamer: Outliers : 3.28 % Allowed : 33.53 % Favored : 63.19 % 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: 1.15 (0.29), residues: 792 helix: 1.28 (0.22), residues: 561 sheet: None (None), residues: 0 loop : -0.39 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 181 TYR 0.023 0.002 TYR N 88 PHE 0.009 0.001 PHE Q 67 TRP 0.008 0.002 TRP H 152 HIS 0.018 0.001 HIS T 82 Details of bonding type rmsd covalent geometry : bond 0.00383 (12896) covalent geometry : angle 0.68718 (18594) hydrogen bonds : bond 0.03914 ( 753) hydrogen bonds : angle 3.19969 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.45 seconds wall clock time: 37 minutes 12.21 seconds (2232.21 seconds total)