Starting phenix.real_space_refine on Wed Aug 5 23:45:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gfm_51313/08_2026/9gfm_51313.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gfm_51313/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9gfm_51313/08_2026/9gfm_51313.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gfm_51313/08_2026/9gfm_51313.map" model { file = "/net/cci-nas-00/data/ceres_data/9gfm_51313/08_2026/9gfm_51313.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gfm_51313/08_2026/9gfm_51313.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.046 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-2.2rc3-6140/lib/python3.11/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: 2.42, per 1000 atoms: 0.20 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: 0.83 Conformation dependent library (CDL) restraints added in 394.1 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: 1.72 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: 2.24 Time building geometry restraints manager: 1.18 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=" C4 DC K 46 " pdb=" N4 DC K 46 " ideal model delta sigma weight residual 1.335 1.294 0.041 9.00e-03 1.23e+04 2.07e+01 bond pdb=" C5' DT L -58 " pdb=" C4' DT L -58 " ideal model delta sigma weight residual 1.512 1.543 -0.031 7.00e-03 2.04e+04 2.01e+01 bond pdb=" C4 DC L 14 " pdb=" N4 DC L 14 " ideal model delta sigma weight residual 1.335 1.295 0.040 9.00e-03 1.23e+04 1.98e+01 bond pdb=" C4 DC L -40 " pdb=" N4 DC L -40 " ideal model delta sigma weight residual 1.335 1.295 0.040 9.00e-03 1.23e+04 1.95e+01 ... (remaining 12891 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.53: 17406 3.53 - 7.06: 1155 7.06 - 10.58: 29 10.58 - 14.11: 3 14.11 - 17.64: 1 Bond angle restraints: 18594 Sorted by residual: angle pdb=" N6 DA L -47 " pdb=" C6 DA L -47 " pdb=" N1 DA L -47 " ideal model delta sigma weight residual 118.60 111.07 7.53 6.00e-01 2.78e+00 1.58e+02 angle pdb=" N6 DA L 28 " pdb=" C6 DA L 28 " pdb=" N1 DA L 28 " ideal model delta sigma weight residual 118.60 111.90 6.70 6.00e-01 2.78e+00 1.25e+02 angle pdb=" O5' DG L -33 " pdb=" C5' DG L -33 " pdb=" C4' DG L -33 " ideal model delta sigma weight residual 109.40 118.02 -8.62 8.00e-01 1.56e+00 1.16e+02 angle pdb=" N6 DA K 48 " pdb=" C6 DA K 48 " pdb=" N1 DA K 48 " ideal model delta sigma weight residual 118.60 112.30 6.30 6.00e-01 2.78e+00 1.10e+02 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 ... (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 - 0.098: 1601 0.098 - 0.195: 451 0.195 - 0.293: 46 0.293 - 0.390: 8 0.390 - 0.488: 3 Chirality restraints: 2109 Sorted by residual: chirality pdb=" C3' DC L 20 " pdb=" C4' DC L 20 " pdb=" O3' DC L 20 " pdb=" C2' DC L 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.24 -0.49 2.00e-01 2.50e+01 5.96e+00 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 ... (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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.650 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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= 1.225 Angle : 1.893 17.640 18594 Z= 1.889 Chirality : 0.088 0.488 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/Z covalent geometry : bond 0.01281 / 1.22 (12896) covalent geometry : angle 1.89278 / 1.89 (18594) hydrogen bonds : bond 0.11870 / 12.29 ( 753) hydrogen bonds : angle 6.45087 / 7.52 ( 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 : 0.270 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: N 80 THR cc_start: 0.9183 (m) cc_final: 0.8950 (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: 0.8527 (mtm-85) REVERT: O 50 TYR cc_start: 0.9215 (t80) cc_final: 0.8965 (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 125 LYS cc_start: 0.8710 (mttt) cc_final: 0.8374 (tppt) REVERT: Q 70 LEU cc_start: 0.9245 (tp) cc_final: 0.8995 (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: 0.9005 (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: 0.8944 (mp) outliers start: 8 outliers final: 2 residues processed: 377 average time/residue: 0.1309 time to fit residues: 66.9118 Evaluate side-chains 282 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 280 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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: 10.0000 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 164 ASN ** P 84 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 = 0.3548 r_free = 0.3548 target = 0.073344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.052491 restraints weight = 46319.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.054121 restraints weight = 22565.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.055231 restraints weight = 15002.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.055939 restraints weight = 11810.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.056337 restraints weight = 10280.060| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 12896 Z= 0.215 Angle : 0.946 9.389 18594 Z= 0.529 Chirality : 0.062 0.276 2109 Planarity : 0.006 0.045 1401 Dihedral : 30.418 174.826 3952 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.38 % Allowed : 2.53 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 19.08 % 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: 0.17 (0.28), residues: 792 helix: 0.49 (0.21), residues: 563 sheet: None (None), residues: 0 loop : -0.59 (0.39), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 134 TYR 0.031 0.003 TYR Q 54 PHE 0.015 0.002 PHE M 67 TRP 0.024 0.005 TRP H 152 HIS 0.006 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.22 (12896) covalent geometry : angle 0.94554 / 0.53 (18594) hydrogen bonds : bond 0.06659 / 5.43 ( 753) hydrogen bonds : angle 3.70415 / 4.16 ( 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 329 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 306 time to evaluate : 0.311 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 153 LEU cc_start: 0.8425 (mt) cc_final: 0.8052 (mp) REVERT: H 180 GLN cc_start: 0.9487 (mt0) cc_final: 0.9092 (mt0) REVERT: M 54 TYR cc_start: 0.9267 (m-10) cc_final: 0.9006 (m-10) REVERT: M 93 GLN cc_start: 0.8933 (tt0) cc_final: 0.8596 (tp40) REVERT: M 108 ASN cc_start: 0.9370 (t0) cc_final: 0.8926 (m-40) REVERT: M 122 LYS cc_start: 0.9020 (ttpt) cc_final: 0.8619 (ttpp) REVERT: N 44 LYS cc_start: 0.9443 (ttpt) cc_final: 0.8906 (ttmm) REVERT: N 80 THR cc_start: 0.9350 (m) cc_final: 0.9045 (p) REVERT: N 84 MET cc_start: 0.8901 (mmm) cc_final: 0.8206 (mmm) REVERT: N 88 TYR cc_start: 0.8691 (m-80) cc_final: 0.8439 (m-80) REVERT: N 98 TYR cc_start: 0.9405 (m-10) cc_final: 0.8896 (m-80) REVERT: O 13 LYS cc_start: 0.8017 (ptmm) cc_final: 0.7735 (tppt) REVERT: O 84 GLN cc_start: 0.9330 (tp40) cc_final: 0.9104 (tp40) REVERT: O 90 ASP cc_start: 0.7702 (t70) cc_final: 0.7209 (t0) REVERT: O 91 GLU cc_start: 0.8695 (pm20) cc_final: 0.8304 (tm-30) REVERT: O 95 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.8999 (ttmm) REVERT: P 68 ASP cc_start: 0.9249 (t70) cc_final: 0.8777 (t0) REVERT: P 71 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8779 (tm-30) REVERT: P 93 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8371 (pt0) REVERT: P 125 LYS cc_start: 0.8423 (mttt) cc_final: 0.7983 (tppt) REVERT: Q 77 ASP cc_start: 0.7954 (m-30) cc_final: 0.7721 (m-30) REVERT: Q 107 THR cc_start: 0.9441 (m) cc_final: 0.9113 (p) REVERT: Q 123 ASP cc_start: 0.8932 (m-30) cc_final: 0.7851 (m-30) REVERT: R 84 MET cc_start: 0.8849 (mmm) cc_final: 0.8429 (mmp) REVERT: R 92 ARG cc_start: 0.9015 (tmm-80) cc_final: 0.8550 (tmm-80) REVERT: S 39 TYR cc_start: 0.8767 (m-80) cc_final: 0.8314 (m-80) REVERT: S 56 GLU cc_start: 0.8755 (tt0) cc_final: 0.8375 (tt0) REVERT: S 59 THR cc_start: 0.9211 (m) cc_final: 0.8877 (p) REVERT: S 61 GLU cc_start: 0.8892 (tp30) cc_final: 0.8600 (tp30) REVERT: S 89 ASN cc_start: 0.9454 (m-40) cc_final: 0.8940 (m-40) REVERT: S 90 ASP cc_start: 0.8787 (t0) cc_final: 0.8184 (t0) REVERT: S 92 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7883 (mt-10) REVERT: S 108 LEU cc_start: 0.9190 (tp) cc_final: 0.8920 (pt) REVERT: S 110 ASN cc_start: 0.8999 (t0) cc_final: 0.8652 (t0) REVERT: T 34 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8741 (mmmm) REVERT: T 47 GLN cc_start: 0.8993 (tp40) cc_final: 0.8735 (tm-30) REVERT: T 51 ASP cc_start: 0.8261 (p0) cc_final: 0.7802 (t0) REVERT: T 57 LYS cc_start: 0.9206 (mppt) cc_final: 0.8926 (mmmt) REVERT: T 64 SER cc_start: 0.9211 (m) cc_final: 0.8380 (p) REVERT: T 68 ASP cc_start: 0.8823 (t0) cc_final: 0.8305 (t0) REVERT: T 108 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8617 (ptpp) outliers start: 23 outliers final: 11 residues processed: 314 average time/residue: 0.1260 time to fit residues: 53.6625 Evaluate side-chains 278 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 265 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 79 LYS Chi-restraints excluded: chain M residue 86 SER Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 95 LYS Chi-restraints excluded: chain O residue 100 VAL Chi-restraints excluded: chain P residue 54 ILE 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 91 SER 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: 0.9990 chunk 102 optimal weight: 0.8980 chunk 94 optimal weight: 0.4980 chunk 7 optimal weight: 20.0000 chunk 39 optimal weight: 0.6980 chunk 30 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 47 GLN ** P 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.073449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.052190 restraints weight = 46981.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.053867 restraints weight = 22946.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.054992 restraints weight = 15266.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.055685 restraints weight = 12037.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.056088 restraints weight = 10522.221| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 12896 Z= 0.189 Angle : 0.813 8.945 18594 Z= 0.468 Chirality : 0.053 0.273 2109 Planarity : 0.006 0.068 1401 Dihedral : 30.453 171.418 3950 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 4.32 % Allowed : 22.95 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.28), residues: 792 helix: 0.68 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 92 TYR 0.029 0.003 TYR P 40 PHE 0.013 0.002 PHE Q 78 TRP 0.015 0.004 TRP H 152 HIS 0.008 0.002 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (12896) covalent geometry : angle 0.81302 / 0.47 (18594) hydrogen bonds : bond 0.05759 / 4.62 ( 753) hydrogen bonds : angle 3.46429 / 3.91 ( 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 310 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.319 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 151 ARG cc_start: 0.9134 (mtt-85) cc_final: 0.8727 (ptt90) REVERT: H 158 LYS cc_start: 0.8970 (ptpp) cc_final: 0.8486 (ptpp) REVERT: H 180 GLN cc_start: 0.9371 (mt0) cc_final: 0.9026 (mt0) REVERT: M 97 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8734 (mt-10) REVERT: M 105 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8315 (mt-10) REVERT: M 108 ASN cc_start: 0.9430 (t0) cc_final: 0.9041 (m-40) REVERT: M 122 LYS cc_start: 0.9185 (ttpt) cc_final: 0.8778 (ttpp) REVERT: N 80 THR cc_start: 0.9344 (m) cc_final: 0.9134 (p) REVERT: N 84 MET cc_start: 0.8798 (mmm) cc_final: 0.8086 (mmm) REVERT: N 88 TYR cc_start: 0.8816 (m-80) cc_final: 0.8524 (m-80) REVERT: N 98 TYR cc_start: 0.9369 (m-10) cc_final: 0.8840 (m-80) REVERT: O 75 LYS cc_start: 0.9376 (mttm) cc_final: 0.9105 (mmmm) REVERT: O 90 ASP cc_start: 0.7694 (t70) cc_final: 0.7198 (t0) REVERT: O 91 GLU cc_start: 0.8717 (pm20) cc_final: 0.8332 (tm-30) REVERT: O 95 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.8987 (ttmm) REVERT: O 104 GLN cc_start: 0.8468 (pm20) cc_final: 0.8162 (pm20) REVERT: P 68 ASP cc_start: 0.9263 (t70) cc_final: 0.8783 (t0) REVERT: P 71 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8382 (tm-30) REVERT: P 84 ASN cc_start: 0.9504 (m-40) cc_final: 0.9092 (m-40) REVERT: P 93 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: P 106 LEU cc_start: 0.9669 (tp) cc_final: 0.9285 (tp) REVERT: P 125 LYS cc_start: 0.8394 (mttt) cc_final: 0.7967 (tppt) REVERT: Q 50 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8779 (mm-30) REVERT: Q 68 GLN cc_start: 0.8699 (tt0) cc_final: 0.8108 (tm-30) REVERT: Q 90 MET cc_start: 0.8653 (ttm) cc_final: 0.8435 (tpp) REVERT: Q 123 ASP cc_start: 0.8989 (m-30) cc_final: 0.7964 (m-30) REVERT: R 36 ARG cc_start: 0.8360 (mtm-85) cc_final: 0.8022 (mtm-85) REVERT: R 39 ARG cc_start: 0.8887 (mmt90) cc_final: 0.8405 (tpp-160) REVERT: R 84 MET cc_start: 0.8756 (mmm) cc_final: 0.8340 (mmp) REVERT: R 92 ARG cc_start: 0.9026 (tmm-80) cc_final: 0.8463 (tmm-80) REVERT: S 56 GLU cc_start: 0.8718 (tt0) cc_final: 0.8351 (tt0) REVERT: S 59 THR cc_start: 0.9189 (m) cc_final: 0.8975 (p) REVERT: S 61 GLU cc_start: 0.8998 (tp30) cc_final: 0.8727 (mm-30) REVERT: S 90 ASP cc_start: 0.8696 (t0) cc_final: 0.8099 (t0) REVERT: S 108 LEU cc_start: 0.9243 (tp) cc_final: 0.9035 (pt) REVERT: T 34 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8705 (mmmm) REVERT: T 35 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7582 (tp30) REVERT: T 47 GLN cc_start: 0.9000 (tp40) cc_final: 0.8758 (tm-30) REVERT: T 51 ASP cc_start: 0.8256 (p0) cc_final: 0.7799 (t0) REVERT: T 57 LYS cc_start: 0.9210 (mppt) cc_final: 0.8919 (mmmt) REVERT: T 64 SER cc_start: 0.9238 (m) cc_final: 0.8408 (p) REVERT: T 68 ASP cc_start: 0.8752 (t0) cc_final: 0.8266 (t0) REVERT: T 80 LEU cc_start: 0.9106 (tt) cc_final: 0.8748 (tt) REVERT: T 108 LYS cc_start: 0.8936 (ptmt) cc_final: 0.8721 (ptmt) outliers start: 29 outliers final: 15 residues processed: 288 average time/residue: 0.1257 time to fit residues: 49.8923 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 : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 95 LYS 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 R residue 46 ILE Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 91 SER Chi-restraints excluded: chain T residue 106 LEU 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: 0.9980 chunk 100 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 0.6980 chunk 94 optimal weight: 0.0770 chunk 56 optimal weight: 0.0970 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 38 ASN R 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.054850 restraints weight = 46534.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.056574 restraints weight = 21974.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.057707 restraints weight = 14292.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.058446 restraints weight = 11133.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.058858 restraints weight = 9619.806| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12896 Z= 0.165 Angle : 0.760 8.543 18594 Z= 0.440 Chirality : 0.051 0.269 2109 Planarity : 0.005 0.049 1401 Dihedral : 30.367 171.480 3950 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 5.07 % Allowed : 22.21 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.28), residues: 792 helix: 0.73 (0.21), residues: 568 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 181 TYR 0.033 0.003 TYR S 39 PHE 0.012 0.001 PHE Q 67 TRP 0.006 0.002 TRP H 152 HIS 0.009 0.001 HIS R 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.17 (12896) covalent geometry : angle 0.76047 / 0.44 (18594) hydrogen bonds : bond 0.05132 / 4.14 ( 753) hydrogen bonds : angle 3.33956 / 3.67 ( 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 307 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 273 time to evaluate : 0.317 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: 0.9122 (mtt-85) cc_final: 0.8780 (ptt90) REVERT: M 48 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8827 (tt) REVERT: M 105 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8463 (mt-10) REVERT: M 108 ASN cc_start: 0.9395 (t0) cc_final: 0.9139 (m-40) REVERT: M 122 LYS cc_start: 0.9199 (ttpt) cc_final: 0.8816 (ttpp) REVERT: N 44 LYS cc_start: 0.9400 (ttpt) cc_final: 0.9037 (ttmm) REVERT: N 80 THR cc_start: 0.9361 (m) cc_final: 0.9155 (p) REVERT: N 84 MET cc_start: 0.8826 (mmm) cc_final: 0.8180 (mmm) REVERT: N 88 TYR cc_start: 0.8805 (m-80) cc_final: 0.8540 (m-80) REVERT: N 98 TYR cc_start: 0.9346 (m-10) cc_final: 0.8806 (m-80) REVERT: O 75 LYS cc_start: 0.9356 (mttm) cc_final: 0.9096 (mmmm) REVERT: O 90 ASP cc_start: 0.7718 (t70) cc_final: 0.7371 (t0) REVERT: O 91 GLU cc_start: 0.8682 (pm20) cc_final: 0.8406 (tm-30) REVERT: O 104 GLN cc_start: 0.8624 (pm20) cc_final: 0.8289 (pm20) REVERT: P 48 VAL cc_start: 0.9608 (t) cc_final: 0.9285 (p) REVERT: P 68 ASP cc_start: 0.9217 (t70) cc_final: 0.8767 (t0) REVERT: P 71 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8726 (tm-30) REVERT: P 84 ASN cc_start: 0.9488 (m-40) cc_final: 0.9129 (m-40) REVERT: P 86 ARG cc_start: 0.8881 (mmm160) cc_final: 0.8327 (mtp85) REVERT: P 125 LYS cc_start: 0.8377 (mttt) cc_final: 0.7909 (tppt) REVERT: Q 50 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8799 (mm-30) REVERT: Q 68 GLN cc_start: 0.8692 (tt0) cc_final: 0.7880 (tm-30) REVERT: Q 110 CYS cc_start: 0.8605 (m) cc_final: 0.8263 (m) REVERT: Q 123 ASP cc_start: 0.8894 (m-30) cc_final: 0.7977 (m-30) REVERT: R 36 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8159 (mtm-85) REVERT: R 37 LEU cc_start: 0.8734 (mt) cc_final: 0.8501 (tt) REVERT: R 39 ARG cc_start: 0.8888 (mmt90) cc_final: 0.8423 (tpp-160) REVERT: R 85 ASP cc_start: 0.8874 (m-30) cc_final: 0.8231 (m-30) REVERT: S 59 THR cc_start: 0.9154 (m) cc_final: 0.8940 (p) REVERT: S 61 GLU cc_start: 0.8953 (tp30) cc_final: 0.8747 (mm-30) REVERT: S 90 ASP cc_start: 0.8630 (t0) cc_final: 0.8105 (t0) REVERT: S 108 LEU cc_start: 0.9238 (tp) cc_final: 0.9021 (pt) REVERT: T 51 ASP cc_start: 0.8171 (p0) cc_final: 0.7679 (t0) REVERT: T 57 LYS cc_start: 0.9153 (mppt) cc_final: 0.8905 (mmmt) REVERT: T 64 SER cc_start: 0.9292 (m) cc_final: 0.8466 (p) REVERT: T 68 ASP cc_start: 0.8692 (t0) cc_final: 0.8281 (t0) REVERT: T 93 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7884 (tp30) outliers start: 34 outliers final: 21 residues processed: 283 average time/residue: 0.1220 time to fit residues: 48.0403 Evaluate side-chains 277 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain M residue 124 ILE Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain S residue 62 ILE Chi-restraints excluded: chain S residue 79 ILE Chi-restraints excluded: chain S residue 83 LEU Chi-restraints excluded: chain T residue 39 ILE Chi-restraints excluded: chain T residue 54 ILE Chi-restraints excluded: chain T residue 61 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 102 LEU Chi-restraints excluded: chain T residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.074518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.054621 restraints weight = 46803.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.056301 restraints weight = 21992.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.057442 restraints weight = 14328.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.058154 restraints weight = 11148.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058575 restraints weight = 9657.291| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12896 Z= 0.168 Angle : 0.737 11.759 18594 Z= 0.425 Chirality : 0.048 0.271 2109 Planarity : 0.004 0.034 1401 Dihedral : 30.280 171.386 3950 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.41 % Favored : 96.34 % Rotamer: Outliers : 4.02 % Allowed : 24.89 % Favored : 71.09 % 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: 0.55 (0.28), residues: 792 helix: 0.88 (0.21), residues: 567 sheet: None (None), residues: 0 loop : -0.78 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 181 TYR 0.022 0.002 TYR T 83 PHE 0.016 0.001 PHE M 67 TRP 0.004 0.001 TRP H 152 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (12896) covalent geometry : angle 0.73709 / 0.43 (18594) hydrogen bonds : bond 0.05019 / 4.04 ( 753) hydrogen bonds : angle 3.27470 / 3.59 ( 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 293 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 266 time to evaluate : 0.333 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: 0.9142 (mtt-85) cc_final: 0.8831 (ptt90) REVERT: H 166 ASP cc_start: 0.8865 (t0) cc_final: 0.8496 (t0) REVERT: H 167 LEU cc_start: 0.7989 (mp) cc_final: 0.7525 (mp) REVERT: H 173 GLU cc_start: 0.9028 (mp0) cc_final: 0.8634 (mp0) REVERT: M 105 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8379 (mt-10) REVERT: M 122 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8868 (ttpp) REVERT: N 44 LYS cc_start: 0.9397 (ttpt) cc_final: 0.8881 (ttmm) REVERT: N 80 THR cc_start: 0.9360 (m) cc_final: 0.9158 (p) REVERT: N 84 MET cc_start: 0.8836 (mmm) cc_final: 0.8190 (mmm) REVERT: N 88 TYR cc_start: 0.8886 (m-10) cc_final: 0.8616 (m-80) REVERT: N 98 TYR cc_start: 0.9383 (m-10) cc_final: 0.8899 (m-80) REVERT: O 75 LYS cc_start: 0.9344 (mttm) cc_final: 0.9094 (mmmm) REVERT: O 90 ASP cc_start: 0.7699 (t70) cc_final: 0.7207 (t70) REVERT: O 91 GLU cc_start: 0.8679 (pm20) cc_final: 0.8338 (tm-30) REVERT: O 92 GLU cc_start: 0.9014 (tp30) cc_final: 0.8668 (tp30) REVERT: O 104 GLN cc_start: 0.8635 (pm20) cc_final: 0.8306 (pm20) REVERT: P 48 VAL cc_start: 0.9575 (t) cc_final: 0.9253 (p) REVERT: P 59 MET cc_start: 0.9132 (tpp) cc_final: 0.8734 (tpp) REVERT: P 68 ASP cc_start: 0.9215 (t70) cc_final: 0.8751 (t0) REVERT: P 71 GLU cc_start: 0.9086 (tm-30) cc_final: 0.8747 (tm-30) REVERT: P 84 ASN cc_start: 0.9478 (m-40) cc_final: 0.9048 (m110) REVERT: P 86 ARG cc_start: 0.8958 (mmm160) cc_final: 0.8684 (mmm-85) REVERT: P 125 LYS cc_start: 0.8385 (mttt) cc_final: 0.7920 (tppt) REVERT: Q 50 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8808 (mm-30) REVERT: Q 68 GLN cc_start: 0.8688 (tt0) cc_final: 0.7845 (tm-30) REVERT: Q 79 LYS cc_start: 0.8582 (tttp) cc_final: 0.8245 (tptp) REVERT: Q 110 CYS cc_start: 0.8871 (m) cc_final: 0.8588 (m) REVERT: Q 123 ASP cc_start: 0.8968 (m-30) cc_final: 0.8205 (m-30) REVERT: R 36 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8060 (mtm-85) REVERT: R 37 LEU cc_start: 0.8847 (mt) cc_final: 0.8541 (tt) REVERT: R 39 ARG cc_start: 0.8908 (mmt90) cc_final: 0.8468 (tpp-160) REVERT: S 19 SER cc_start: 0.9538 (t) cc_final: 0.9095 (p) REVERT: S 41 GLU cc_start: 0.8586 (pm20) cc_final: 0.8378 (pm20) REVERT: S 59 THR cc_start: 0.9290 (m) cc_final: 0.9076 (p) REVERT: S 61 GLU cc_start: 0.8981 (tp30) cc_final: 0.8730 (mm-30) REVERT: S 90 ASP cc_start: 0.8714 (t0) cc_final: 0.8138 (t0) REVERT: S 108 LEU cc_start: 0.9211 (tp) cc_final: 0.8944 (pp) REVERT: T 51 ASP cc_start: 0.8160 (p0) cc_final: 0.7650 (t0) REVERT: T 57 LYS cc_start: 0.9136 (mppt) cc_final: 0.8894 (mmmt) REVERT: T 64 SER cc_start: 0.9274 (m) cc_final: 0.8473 (p) REVERT: T 68 ASP cc_start: 0.8674 (t0) cc_final: 0.8295 (t0) REVERT: T 79 ARG cc_start: 0.8748 (ttp-110) cc_final: 0.7712 (mtm-85) REVERT: T 105 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8385 (mm-30) REVERT: T 108 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8629 (ptpp) outliers start: 27 outliers final: 17 residues processed: 271 average time/residue: 0.1179 time to fit residues: 45.0775 Evaluate side-chains 271 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 86 SER 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 61 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 108 LYS 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: 0.9990 chunk 69 optimal weight: 0.0870 chunk 95 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 18 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3526 r_free = 0.3526 target = 0.073550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.052384 restraints weight = 47168.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.054058 restraints weight = 22017.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.055208 restraints weight = 14405.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055905 restraints weight = 11265.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.056307 restraints weight = 9823.917| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12896 Z= 0.164 Angle : 0.717 12.713 18594 Z= 0.415 Chirality : 0.047 0.273 2109 Planarity : 0.004 0.033 1401 Dihedral : 30.240 171.545 3950 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.16 % Favored : 96.59 % Rotamer: Outliers : 4.47 % Allowed : 25.19 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.29), residues: 792 helix: 0.96 (0.21), residues: 570 sheet: None (None), residues: 0 loop : -0.75 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 181 TYR 0.034 0.002 TYR P 40 PHE 0.015 0.001 PHE M 67 TRP 0.004 0.001 TRP H 152 HIS 0.007 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.16 (12896) covalent geometry : angle 0.71689 / 0.41 (18594) hydrogen bonds : bond 0.04702 / 3.82 ( 753) hydrogen bonds : angle 3.19605 / 3.50 ( 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 294 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.350 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 148 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8040 (tm-30) REVERT: H 151 ARG cc_start: 0.9163 (mtt-85) cc_final: 0.8811 (ptt90) REVERT: H 173 GLU cc_start: 0.9067 (mp0) cc_final: 0.8678 (mp0) REVERT: M 73 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8218 (mm-30) REVERT: M 105 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8501 (mt-10) REVERT: M 108 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8677 (m-40) REVERT: M 122 LYS cc_start: 0.9205 (ttpt) cc_final: 0.8820 (ttpp) REVERT: N 22 LEU cc_start: 0.6747 (OUTLIER) cc_final: 0.6492 (mt) REVERT: N 44 LYS cc_start: 0.9375 (ttpt) cc_final: 0.8817 (ttmm) REVERT: N 80 THR cc_start: 0.9331 (m) cc_final: 0.9117 (p) REVERT: N 84 MET cc_start: 0.8844 (mmm) cc_final: 0.8133 (mmm) REVERT: N 88 TYR cc_start: 0.8873 (m-10) cc_final: 0.8608 (m-80) REVERT: N 98 TYR cc_start: 0.9358 (m-10) cc_final: 0.8847 (m-80) REVERT: O 36 LYS cc_start: 0.9518 (mmmt) cc_final: 0.9313 (mtmt) REVERT: O 39 TYR cc_start: 0.8950 (m-80) cc_final: 0.8597 (m-80) REVERT: O 75 LYS cc_start: 0.9331 (mttm) cc_final: 0.9110 (mmmm) REVERT: O 90 ASP cc_start: 0.7583 (t70) cc_final: 0.7060 (t70) REVERT: O 91 GLU cc_start: 0.8737 (pm20) cc_final: 0.8320 (tm-30) REVERT: O 92 GLU cc_start: 0.9070 (tp30) cc_final: 0.8809 (tp30) REVERT: O 104 GLN cc_start: 0.8645 (pm20) cc_final: 0.8229 (pm20) REVERT: P 48 VAL cc_start: 0.9569 (t) cc_final: 0.9252 (p) REVERT: P 59 MET cc_start: 0.9162 (tpp) cc_final: 0.8900 (tpp) REVERT: P 68 ASP cc_start: 0.9193 (t70) cc_final: 0.8779 (t0) REVERT: P 71 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8752 (tm-30) REVERT: P 84 ASN cc_start: 0.9464 (m-40) cc_final: 0.9032 (m110) REVERT: P 86 ARG cc_start: 0.8989 (mmm160) cc_final: 0.8426 (mtp85) REVERT: P 93 GLU cc_start: 0.8607 (pt0) cc_final: 0.8374 (pm20) REVERT: P 125 LYS cc_start: 0.8412 (mttt) cc_final: 0.7969 (tppt) REVERT: Q 50 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8844 (mm-30) REVERT: Q 68 GLN cc_start: 0.8690 (tt0) cc_final: 0.7822 (tm-30) REVERT: Q 79 LYS cc_start: 0.8578 (tttp) cc_final: 0.8304 (tptp) REVERT: Q 123 ASP cc_start: 0.9073 (m-30) cc_final: 0.8175 (m-30) REVERT: R 37 LEU cc_start: 0.8744 (mt) cc_final: 0.8474 (tt) REVERT: R 39 ARG cc_start: 0.8844 (mmt90) cc_final: 0.8359 (tpp-160) REVERT: S 19 SER cc_start: 0.9542 (t) cc_final: 0.9091 (p) REVERT: S 41 GLU cc_start: 0.8721 (pm20) cc_final: 0.8501 (pm20) REVERT: S 59 THR cc_start: 0.9252 (m) cc_final: 0.9014 (p) REVERT: S 61 GLU cc_start: 0.9029 (tp30) cc_final: 0.8768 (mm-30) REVERT: S 90 ASP cc_start: 0.8625 (t0) cc_final: 0.7493 (t0) REVERT: S 110 ASN cc_start: 0.9087 (t0) cc_final: 0.8849 (t0) REVERT: T 51 ASP cc_start: 0.8216 (p0) cc_final: 0.7717 (t0) REVERT: T 57 LYS cc_start: 0.9089 (mppt) cc_final: 0.8818 (mmmt) REVERT: T 64 SER cc_start: 0.9222 (m) cc_final: 0.8417 (p) REVERT: T 68 ASP cc_start: 0.8789 (t0) cc_final: 0.8383 (t0) REVERT: T 79 ARG cc_start: 0.8668 (ttp-110) cc_final: 0.8370 (ttp80) REVERT: T 105 GLU cc_start: 0.8937 (mm-30) cc_final: 0.7915 (mm-30) REVERT: T 108 LYS cc_start: 0.8911 (ptmt) cc_final: 0.8604 (ptpp) outliers start: 30 outliers final: 20 residues processed: 274 average time/residue: 0.1089 time to fit residues: 42.3282 Evaluate side-chains 277 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 255 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain M residue 108 ASN Chi-restraints excluded: chain M residue 112 ILE Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 114 VAL Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE 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 61 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: 8.9990 chunk 49 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.073924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.052443 restraints weight = 47303.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054122 restraints weight = 22366.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055287 restraints weight = 14708.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.056007 restraints weight = 11524.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.056436 restraints weight = 10030.483| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12896 Z= 0.165 Angle : 0.721 13.244 18594 Z= 0.417 Chirality : 0.047 0.268 2109 Planarity : 0.004 0.046 1401 Dihedral : 30.233 171.650 3950 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.90 % Favored : 96.84 % Rotamer: Outliers : 3.73 % Allowed : 27.12 % Favored : 69.15 % 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: 0.77 (0.29), residues: 792 helix: 0.99 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.59 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 36 TYR 0.028 0.002 TYR P 40 PHE 0.015 0.001 PHE M 67 TRP 0.006 0.001 TRP H 152 HIS 0.006 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (12896) covalent geometry : angle 0.72057 / 0.42 (18594) hydrogen bonds : bond 0.04633 / 3.76 ( 753) hydrogen bonds : angle 3.20573 / 3.48 ( 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: 25 poor density : 265 time to evaluate : 0.332 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: 0.8632 (tm-30) cc_final: 0.8100 (tm-30) REVERT: H 151 ARG cc_start: 0.9143 (mtt-85) cc_final: 0.8790 (ptt90) REVERT: H 161 LEU cc_start: 0.8843 (tp) cc_final: 0.8443 (tp) REVERT: H 173 GLU cc_start: 0.9063 (mp0) cc_final: 0.8734 (mp0) REVERT: M 73 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8210 (mm-30) REVERT: M 105 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8471 (mt-10) REVERT: M 122 LYS cc_start: 0.9209 (ttpt) cc_final: 0.8857 (ttpp) REVERT: N 22 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6505 (mt) REVERT: N 44 LYS cc_start: 0.9357 (ttpt) cc_final: 0.8943 (ttmt) REVERT: N 80 THR cc_start: 0.9326 (m) cc_final: 0.9103 (p) REVERT: N 84 MET cc_start: 0.8832 (mmm) cc_final: 0.8156 (mmm) REVERT: N 88 TYR cc_start: 0.8883 (m-10) cc_final: 0.8602 (m-80) REVERT: N 98 TYR cc_start: 0.9343 (m-10) cc_final: 0.8870 (m-80) REVERT: O 39 TYR cc_start: 0.8950 (m-80) cc_final: 0.8496 (m-80) REVERT: O 75 LYS cc_start: 0.9325 (mttm) cc_final: 0.9090 (mmmm) REVERT: O 81 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8794 (tpt170) REVERT: O 90 ASP cc_start: 0.7603 (t70) cc_final: 0.7050 (t70) REVERT: O 91 GLU cc_start: 0.8758 (pm20) cc_final: 0.8345 (tm-30) REVERT: O 92 GLU cc_start: 0.9040 (tp30) cc_final: 0.8808 (tp30) REVERT: O 104 GLN cc_start: 0.8646 (pm20) cc_final: 0.8246 (pm20) REVERT: P 48 VAL cc_start: 0.9565 (t) cc_final: 0.9258 (p) REVERT: P 59 MET cc_start: 0.9153 (tpp) cc_final: 0.8897 (tpp) REVERT: P 68 ASP cc_start: 0.9190 (t70) cc_final: 0.8775 (t0) REVERT: P 71 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8755 (tm-30) REVERT: P 84 ASN cc_start: 0.9464 (m-40) cc_final: 0.9023 (m110) REVERT: P 125 LYS cc_start: 0.8409 (mttt) cc_final: 0.7898 (tppt) REVERT: Q 50 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8857 (mm-30) REVERT: Q 68 GLN cc_start: 0.8682 (tt0) cc_final: 0.8191 (tp40) REVERT: Q 79 LYS cc_start: 0.8575 (tttp) cc_final: 0.8296 (tptp) REVERT: Q 123 ASP cc_start: 0.9084 (m-30) cc_final: 0.8309 (m-30) REVERT: R 37 LEU cc_start: 0.8732 (mt) cc_final: 0.8524 (tt) REVERT: R 39 ARG cc_start: 0.8849 (mmt90) cc_final: 0.8372 (tpp-160) REVERT: S 19 SER cc_start: 0.9549 (t) cc_final: 0.9066 (p) REVERT: S 41 GLU cc_start: 0.8742 (pm20) cc_final: 0.8495 (pm20) REVERT: S 59 THR cc_start: 0.9255 (m) cc_final: 0.9019 (p) REVERT: S 61 GLU cc_start: 0.9026 (tp30) cc_final: 0.8762 (mm-30) REVERT: S 90 ASP cc_start: 0.8477 (t0) cc_final: 0.7633 (t0) REVERT: S 92 GLU cc_start: 0.8574 (mp0) cc_final: 0.7307 (pm20) REVERT: S 110 ASN cc_start: 0.9209 (t0) cc_final: 0.8992 (t0) REVERT: T 51 ASP cc_start: 0.8226 (p0) cc_final: 0.7711 (t0) REVERT: T 57 LYS cc_start: 0.9089 (mppt) cc_final: 0.8832 (mmmt) REVERT: T 64 SER cc_start: 0.9215 (m) cc_final: 0.8427 (p) REVERT: T 68 ASP cc_start: 0.8785 (t0) cc_final: 0.8394 (t0) REVERT: T 76 GLU cc_start: 0.9019 (tp30) cc_final: 0.8779 (tp30) REVERT: T 79 ARG cc_start: 0.8728 (ttp-110) cc_final: 0.8500 (ttp80) REVERT: T 93 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8034 (tp30) outliers start: 25 outliers final: 17 residues processed: 277 average time/residue: 0.1067 time to fit residues: 41.7834 Evaluate side-chains 272 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 253 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE 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 61 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 40.0000 chunk 45 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 86 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 68 GLN ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.073778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.052528 restraints weight = 47502.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.054180 restraints weight = 22938.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.055290 restraints weight = 15205.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.056023 restraints weight = 11994.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.056455 restraints weight = 10433.980| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12896 Z= 0.170 Angle : 0.725 13.351 18594 Z= 0.415 Chirality : 0.046 0.262 2109 Planarity : 0.004 0.044 1401 Dihedral : 30.259 171.686 3950 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.90 % Favored : 96.84 % Rotamer: Outliers : 4.17 % Allowed : 26.83 % Favored : 69.00 % 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: 0.82 (0.29), residues: 792 helix: 1.03 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.58 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 36 TYR 0.031 0.002 TYR P 40 PHE 0.015 0.002 PHE O 25 TRP 0.006 0.002 TRP H 152 HIS 0.011 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.17 (12896) covalent geometry : angle 0.72540 / 0.42 (18594) hydrogen bonds : bond 0.04584 / 3.72 ( 753) hydrogen bonds : angle 3.24983 / 3.53 ( 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 290 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 262 time to evaluate : 0.329 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 148 GLU cc_start: 0.8691 (tm-30) cc_final: 0.8160 (tm-30) REVERT: H 151 ARG cc_start: 0.9172 (mtt-85) cc_final: 0.8793 (ptt90) REVERT: H 161 LEU cc_start: 0.8663 (tp) cc_final: 0.8443 (tp) REVERT: H 173 GLU cc_start: 0.9056 (mp0) cc_final: 0.8685 (mp0) REVERT: M 73 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8141 (mm-30) REVERT: M 105 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8486 (mt-10) REVERT: M 122 LYS cc_start: 0.9235 (ttpt) cc_final: 0.8876 (ttpp) REVERT: N 22 LEU cc_start: 0.6727 (OUTLIER) cc_final: 0.6443 (mt) REVERT: N 44 LYS cc_start: 0.9394 (ttpt) cc_final: 0.8945 (ttmt) REVERT: N 80 THR cc_start: 0.9312 (m) cc_final: 0.8966 (p) REVERT: N 84 MET cc_start: 0.8839 (mmm) cc_final: 0.8197 (mmm) REVERT: N 88 TYR cc_start: 0.8909 (m-10) cc_final: 0.8640 (m-80) REVERT: O 36 LYS cc_start: 0.9333 (mmmm) cc_final: 0.8985 (mmmt) REVERT: O 39 TYR cc_start: 0.8913 (m-80) cc_final: 0.8416 (m-80) REVERT: O 75 LYS cc_start: 0.9306 (mttm) cc_final: 0.9079 (mmmm) REVERT: O 81 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8747 (tpt170) REVERT: O 90 ASP cc_start: 0.7581 (t70) cc_final: 0.7014 (t70) REVERT: O 91 GLU cc_start: 0.8763 (pm20) cc_final: 0.8360 (tm-30) REVERT: O 92 GLU cc_start: 0.9047 (tp30) cc_final: 0.8737 (tp30) REVERT: O 104 GLN cc_start: 0.8655 (pm20) cc_final: 0.8244 (pm20) REVERT: P 48 VAL cc_start: 0.9565 (t) cc_final: 0.9270 (p) REVERT: P 68 ASP cc_start: 0.9192 (t70) cc_final: 0.8786 (t0) REVERT: P 71 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8762 (tm-30) REVERT: P 76 GLU cc_start: 0.7721 (tp30) cc_final: 0.7374 (tp30) REVERT: P 79 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: P 84 ASN cc_start: 0.9424 (m-40) cc_final: 0.8967 (m-40) REVERT: P 86 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8282 (mtt90) REVERT: P 125 LYS cc_start: 0.8429 (mttt) cc_final: 0.7907 (tppt) REVERT: Q 68 GLN cc_start: 0.8664 (tt0) cc_final: 0.8076 (tp40) REVERT: Q 123 ASP cc_start: 0.9131 (m-30) cc_final: 0.8465 (m-30) REVERT: R 36 ARG cc_start: 0.8541 (mtm-85) cc_final: 0.8178 (mtm-85) REVERT: R 37 LEU cc_start: 0.8733 (mt) cc_final: 0.8533 (tt) REVERT: R 39 ARG cc_start: 0.8878 (mmt90) cc_final: 0.8426 (tpp-160) REVERT: S 19 SER cc_start: 0.9541 (t) cc_final: 0.9060 (p) REVERT: S 56 GLU cc_start: 0.8735 (tt0) cc_final: 0.8396 (tt0) REVERT: S 59 THR cc_start: 0.9258 (m) cc_final: 0.9009 (p) REVERT: S 61 GLU cc_start: 0.9023 (tp30) cc_final: 0.8757 (mm-30) REVERT: S 90 ASP cc_start: 0.8466 (t0) cc_final: 0.7517 (t0) REVERT: T 51 ASP cc_start: 0.8259 (p0) cc_final: 0.7760 (t0) REVERT: T 57 LYS cc_start: 0.9081 (mppt) cc_final: 0.8824 (mmmt) REVERT: T 64 SER cc_start: 0.9212 (m) cc_final: 0.8787 (p) REVERT: T 68 ASP cc_start: 0.8796 (t0) cc_final: 0.8471 (t0) REVERT: T 79 ARG cc_start: 0.8721 (ttp-110) cc_final: 0.8425 (ttp80) REVERT: T 93 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8344 (tp30) outliers start: 28 outliers final: 22 residues processed: 273 average time/residue: 0.1090 time to fit residues: 41.8302 Evaluate side-chains 275 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 251 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain O residue 81 ARG Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 LEU Chi-restraints excluded: chain S residue 64 GLU 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 61 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.073951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.052616 restraints weight = 46929.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.054330 restraints weight = 22276.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.055487 restraints weight = 14619.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.056228 restraints weight = 11441.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.056651 restraints weight = 9944.148| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12896 Z= 0.168 Angle : 0.742 13.579 18594 Z= 0.420 Chirality : 0.047 0.262 2109 Planarity : 0.004 0.048 1401 Dihedral : 30.284 171.966 3950 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.65 % Favored : 97.10 % Rotamer: Outliers : 4.02 % Allowed : 27.57 % Favored : 68.41 % 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: 0.82 (0.29), residues: 792 helix: 1.03 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -0.58 (0.39), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG R 36 TYR 0.028 0.002 TYR P 40 PHE 0.014 0.001 PHE M 67 TRP 0.005 0.001 TRP H 152 HIS 0.015 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (12896) covalent geometry : angle 0.74183 / 0.42 (18594) hydrogen bonds : bond 0.04498 / 3.69 ( 753) hydrogen bonds : angle 3.24129 / 3.52 ( 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 281 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.318 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 148 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8045 (tm-30) REVERT: H 151 ARG cc_start: 0.9162 (mtt-85) cc_final: 0.8797 (ptt90) REVERT: H 161 LEU cc_start: 0.8710 (tp) cc_final: 0.8488 (tp) REVERT: H 173 GLU cc_start: 0.9125 (mp0) cc_final: 0.8772 (mp0) REVERT: M 73 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8197 (mm-30) REVERT: M 94 GLU cc_start: 0.8706 (mm-30) cc_final: 0.7628 (mm-30) REVERT: M 105 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8496 (mt-10) REVERT: M 122 LYS cc_start: 0.9286 (ttpt) cc_final: 0.8902 (ttpp) REVERT: N 22 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6409 (mt) REVERT: N 44 LYS cc_start: 0.9373 (ttpt) cc_final: 0.8954 (ttmt) REVERT: N 80 THR cc_start: 0.9305 (m) cc_final: 0.8979 (p) REVERT: N 84 MET cc_start: 0.8899 (mmm) cc_final: 0.8095 (mmm) REVERT: N 88 TYR cc_start: 0.8920 (m-10) cc_final: 0.8557 (m-80) REVERT: O 36 LYS cc_start: 0.9327 (mmmm) cc_final: 0.8994 (mmmt) REVERT: O 39 TYR cc_start: 0.8909 (m-80) cc_final: 0.8400 (m-80) REVERT: O 75 LYS cc_start: 0.9314 (mttm) cc_final: 0.9094 (mmmm) REVERT: O 90 ASP cc_start: 0.7580 (t70) cc_final: 0.7027 (t70) REVERT: O 91 GLU cc_start: 0.8741 (pm20) cc_final: 0.8351 (tm-30) REVERT: O 92 GLU cc_start: 0.9046 (tp30) cc_final: 0.8753 (tp30) REVERT: O 104 GLN cc_start: 0.8676 (pm20) cc_final: 0.8257 (pm20) REVERT: P 68 ASP cc_start: 0.9210 (t70) cc_final: 0.8853 (t0) REVERT: P 71 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8766 (tm-30) REVERT: P 84 ASN cc_start: 0.9416 (m-40) cc_final: 0.8981 (m-40) REVERT: P 125 LYS cc_start: 0.8423 (mttt) cc_final: 0.7874 (tppt) REVERT: Q 68 GLN cc_start: 0.8657 (tt0) cc_final: 0.8060 (tm-30) REVERT: Q 123 ASP cc_start: 0.9109 (m-30) cc_final: 0.8481 (m-30) REVERT: R 39 ARG cc_start: 0.8662 (mmt90) cc_final: 0.8415 (tpp-160) REVERT: S 19 SER cc_start: 0.9529 (t) cc_final: 0.9056 (p) REVERT: S 56 GLU cc_start: 0.8719 (tt0) cc_final: 0.8401 (tt0) REVERT: S 59 THR cc_start: 0.9229 (m) cc_final: 0.8972 (p) REVERT: S 61 GLU cc_start: 0.9049 (tp30) cc_final: 0.8772 (mm-30) REVERT: S 90 ASP cc_start: 0.8169 (t0) cc_final: 0.7910 (t0) REVERT: S 104 GLN cc_start: 0.8769 (mt0) cc_final: 0.8374 (mm-40) REVERT: T 51 ASP cc_start: 0.8239 (p0) cc_final: 0.7761 (t0) REVERT: T 57 LYS cc_start: 0.9084 (mppt) cc_final: 0.8825 (mmmt) REVERT: T 64 SER cc_start: 0.9197 (m) cc_final: 0.8773 (p) REVERT: T 68 ASP cc_start: 0.8792 (t0) cc_final: 0.8469 (t0) REVERT: T 105 GLU cc_start: 0.8091 (pm20) cc_final: 0.7839 (pm20) outliers start: 27 outliers final: 21 residues processed: 265 average time/residue: 0.1107 time to fit residues: 41.3290 Evaluate side-chains 269 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain P residue 62 MET Chi-restraints excluded: chain Q residue 48 LEU Chi-restraints excluded: chain Q residue 51 ILE Chi-restraints excluded: chain Q residue 112 ILE Chi-restraints excluded: chain R residue 43 VAL Chi-restraints excluded: chain R residue 58 LEU 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 61 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 68 GLN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.053006 restraints weight = 47512.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.054725 restraints weight = 22315.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055896 restraints weight = 14553.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056661 restraints weight = 11345.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.057108 restraints weight = 9796.799| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12896 Z= 0.169 Angle : 0.748 13.598 18594 Z= 0.421 Chirality : 0.046 0.260 2109 Planarity : 0.004 0.048 1401 Dihedral : 30.294 172.477 3950 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.90 % Favored : 96.84 % Rotamer: Outliers : 3.28 % Allowed : 28.46 % Favored : 68.26 % 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: 0.85 (0.29), residues: 792 helix: 1.05 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 36 TYR 0.026 0.002 TYR P 40 PHE 0.015 0.001 PHE M 67 TRP 0.005 0.001 TRP H 152 HIS 0.010 0.001 HIS N 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12896) covalent geometry : angle 0.74773 / 0.42 (18594) hydrogen bonds : bond 0.04452 / 3.69 ( 753) hydrogen bonds : angle 3.28586 / 3.54 ( 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 280 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 258 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: 0.8672 (tm-30) cc_final: 0.8201 (tm-30) REVERT: H 151 ARG cc_start: 0.9141 (mtt-85) cc_final: 0.8794 (ptt90) REVERT: H 161 LEU cc_start: 0.8742 (tp) cc_final: 0.8524 (tp) REVERT: H 173 GLU cc_start: 0.9066 (mp0) cc_final: 0.8695 (mp0) REVERT: M 73 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8045 (mm-30) REVERT: M 94 GLU cc_start: 0.8720 (mm-30) cc_final: 0.7710 (mm-30) REVERT: M 105 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8491 (mt-10) REVERT: M 122 LYS cc_start: 0.9253 (ttpt) cc_final: 0.8858 (ttpp) REVERT: N 22 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.5953 (mp) REVERT: N 44 LYS cc_start: 0.9344 (ttpt) cc_final: 0.8929 (ttmt) REVERT: N 80 THR cc_start: 0.9326 (m) cc_final: 0.9007 (p) REVERT: N 84 MET cc_start: 0.8894 (mmm) cc_final: 0.8104 (mmm) REVERT: N 88 TYR cc_start: 0.8918 (m-10) cc_final: 0.8550 (m-80) REVERT: N 92 ARG cc_start: 0.8928 (ttp80) cc_final: 0.8097 (ttp80) REVERT: O 36 LYS cc_start: 0.9316 (mmmm) cc_final: 0.8969 (mmmt) REVERT: O 39 TYR cc_start: 0.8870 (m-80) cc_final: 0.8182 (m-80) REVERT: O 75 LYS cc_start: 0.9308 (mttm) cc_final: 0.9079 (mmmm) REVERT: O 90 ASP cc_start: 0.7534 (t70) cc_final: 0.7003 (t70) REVERT: O 91 GLU cc_start: 0.8735 (pm20) cc_final: 0.8349 (tm-30) REVERT: O 92 GLU cc_start: 0.9056 (tp30) cc_final: 0.8761 (tp30) REVERT: P 68 ASP cc_start: 0.9210 (t70) cc_final: 0.8853 (t0) REVERT: P 71 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8777 (tm-30) REVERT: P 84 ASN cc_start: 0.9418 (m-40) cc_final: 0.9000 (m-40) REVERT: P 86 ARG cc_start: 0.8996 (mmm160) cc_final: 0.8298 (mtp85) REVERT: P 125 LYS cc_start: 0.8372 (mttt) cc_final: 0.7815 (tppt) REVERT: Q 68 GLN cc_start: 0.8655 (tt0) cc_final: 0.8051 (tm-30) REVERT: Q 123 ASP cc_start: 0.9076 (m-30) cc_final: 0.8485 (m-30) REVERT: R 36 ARG cc_start: 0.8616 (mtm-85) cc_final: 0.8271 (mtm-85) REVERT: S 19 SER cc_start: 0.9527 (t) cc_final: 0.9064 (p) REVERT: S 56 GLU cc_start: 0.8740 (tt0) cc_final: 0.8438 (tt0) REVERT: S 59 THR cc_start: 0.9232 (m) cc_final: 0.8979 (p) REVERT: S 61 GLU cc_start: 0.8963 (tp30) cc_final: 0.8676 (mm-30) REVERT: S 90 ASP cc_start: 0.8381 (t0) cc_final: 0.7772 (t0) REVERT: S 104 GLN cc_start: 0.8773 (mt0) cc_final: 0.8406 (mm-40) REVERT: T 51 ASP cc_start: 0.8236 (p0) cc_final: 0.7791 (t0) REVERT: T 57 LYS cc_start: 0.9059 (mppt) cc_final: 0.8801 (mmmt) REVERT: T 64 SER cc_start: 0.9208 (m) cc_final: 0.8771 (p) REVERT: T 68 ASP cc_start: 0.8795 (t0) cc_final: 0.8478 (t0) outliers start: 22 outliers final: 21 residues processed: 266 average time/residue: 0.1078 time to fit residues: 40.2848 Evaluate side-chains 267 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 87 SER Chi-restraints excluded: chain M residue 107 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 49 LEU Chi-restraints excluded: chain N residue 93 GLN Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain P residue 62 MET 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 43 VAL Chi-restraints excluded: chain R residue 58 LEU 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 61 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 77 optimal weight: 0.0770 chunk 91 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... T 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.074456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.053126 restraints weight = 47132.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.054845 restraints weight = 22264.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.056022 restraints weight = 14589.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.056750 restraints weight = 11415.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.057221 restraints weight = 9926.057| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12896 Z= 0.162 Angle : 0.750 13.976 18594 Z= 0.422 Chirality : 0.045 0.259 2109 Planarity : 0.004 0.050 1401 Dihedral : 30.286 173.092 3950 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.25 % Allowed : 2.78 % Favored : 96.97 % Rotamer: Outliers : 2.98 % Allowed : 28.91 % 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: 0.81 (0.29), residues: 792 helix: 1.01 (0.21), residues: 571 sheet: None (None), residues: 0 loop : -0.54 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 36 TYR 0.025 0.002 TYR P 40 PHE 0.019 0.001 PHE Q 67 TRP 0.006 0.001 TRP H 152 HIS 0.017 0.002 HIS T 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (12896) covalent geometry : angle 0.74990 / 0.42 (18594) hydrogen bonds : bond 0.04377 / 3.66 ( 753) hydrogen bonds : angle 3.27651 / 3.59 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2118.34 seconds wall clock time: 37 minutes 10.89 seconds (2230.89 seconds total)