Starting phenix.real_space_refine on Wed Mar 4 04:24:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.map" model { file = "/net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cg4_30350/03_2026/7cg4_30350.cif" } resolution = 3.6 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= 0.002 sd= 0.049 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: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 7153 2.51 5 N 1775 2.21 5 O 1923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10943 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 536 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 1, 'TRANS': 69} Chain: "b" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 526 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "c" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "d" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "e" Number of atoms: 543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 543 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "f" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 293 Classifications: {'peptide': 39} Link IDs: {'TRANS': 38} Chain: "r" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1608 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 1 Chain: "s" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1608 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain breaks: 1 Chain: "t" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1601 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 13, 'TRANS': 192} Chain breaks: 1 Chain: "u" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1583 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain breaks: 1 Chain: "v" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1559 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 14, 'TRANS': 185} Chain breaks: 2 Time building chain proxies: 2.31, per 1000 atoms: 0.21 Number of scatterers: 10943 At special positions: 0 Unit cell: (105.867, 101.946, 130.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 1923 8.00 N 1775 7.00 C 7153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 496.0 milliseconds 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2698 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 84.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'a' and resid 34 through 61 removed outlier: 3.864A pdb=" N ASP a 47 " --> pdb=" O ASP a 43 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG a 48 " --> pdb=" O ARG a 44 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 100 Processing helix chain 'b' and resid 37 through 61 removed outlier: 3.924A pdb=" N ALA b 52 " --> pdb=" O ARG b 48 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LEU b 61 " --> pdb=" O GLU b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 69 through 101 Processing helix chain 'c' and resid 34 through 61 removed outlier: 3.727A pdb=" N ARG c 48 " --> pdb=" O ARG c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 102 removed outlier: 4.337A pdb=" N ALA c 73 " --> pdb=" O ASN c 69 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N MET c 102 " --> pdb=" O GLU c 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 34 through 61 Processing helix chain 'd' and resid 70 through 101 removed outlier: 4.465A pdb=" N GLN d 76 " --> pdb=" O MET d 72 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS d 77 " --> pdb=" O ALA d 73 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N SER d 79 " --> pdb=" O MET d 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 34 through 61 removed outlier: 3.676A pdb=" N LEU e 38 " --> pdb=" O PHE e 34 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N HIS e 39 " --> pdb=" O ALA e 35 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ARG e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN e 49 " --> pdb=" O ILE e 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 100 removed outlier: 3.671A pdb=" N GLN e 76 " --> pdb=" O MET e 72 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 100 Processing helix chain 'r' and resid 42 through 61 removed outlier: 3.554A pdb=" N THR r 52 " --> pdb=" O ILE r 48 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE r 53 " --> pdb=" O THR r 49 " (cutoff:3.500A) Proline residue: r 55 - end of helix Processing helix chain 'r' and resid 64 through 78 removed outlier: 3.931A pdb=" N ILE r 68 " --> pdb=" O PHE r 64 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE r 69 " --> pdb=" O THR r 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 88 through 101 removed outlier: 4.255A pdb=" N LEU r 94 " --> pdb=" O LEU r 90 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR r 97 " --> pdb=" O ALA r 93 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 117 Proline residue: r 115 - end of helix Processing helix chain 'r' and resid 122 through 142 removed outlier: 4.460A pdb=" N ASP r 128 " --> pdb=" O GLN r 124 " (cutoff:3.500A) Proline residue: r 133 - end of helix removed outlier: 3.605A pdb=" N GLN r 141 " --> pdb=" O PHE r 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR r 142 " --> pdb=" O MET r 138 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 155 removed outlier: 3.799A pdb=" N ALA r 148 " --> pdb=" O GLU r 144 " (cutoff:3.500A) Processing helix chain 'r' and resid 166 through 207 removed outlier: 3.679A pdb=" N LEU r 171 " --> pdb=" O MET r 167 " (cutoff:3.500A) Proline residue: r 172 - end of helix removed outlier: 3.696A pdb=" N SER r 177 " --> pdb=" O ALA r 173 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR r 181 " --> pdb=" O SER r 177 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE r 183 " --> pdb=" O LEU r 179 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN r 184 " --> pdb=" O LYS r 180 " (cutoff:3.500A) Proline residue: r 192 - end of helix Processing helix chain 'r' and resid 214 through 229 Proline residue: r 220 - end of helix Processing helix chain 'r' and resid 230 through 245 Processing helix chain 's' and resid 39 through 59 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 64 through 78 removed outlier: 3.800A pdb=" N ILE s 68 " --> pdb=" O PHE s 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE s 69 " --> pdb=" O THR s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 85 through 117 removed outlier: 3.618A pdb=" N LEU s 89 " --> pdb=" O PRO s 85 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR s 97 " --> pdb=" O ALA s 93 " (cutoff:3.500A) Proline residue: s 103 - end of helix Proline residue: s 115 - end of helix Processing helix chain 's' and resid 122 through 142 removed outlier: 4.630A pdb=" N ASP s 128 " --> pdb=" O GLN s 124 " (cutoff:3.500A) Proline residue: s 133 - end of helix removed outlier: 4.546A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN s 141 " --> pdb=" O PHE s 137 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR s 142 " --> pdb=" O MET s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 143 through 155 Processing helix chain 's' and resid 170 through 206 removed outlier: 3.780A pdb=" N SER s 177 " --> pdb=" O ALA s 173 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR s 181 " --> pdb=" O SER s 177 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE s 183 " --> pdb=" O LEU s 179 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN s 184 " --> pdb=" O LYS s 180 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR s 188 " --> pdb=" O GLN s 184 " (cutoff:3.500A) Proline residue: s 192 - end of helix Processing helix chain 's' and resid 214 through 229 Proline residue: s 220 - end of helix Processing helix chain 's' and resid 230 through 245 Processing helix chain 't' and resid 39 through 61 removed outlier: 3.792A pdb=" N THR t 52 " --> pdb=" O ILE t 48 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE t 53 " --> pdb=" O THR t 49 " (cutoff:3.500A) Proline residue: t 55 - end of helix Processing helix chain 't' and resid 64 through 78 removed outlier: 3.644A pdb=" N ILE t 68 " --> pdb=" O PHE t 64 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE t 69 " --> pdb=" O THR t 65 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL t 70 " --> pdb=" O ARG t 66 " (cutoff:3.500A) Processing helix chain 't' and resid 85 through 101 removed outlier: 3.600A pdb=" N LEU t 94 " --> pdb=" O LEU t 90 " (cutoff:3.500A) Processing helix chain 't' and resid 101 through 114 removed outlier: 3.511A pdb=" N ILE t 105 " --> pdb=" O MET t 101 " (cutoff:3.500A) Processing helix chain 't' and resid 122 through 141 removed outlier: 4.475A pdb=" N ASP t 128 " --> pdb=" O GLN t 124 " (cutoff:3.500A) Proline residue: t 133 - end of helix Processing helix chain 't' and resid 143 through 155 removed outlier: 4.036A pdb=" N LEU t 147 " --> pdb=" O ARG t 143 " (cutoff:3.500A) Processing helix chain 't' and resid 170 through 207 removed outlier: 3.549A pdb=" N SER t 177 " --> pdb=" O ALA t 173 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR t 181 " --> pdb=" O SER t 177 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE t 183 " --> pdb=" O LEU t 179 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N THR t 188 " --> pdb=" O GLN t 184 " (cutoff:3.500A) Proline residue: t 192 - end of helix removed outlier: 3.618A pdb=" N LEU t 207 " --> pdb=" O VAL t 203 " (cutoff:3.500A) Processing helix chain 't' and resid 214 through 229 Proline residue: t 220 - end of helix Processing helix chain 't' and resid 230 through 244 removed outlier: 4.032A pdb=" N GLY t 237 " --> pdb=" O GLN t 233 " (cutoff:3.500A) Processing helix chain 'u' and resid 39 through 60 removed outlier: 3.661A pdb=" N LEU u 51 " --> pdb=" O PHE u 47 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR u 52 " --> pdb=" O ILE u 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE u 53 " --> pdb=" O THR u 49 " (cutoff:3.500A) Proline residue: u 55 - end of helix Processing helix chain 'u' and resid 64 through 78 Processing helix chain 'u' and resid 85 through 101 removed outlier: 4.187A pdb=" N GLY u 91 " --> pdb=" O GLN u 87 " (cutoff:3.500A) Processing helix chain 'u' and resid 101 through 118 Proline residue: u 115 - end of helix removed outlier: 3.914A pdb=" N GLU u 118 " --> pdb=" O GLN u 114 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 142 removed outlier: 4.834A pdb=" N ASP u 128 " --> pdb=" O GLN u 124 " (cutoff:3.500A) Proline residue: u 133 - end of helix removed outlier: 4.017A pdb=" N ARG u 140 " --> pdb=" O ALA u 136 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN u 141 " --> pdb=" O PHE u 137 " (cutoff:3.500A) Processing helix chain 'u' and resid 145 through 152 removed outlier: 3.780A pdb=" N LEU u 149 " --> pdb=" O ALA u 145 " (cutoff:3.500A) Processing helix chain 'u' and resid 166 through 207 removed outlier: 3.601A pdb=" N LEU u 170 " --> pdb=" O PRO u 166 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU u 171 " --> pdb=" O MET u 167 " (cutoff:3.500A) Proline residue: u 172 - end of helix removed outlier: 4.144A pdb=" N SER u 177 " --> pdb=" O ALA u 173 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR u 181 " --> pdb=" O SER u 177 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN u 184 " --> pdb=" O LYS u 180 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR u 188 " --> pdb=" O GLN u 184 " (cutoff:3.500A) Proline residue: u 192 - end of helix Processing helix chain 'u' and resid 213 through 229 removed outlier: 4.064A pdb=" N ILE u 217 " --> pdb=" O PRO u 213 " (cutoff:3.500A) Proline residue: u 220 - end of helix Processing helix chain 'u' and resid 230 through 245 Processing helix chain 'v' and resid 39 through 53 Processing helix chain 'v' and resid 53 through 60 removed outlier: 3.554A pdb=" N ILE v 57 " --> pdb=" O PHE v 53 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU v 58 " --> pdb=" O LEU v 54 " (cutoff:3.500A) Processing helix chain 'v' and resid 66 through 78 Processing helix chain 'v' and resid 85 through 101 removed outlier: 4.151A pdb=" N GLY v 91 " --> pdb=" O GLN v 87 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 118 removed outlier: 3.554A pdb=" N ILE v 105 " --> pdb=" O MET v 101 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN v 114 " --> pdb=" O VAL v 110 " (cutoff:3.500A) Proline residue: v 115 - end of helix Processing helix chain 'v' and resid 122 through 141 Proline residue: v 133 - end of helix Processing helix chain 'v' and resid 145 through 155 removed outlier: 4.212A pdb=" N LEU v 149 " --> pdb=" O ALA v 145 " (cutoff:3.500A) Processing helix chain 'v' and resid 166 through 202 removed outlier: 3.797A pdb=" N LEU v 170 " --> pdb=" O PRO v 166 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU v 171 " --> pdb=" O MET v 167 " (cutoff:3.500A) Proline residue: v 172 - end of helix removed outlier: 3.649A pdb=" N SER v 177 " --> pdb=" O ALA v 173 " (cutoff:3.500A) Proline residue: v 192 - end of helix Processing helix chain 'v' and resid 213 through 230 removed outlier: 3.785A pdb=" N ILE v 217 " --> pdb=" O PRO v 213 " (cutoff:3.500A) Proline residue: v 220 - end of helix Processing helix chain 'v' and resid 230 through 245 removed outlier: 4.111A pdb=" N LEU v 234 " --> pdb=" O ASP v 230 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.41 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1734 1.31 - 1.44: 2730 1.44 - 1.56: 6496 1.56 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 11144 Sorted by residual: bond pdb=" C MET c 75 " pdb=" O MET c 75 " ideal model delta sigma weight residual 1.237 1.185 0.052 1.16e-02 7.43e+03 2.00e+01 bond pdb=" C MET c 75 " pdb=" N GLN c 76 " ideal model delta sigma weight residual 1.335 1.292 0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" C GLN e 83 " pdb=" O GLN e 83 " ideal model delta sigma weight residual 1.237 1.201 0.035 1.16e-02 7.43e+03 9.22e+00 bond pdb=" N VAL v 88 " pdb=" CA VAL v 88 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.92e+00 bond pdb=" C ASP c 74 " pdb=" N MET c 75 " ideal model delta sigma weight residual 1.334 1.297 0.037 1.33e-02 5.65e+03 7.87e+00 ... (remaining 11139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 14949 2.91 - 5.82: 133 5.82 - 8.72: 8 8.72 - 11.63: 1 11.63 - 14.54: 1 Bond angle restraints: 15092 Sorted by residual: angle pdb=" CB MET c 75 " pdb=" CG MET c 75 " pdb=" SD MET c 75 " ideal model delta sigma weight residual 112.70 98.16 14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" N MET c 75 " pdb=" CA MET c 75 " pdb=" C MET c 75 " ideal model delta sigma weight residual 111.14 106.44 4.70 1.08e+00 8.57e-01 1.89e+01 angle pdb=" N GLN e 83 " pdb=" CA GLN e 83 " pdb=" C GLN e 83 " ideal model delta sigma weight residual 111.14 106.83 4.31 1.08e+00 8.57e-01 1.59e+01 angle pdb=" CA GLN e 83 " pdb=" C GLN e 83 " pdb=" O GLN e 83 " ideal model delta sigma weight residual 120.70 117.12 3.58 1.03e+00 9.43e-01 1.21e+01 angle pdb=" CA ASP c 74 " pdb=" C ASP c 74 " pdb=" N MET c 75 " ideal model delta sigma weight residual 117.63 113.41 4.22 1.25e+00 6.40e-01 1.14e+01 ... (remaining 15087 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6077 17.89 - 35.77: 570 35.77 - 53.66: 105 53.66 - 71.55: 14 71.55 - 89.43: 18 Dihedral angle restraints: 6784 sinusoidal: 2658 harmonic: 4126 Sorted by residual: dihedral pdb=" CA SER u 177 " pdb=" C SER u 177 " pdb=" N GLU u 178 " pdb=" CA GLU u 178 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LEU t 58 " pdb=" C LEU t 58 " pdb=" N LEU t 59 " pdb=" CA LEU t 59 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR u 62 " pdb=" C THR u 62 " pdb=" N SER u 63 " pdb=" CA SER u 63 " ideal model delta harmonic sigma weight residual -180.00 -158.58 -21.42 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 6781 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1511 0.053 - 0.107: 271 0.107 - 0.160: 28 0.160 - 0.213: 3 0.213 - 0.266: 3 Chirality restraints: 1816 Sorted by residual: chirality pdb=" CA MET c 75 " pdb=" N MET c 75 " pdb=" C MET c 75 " pdb=" CB MET c 75 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA MET u 236 " pdb=" N MET u 236 " pdb=" C MET u 236 " pdb=" CB MET u 236 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CA MET t 236 " pdb=" N MET t 236 " pdb=" C MET t 236 " pdb=" CB MET t 236 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1813 not shown) Planarity restraints: 1885 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL u 110 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.31e+00 pdb=" C VAL u 110 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL u 110 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP u 111 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP c 74 " -0.011 2.00e-02 2.50e+03 2.35e-02 5.54e+00 pdb=" C ASP c 74 " 0.041 2.00e-02 2.50e+03 pdb=" O ASP c 74 " -0.016 2.00e-02 2.50e+03 pdb=" N MET c 75 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN t 114 " 0.037 5.00e-02 4.00e+02 5.50e-02 4.83e+00 pdb=" N PRO t 115 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO t 115 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO t 115 " 0.030 5.00e-02 4.00e+02 ... (remaining 1882 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 792 2.73 - 3.27: 11956 3.27 - 3.82: 17650 3.82 - 4.36: 18716 4.36 - 4.90: 32588 Nonbonded interactions: 81702 Sorted by model distance: nonbonded pdb=" NE2 GLN v 141 " pdb=" O PHE v 243 " model vdw 2.192 3.120 nonbonded pdb=" O ARG t 140 " pdb=" NH1 ARG t 140 " model vdw 2.217 3.120 nonbonded pdb=" NE ARG r 66 " pdb=" OE2 GLU r 178 " model vdw 2.264 3.120 nonbonded pdb=" OH TYR t 174 " pdb=" OE2 GLU t 178 " model vdw 2.267 3.040 nonbonded pdb=" NH1 ARG s 75 " pdb=" OD1 ASN s 86 " model vdw 2.282 3.120 ... (remaining 81697 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 'a' and resid 35 through 103) selection = (chain 'b' and resid 35 through 103) selection = (chain 'c' and resid 35 through 103) selection = (chain 'd' and resid 35 through 103) selection = (chain 'e' and resid 35 through 103) } ncs_group { reference = (chain 'r' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 's' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 't' and (resid 35 through 154 or resid 163 through 204 or resid 212 throu \ gh 245)) selection = (chain 'u' and (resid 35 through 204 or resid 212 through 245)) selection = (chain 'v' and (resid 35 through 154 or resid 163 through 245)) } 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: 9.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 10.280 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.003 0.054 11144 Z= 0.186 Angle : 0.691 14.541 15092 Z= 0.379 Chirality : 0.041 0.266 1816 Planarity : 0.004 0.055 1885 Dihedral : 14.904 89.431 4086 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.34 % Allowed : 5.57 % Favored : 94.09 % 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: -2.88 (0.20), residues: 1385 helix: -1.37 (0.14), residues: 1117 sheet: None (None), residues: 0 loop : -3.56 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG r 168 TYR 0.013 0.001 TYR s 244 PHE 0.017 0.001 PHE v 64 TRP 0.013 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00328 (11144) covalent geometry : angle 0.69137 (15092) hydrogen bonds : bond 0.12108 ( 809) hydrogen bonds : angle 5.57778 ( 2427) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 453 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 47 ASP cc_start: 0.7718 (t70) cc_final: 0.7490 (t70) REVERT: b 83 GLN cc_start: 0.9103 (tp40) cc_final: 0.8843 (tp40) REVERT: b 96 TYR cc_start: 0.8284 (t80) cc_final: 0.7930 (t80) REVERT: d 34 PHE cc_start: 0.7446 (t80) cc_final: 0.7207 (t80) REVERT: e 83 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7156 (tm-30) REVERT: f 69 ASN cc_start: 0.6201 (t0) cc_final: 0.5896 (t0) REVERT: f 77 LYS cc_start: 0.7610 (mttt) cc_final: 0.7394 (mmmt) REVERT: f 91 LYS cc_start: 0.7852 (ttpt) cc_final: 0.7489 (ttpp) REVERT: r 76 ASN cc_start: 0.8599 (t0) cc_final: 0.8320 (t0) REVERT: r 211 MET cc_start: 0.6803 (mmp) cc_final: 0.6557 (mmp) REVERT: r 241 GLN cc_start: 0.8186 (tm-30) cc_final: 0.7954 (tm-30) REVERT: s 101 MET cc_start: 0.7667 (mmt) cc_final: 0.7278 (mmt) REVERT: v 98 PHE cc_start: 0.7870 (t80) cc_final: 0.7663 (t80) REVERT: v 123 MET cc_start: 0.6136 (tpt) cc_final: 0.5891 (tpt) outliers start: 4 outliers final: 1 residues processed: 454 average time/residue: 0.0966 time to fit residues: 62.6111 Evaluate side-chains 405 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 403 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain v residue 144 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 98 optimal weight: 0.0470 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0370 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.0870 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN d 49 GLN e 49 GLN r 141 GLN t 43 GLN u 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.146813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130897 restraints weight = 18784.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134345 restraints weight = 8660.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136445 restraints weight = 4830.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.137727 restraints weight = 3126.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138674 restraints weight = 2313.006| |-----------------------------------------------------------------------------| r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11144 Z= 0.134 Angle : 0.715 9.770 15092 Z= 0.335 Chirality : 0.040 0.174 1816 Planarity : 0.005 0.066 1885 Dihedral : 5.237 59.726 1490 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 2.95 % Allowed : 18.23 % Favored : 78.82 % 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: -0.60 (0.23), residues: 1385 helix: 0.25 (0.16), residues: 1122 sheet: None (None), residues: 0 loop : -2.96 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 89 TYR 0.011 0.001 TYR r 109 PHE 0.018 0.001 PHE c 34 TRP 0.012 0.001 TRP s 232 HIS 0.004 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00272 (11144) covalent geometry : angle 0.71481 (15092) hydrogen bonds : bond 0.04235 ( 809) hydrogen bonds : angle 4.50406 ( 2427) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 419 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 57 GLU cc_start: 0.8027 (tt0) cc_final: 0.7470 (tp30) REVERT: c 75 MET cc_start: 0.8101 (tmm) cc_final: 0.7824 (tpt) REVERT: d 82 MET cc_start: 0.8572 (tpp) cc_final: 0.8346 (tpp) REVERT: e 83 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7036 (tm-30) REVERT: e 84 MET cc_start: 0.7428 (tmm) cc_final: 0.6820 (tmm) REVERT: f 77 LYS cc_start: 0.8002 (mttt) cc_final: 0.7626 (mmtt) REVERT: f 91 LYS cc_start: 0.8067 (ttpt) cc_final: 0.7706 (ttpp) REVERT: r 76 ASN cc_start: 0.9004 (t0) cc_final: 0.8731 (t0) REVERT: r 211 MET cc_start: 0.7146 (mmp) cc_final: 0.6831 (mmm) REVERT: r 241 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8043 (tm-30) REVERT: s 60 MET cc_start: 0.7856 (mmt) cc_final: 0.6265 (ttt) REVERT: s 61 MET cc_start: 0.7851 (ptp) cc_final: 0.7380 (ptp) REVERT: s 101 MET cc_start: 0.7452 (mmt) cc_final: 0.7241 (mmt) REVERT: s 211 MET cc_start: 0.8414 (pmm) cc_final: 0.8139 (pmm) REVERT: u 178 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: v 190 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8416 (t80) REVERT: v 195 ILE cc_start: 0.9213 (tt) cc_final: 0.8971 (tp) outliers start: 35 outliers final: 23 residues processed: 429 average time/residue: 0.0880 time to fit residues: 55.0173 Evaluate side-chains 416 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 390 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 49 GLN Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 225 LEU Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 94 LEU Chi-restraints excluded: chain s residue 225 LEU Chi-restraints excluded: chain s residue 227 VAL Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain u residue 80 THR Chi-restraints excluded: chain u residue 178 GLU Chi-restraints excluded: chain u residue 179 LEU Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 65 THR Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 100 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 96 optimal weight: 0.0870 chunk 134 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN c 83 GLN ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 36 GLN u 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.124784 restraints weight = 19162.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.128164 restraints weight = 8791.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.130236 restraints weight = 4916.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131577 restraints weight = 3194.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132436 restraints weight = 2338.436| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11144 Z= 0.204 Angle : 0.756 8.716 15092 Z= 0.366 Chirality : 0.042 0.151 1816 Planarity : 0.004 0.056 1885 Dihedral : 5.305 54.161 1490 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 5.32 % Allowed : 21.35 % Favored : 73.33 % 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: -0.26 (0.24), residues: 1385 helix: 0.46 (0.16), residues: 1133 sheet: None (None), residues: 0 loop : -2.86 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 53 TYR 0.020 0.002 TYR s 244 PHE 0.019 0.002 PHE e 59 TRP 0.025 0.002 TRP t 232 HIS 0.010 0.002 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00441 (11144) covalent geometry : angle 0.75585 (15092) hydrogen bonds : bond 0.04780 ( 809) hydrogen bonds : angle 4.70443 ( 2427) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 407 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7678 (mtp-110) cc_final: 0.7473 (mtp-110) REVERT: a 47 ASP cc_start: 0.7771 (t70) cc_final: 0.7443 (t70) REVERT: c 57 GLU cc_start: 0.8006 (tt0) cc_final: 0.7526 (tp30) REVERT: d 53 ARG cc_start: 0.7955 (ttp80) cc_final: 0.7722 (tmm-80) REVERT: d 82 MET cc_start: 0.8734 (tpp) cc_final: 0.8487 (tpp) REVERT: e 74 ASP cc_start: 0.8457 (t70) cc_final: 0.8148 (t70) REVERT: e 83 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: e 84 MET cc_start: 0.7538 (tmm) cc_final: 0.6785 (tmm) REVERT: f 72 MET cc_start: 0.8974 (tpp) cc_final: 0.8636 (mmm) REVERT: f 77 LYS cc_start: 0.8049 (mttt) cc_final: 0.7673 (mmtt) REVERT: f 91 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7843 (ttpp) REVERT: f 100 MET cc_start: 0.8000 (tpp) cc_final: 0.7767 (tpp) REVERT: r 76 ASN cc_start: 0.9056 (t0) cc_final: 0.8793 (t0) REVERT: r 190 PHE cc_start: 0.8428 (OUTLIER) cc_final: 0.8145 (t80) REVERT: r 211 MET cc_start: 0.7087 (mmp) cc_final: 0.6764 (mmm) REVERT: r 224 MET cc_start: 0.7493 (tmm) cc_final: 0.7118 (ttt) REVERT: r 241 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8080 (tm-30) REVERT: s 60 MET cc_start: 0.7999 (mmt) cc_final: 0.6274 (ttt) REVERT: s 80 THR cc_start: 0.7633 (OUTLIER) cc_final: 0.7423 (t) REVERT: s 101 MET cc_start: 0.7778 (mmt) cc_final: 0.7372 (mmt) REVERT: s 209 MET cc_start: 0.8503 (mpp) cc_final: 0.8288 (mpp) REVERT: t 107 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8095 (ttpt) REVERT: t 127 LEU cc_start: 0.8713 (tp) cc_final: 0.8156 (tt) REVERT: t 178 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7797 (mt-10) REVERT: t 210 MET cc_start: 0.8007 (tmm) cc_final: 0.7040 (tmm) REVERT: t 224 MET cc_start: 0.7700 (ttt) cc_final: 0.7348 (ttm) REVERT: u 209 MET cc_start: 0.8894 (tpp) cc_final: 0.8609 (tpp) REVERT: u 224 MET cc_start: 0.7634 (ppp) cc_final: 0.7353 (ppp) REVERT: v 66 ARG cc_start: 0.7499 (ptp-170) cc_final: 0.7231 (ptp-170) REVERT: v 111 ASP cc_start: 0.3914 (OUTLIER) cc_final: 0.3616 (m-30) REVERT: v 190 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8442 (t80) REVERT: v 195 ILE cc_start: 0.9215 (tt) cc_final: 0.8979 (tp) outliers start: 63 outliers final: 42 residues processed: 428 average time/residue: 0.0899 time to fit residues: 55.8071 Evaluate side-chains 445 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 398 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 93 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain c residue 80 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 93 VAL Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 189 ILE Chi-restraints excluded: chain r residue 190 PHE Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 80 THR Chi-restraints excluded: chain s residue 94 LEU Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 57 ILE Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 70 VAL Chi-restraints excluded: chain t residue 140 ARG Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 203 VAL Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 80 THR Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 52 THR Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 111 ASP Chi-restraints excluded: chain v residue 122 SER Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 107 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 117 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.143932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.127713 restraints weight = 18786.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131172 restraints weight = 8557.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.133299 restraints weight = 4746.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.134667 restraints weight = 3062.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135452 restraints weight = 2232.969| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11144 Z= 0.140 Angle : 0.707 10.063 15092 Z= 0.332 Chirality : 0.040 0.179 1816 Planarity : 0.004 0.055 1885 Dihedral : 5.117 48.535 1490 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 4.14 % Allowed : 24.05 % Favored : 71.81 % 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: 0.24 (0.24), residues: 1385 helix: 0.82 (0.16), residues: 1134 sheet: None (None), residues: 0 loop : -2.72 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 53 TYR 0.014 0.001 TYR a 96 PHE 0.014 0.001 PHE r 187 TRP 0.011 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00303 (11144) covalent geometry : angle 0.70719 (15092) hydrogen bonds : bond 0.04214 ( 809) hydrogen bonds : angle 4.45908 ( 2427) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 405 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7660 (mtp-110) cc_final: 0.7456 (mtp-110) REVERT: c 57 GLU cc_start: 0.7972 (tt0) cc_final: 0.7561 (tp30) REVERT: d 53 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7769 (tmm-80) REVERT: d 75 MET cc_start: 0.8229 (mmm) cc_final: 0.8026 (mmp) REVERT: d 82 MET cc_start: 0.8700 (tpp) cc_final: 0.8469 (tpp) REVERT: e 74 ASP cc_start: 0.8410 (t70) cc_final: 0.8036 (t70) REVERT: e 83 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: e 84 MET cc_start: 0.7649 (tmm) cc_final: 0.6861 (tmm) REVERT: f 72 MET cc_start: 0.8984 (tpp) cc_final: 0.8595 (mmm) REVERT: f 77 LYS cc_start: 0.8037 (mttt) cc_final: 0.7665 (mmtt) REVERT: f 91 LYS cc_start: 0.8252 (ttpt) cc_final: 0.7849 (ttpp) REVERT: f 100 MET cc_start: 0.7817 (tpp) cc_final: 0.7508 (tpp) REVERT: r 61 MET cc_start: 0.8616 (ptp) cc_final: 0.8382 (ptp) REVERT: r 101 MET cc_start: 0.7740 (mmp) cc_final: 0.7469 (mmm) REVERT: r 177 SER cc_start: 0.8729 (m) cc_final: 0.8438 (m) REVERT: r 190 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8107 (t80) REVERT: r 224 MET cc_start: 0.7565 (tmm) cc_final: 0.6985 (ttt) REVERT: r 241 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8024 (tm-30) REVERT: s 60 MET cc_start: 0.7984 (mmt) cc_final: 0.6344 (ttt) REVERT: s 61 MET cc_start: 0.7824 (ptp) cc_final: 0.7452 (ptp) REVERT: s 80 THR cc_start: 0.7642 (OUTLIER) cc_final: 0.7437 (t) REVERT: s 101 MET cc_start: 0.7679 (mmt) cc_final: 0.7286 (mmt) REVERT: s 120 LYS cc_start: 0.9153 (mtpp) cc_final: 0.8837 (mtpp) REVERT: s 190 PHE cc_start: 0.8243 (OUTLIER) cc_final: 0.7905 (t80) REVERT: s 211 MET cc_start: 0.8366 (pmm) cc_final: 0.8139 (pmm) REVERT: t 36 GLN cc_start: 0.8332 (pm20) cc_final: 0.7865 (pm20) REVERT: t 107 LYS cc_start: 0.8307 (ttmm) cc_final: 0.8019 (ttpt) REVERT: t 168 ARG cc_start: 0.8217 (mtm-85) cc_final: 0.7935 (mtm110) REVERT: t 210 MET cc_start: 0.7559 (tmm) cc_final: 0.7188 (tmm) REVERT: t 236 MET cc_start: 0.7196 (mtm) cc_final: 0.6978 (mtm) REVERT: u 187 PHE cc_start: 0.6647 (OUTLIER) cc_final: 0.5879 (t80) REVERT: v 111 ASP cc_start: 0.3612 (OUTLIER) cc_final: 0.3400 (m-30) REVERT: v 190 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.8423 (t80) REVERT: v 195 ILE cc_start: 0.9209 (tt) cc_final: 0.8972 (tp) outliers start: 49 outliers final: 31 residues processed: 425 average time/residue: 0.0899 time to fit residues: 55.0639 Evaluate side-chains 434 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 190 PHE Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 80 THR Chi-restraints excluded: chain s residue 94 LEU Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 227 VAL Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 57 ILE Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain u residue 80 THR Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 65 THR Chi-restraints excluded: chain v residue 111 ASP Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 132 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 126 optimal weight: 4.9990 chunk 82 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN b 49 GLN c 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.144521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128371 restraints weight = 18939.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.131806 restraints weight = 8714.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.133915 restraints weight = 4857.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135247 restraints weight = 3131.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136026 restraints weight = 2290.993| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11144 Z= 0.135 Angle : 0.706 10.820 15092 Z= 0.330 Chirality : 0.040 0.216 1816 Planarity : 0.004 0.051 1885 Dihedral : 4.970 48.707 1490 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 5.23 % Allowed : 24.81 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1385 helix: 0.97 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -2.65 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 53 TYR 0.014 0.001 TYR s 244 PHE 0.014 0.001 PHE r 187 TRP 0.029 0.001 TRP t 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00292 (11144) covalent geometry : angle 0.70590 (15092) hydrogen bonds : bond 0.04022 ( 809) hydrogen bonds : angle 4.36103 ( 2427) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 410 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7728 (mtp-110) cc_final: 0.7459 (mtp-110) REVERT: a 84 MET cc_start: 0.7356 (tmm) cc_final: 0.7099 (tmm) REVERT: c 57 GLU cc_start: 0.7957 (tt0) cc_final: 0.7563 (tp30) REVERT: d 53 ARG cc_start: 0.7942 (ttp80) cc_final: 0.7730 (tmm-80) REVERT: d 82 MET cc_start: 0.8747 (tpp) cc_final: 0.8501 (tpp) REVERT: e 74 ASP cc_start: 0.8397 (t70) cc_final: 0.8014 (t70) REVERT: e 83 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: e 84 MET cc_start: 0.7676 (tmm) cc_final: 0.7397 (tmm) REVERT: f 72 MET cc_start: 0.9040 (tpp) cc_final: 0.8634 (mmm) REVERT: f 77 LYS cc_start: 0.8059 (mttt) cc_final: 0.7670 (mmtt) REVERT: f 91 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7828 (ttpp) REVERT: r 61 MET cc_start: 0.8607 (ptp) cc_final: 0.8372 (ptp) REVERT: r 66 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8547 (ptm160) REVERT: r 101 MET cc_start: 0.7718 (mmp) cc_final: 0.7499 (mmm) REVERT: r 177 SER cc_start: 0.8634 (m) cc_final: 0.8353 (m) REVERT: r 190 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.8042 (t80) REVERT: r 210 MET cc_start: 0.7149 (tmm) cc_final: 0.6801 (tmm) REVERT: r 224 MET cc_start: 0.7570 (tmm) cc_final: 0.7002 (ttt) REVERT: r 241 GLN cc_start: 0.8293 (tm-30) cc_final: 0.8013 (tm-30) REVERT: s 60 MET cc_start: 0.7978 (mmt) cc_final: 0.6367 (ttt) REVERT: s 61 MET cc_start: 0.7855 (ptp) cc_final: 0.7385 (ptp) REVERT: s 101 MET cc_start: 0.7636 (mmt) cc_final: 0.7284 (mmt) REVERT: s 190 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7931 (t80) REVERT: s 224 MET cc_start: 0.7049 (tpt) cc_final: 0.6822 (tpp) REVERT: t 98 PHE cc_start: 0.7599 (OUTLIER) cc_final: 0.7370 (t80) REVERT: t 107 LYS cc_start: 0.8344 (ttmm) cc_final: 0.7999 (ttpt) REVERT: t 138 MET cc_start: 0.8090 (mtt) cc_final: 0.7849 (mmt) REVERT: t 168 ARG cc_start: 0.8227 (mtm-85) cc_final: 0.7922 (mtm110) REVERT: t 210 MET cc_start: 0.7985 (tmm) cc_final: 0.7628 (tmm) REVERT: t 224 MET cc_start: 0.7660 (ttt) cc_final: 0.7288 (ttm) REVERT: u 211 MET cc_start: 0.7470 (mpp) cc_final: 0.7251 (mpp) REVERT: v 76 ASN cc_start: 0.8957 (t0) cc_final: 0.8316 (m110) REVERT: v 144 GLU cc_start: 0.3175 (OUTLIER) cc_final: 0.2301 (pt0) REVERT: v 190 PHE cc_start: 0.8806 (OUTLIER) cc_final: 0.8431 (t80) REVERT: v 195 ILE cc_start: 0.9287 (tt) cc_final: 0.9059 (tp) outliers start: 62 outliers final: 37 residues processed: 441 average time/residue: 0.0962 time to fit residues: 60.4910 Evaluate side-chains 441 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 66 ARG Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 189 ILE Chi-restraints excluded: chain r residue 190 PHE Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 98 PHE Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 80 THR Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 65 THR Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 119 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.145059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128838 restraints weight = 18891.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132324 restraints weight = 8661.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134453 restraints weight = 4804.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135819 restraints weight = 3091.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136689 restraints weight = 2248.984| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11144 Z= 0.140 Angle : 0.733 13.082 15092 Z= 0.343 Chirality : 0.041 0.307 1816 Planarity : 0.004 0.052 1885 Dihedral : 4.913 48.693 1490 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 4.81 % Allowed : 26.33 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.24), residues: 1385 helix: 1.07 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -2.46 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG v 143 TYR 0.018 0.001 TYR a 96 PHE 0.012 0.001 PHE v 64 TRP 0.017 0.001 TRP t 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00305 (11144) covalent geometry : angle 0.73317 (15092) hydrogen bonds : bond 0.03997 ( 809) hydrogen bonds : angle 4.31802 ( 2427) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8867 (tp40) cc_final: 0.7488 (tm-30) REVERT: a 84 MET cc_start: 0.7378 (tmm) cc_final: 0.7055 (tmm) REVERT: c 57 GLU cc_start: 0.7938 (tt0) cc_final: 0.7560 (tp30) REVERT: d 53 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7765 (tmm-80) REVERT: d 82 MET cc_start: 0.8760 (tpp) cc_final: 0.8504 (tpp) REVERT: e 74 ASP cc_start: 0.8438 (t70) cc_final: 0.8029 (t70) REVERT: e 83 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.7182 (tm-30) REVERT: e 84 MET cc_start: 0.7701 (tmm) cc_final: 0.7440 (tmm) REVERT: f 72 MET cc_start: 0.9038 (tpp) cc_final: 0.8694 (mmm) REVERT: f 77 LYS cc_start: 0.8076 (mttt) cc_final: 0.7673 (mmtt) REVERT: f 91 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7801 (ttpp) REVERT: r 61 MET cc_start: 0.8620 (ptp) cc_final: 0.8355 (ptp) REVERT: r 101 MET cc_start: 0.7771 (mmp) cc_final: 0.7553 (mmm) REVERT: r 177 SER cc_start: 0.8594 (m) cc_final: 0.8314 (m) REVERT: r 190 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7947 (t80) REVERT: r 210 MET cc_start: 0.6985 (tmm) cc_final: 0.6472 (tmm) REVERT: r 224 MET cc_start: 0.7593 (tmm) cc_final: 0.7037 (ttt) REVERT: r 241 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8042 (tm-30) REVERT: s 60 MET cc_start: 0.7997 (mmt) cc_final: 0.6381 (ttt) REVERT: s 61 MET cc_start: 0.7755 (ptp) cc_final: 0.7279 (ptp) REVERT: s 101 MET cc_start: 0.7626 (mmt) cc_final: 0.7331 (mmt) REVERT: s 190 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7923 (t80) REVERT: t 36 GLN cc_start: 0.8219 (pm20) cc_final: 0.7824 (pm20) REVERT: t 107 LYS cc_start: 0.8280 (ttmm) cc_final: 0.8005 (ttpt) REVERT: t 168 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7837 (mtm110) REVERT: t 178 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7842 (mt-10) REVERT: t 210 MET cc_start: 0.7998 (tmm) cc_final: 0.7236 (tmm) REVERT: t 224 MET cc_start: 0.7681 (ttt) cc_final: 0.7375 (ttm) REVERT: v 76 ASN cc_start: 0.8970 (t0) cc_final: 0.8406 (m110) REVERT: v 144 GLU cc_start: 0.3232 (OUTLIER) cc_final: 0.2491 (pm20) REVERT: v 190 PHE cc_start: 0.8797 (OUTLIER) cc_final: 0.8431 (t80) REVERT: v 195 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9062 (tp) outliers start: 57 outliers final: 40 residues processed: 427 average time/residue: 0.0924 time to fit residues: 56.9861 Evaluate side-chains 437 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 391 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain b residue 102 MET Chi-restraints excluded: chain c residue 53 ARG Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 83 GLN Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 189 ILE Chi-restraints excluded: chain r residue 190 PHE Chi-restraints excluded: chain r residue 198 LEU Chi-restraints excluded: chain r residue 209 MET Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 94 LEU Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN b 49 GLN c 83 GLN e 83 GLN f 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.128557 restraints weight = 18771.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.131957 restraints weight = 8620.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134059 restraints weight = 4801.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135363 restraints weight = 3099.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136229 restraints weight = 2281.298| |-----------------------------------------------------------------------------| r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11144 Z= 0.148 Angle : 0.749 12.505 15092 Z= 0.349 Chirality : 0.041 0.255 1816 Planarity : 0.004 0.049 1885 Dihedral : 4.873 48.658 1490 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 4.39 % Allowed : 27.51 % Favored : 68.10 % 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: 0.80 (0.24), residues: 1385 helix: 1.16 (0.16), residues: 1136 sheet: None (None), residues: 0 loop : -2.29 (0.43), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG t 66 TYR 0.015 0.001 TYR a 96 PHE 0.025 0.001 PHE t 98 TRP 0.010 0.001 TRP s 232 HIS 0.007 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00325 (11144) covalent geometry : angle 0.74911 (15092) hydrogen bonds : bond 0.04009 ( 809) hydrogen bonds : angle 4.32480 ( 2427) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 397 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7423 (mtp-110) cc_final: 0.7214 (mtp-110) REVERT: a 83 GLN cc_start: 0.8825 (tp40) cc_final: 0.7498 (tm-30) REVERT: a 84 MET cc_start: 0.7363 (tmm) cc_final: 0.7040 (tmm) REVERT: c 57 GLU cc_start: 0.7940 (tt0) cc_final: 0.7570 (tp30) REVERT: d 82 MET cc_start: 0.8761 (tpp) cc_final: 0.8515 (tpp) REVERT: e 74 ASP cc_start: 0.8446 (t70) cc_final: 0.8030 (t70) REVERT: f 72 MET cc_start: 0.9033 (tpp) cc_final: 0.8683 (mmm) REVERT: f 77 LYS cc_start: 0.8043 (mttt) cc_final: 0.7632 (mmtt) REVERT: f 91 LYS cc_start: 0.8213 (ttpt) cc_final: 0.7803 (ttpp) REVERT: r 61 MET cc_start: 0.8615 (ptp) cc_final: 0.8345 (ptp) REVERT: r 101 MET cc_start: 0.7810 (mmp) cc_final: 0.7608 (mmm) REVERT: r 177 SER cc_start: 0.8589 (m) cc_final: 0.8306 (m) REVERT: r 210 MET cc_start: 0.6929 (tmm) cc_final: 0.6707 (tmm) REVERT: r 224 MET cc_start: 0.7652 (tmm) cc_final: 0.7120 (ttt) REVERT: r 241 GLN cc_start: 0.8312 (tm-30) cc_final: 0.8045 (tm-30) REVERT: r 243 PHE cc_start: 0.7605 (t80) cc_final: 0.7399 (t80) REVERT: s 60 MET cc_start: 0.7963 (mmt) cc_final: 0.6321 (ttt) REVERT: s 105 ILE cc_start: 0.8338 (OUTLIER) cc_final: 0.8119 (mt) REVERT: s 129 LYS cc_start: 0.7639 (mmmm) cc_final: 0.7399 (mmmm) REVERT: s 190 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7908 (t80) REVERT: t 36 GLN cc_start: 0.8238 (pm20) cc_final: 0.7763 (pm20) REVERT: t 107 LYS cc_start: 0.8275 (ttmm) cc_final: 0.8014 (ttpt) REVERT: t 168 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7839 (mtm110) REVERT: t 178 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7711 (mt-10) REVERT: t 210 MET cc_start: 0.7808 (tmm) cc_final: 0.7458 (tmm) REVERT: t 224 MET cc_start: 0.7643 (ttt) cc_final: 0.7327 (ttm) REVERT: v 76 ASN cc_start: 0.8908 (t0) cc_final: 0.8368 (m110) REVERT: v 144 GLU cc_start: 0.3199 (OUTLIER) cc_final: 0.2436 (pm20) REVERT: v 190 PHE cc_start: 0.8798 (OUTLIER) cc_final: 0.8428 (t80) REVERT: v 195 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9064 (tp) outliers start: 52 outliers final: 41 residues processed: 416 average time/residue: 0.0911 time to fit residues: 54.8900 Evaluate side-chains 437 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 391 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 54 VAL Chi-restraints excluded: chain d residue 60 THR Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 198 LEU Chi-restraints excluded: chain r residue 209 MET Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 105 ILE Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 194 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 49 THR Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 68 ILE Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN b 49 GLN c 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.129210 restraints weight = 18821.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.132626 restraints weight = 8689.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134729 restraints weight = 4849.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136075 restraints weight = 3139.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.136817 restraints weight = 2294.270| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11144 Z= 0.142 Angle : 0.755 13.085 15092 Z= 0.351 Chirality : 0.042 0.279 1816 Planarity : 0.004 0.049 1885 Dihedral : 4.540 34.436 1487 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.20 % Favored : 94.73 % Rotamer: Outliers : 3.88 % Allowed : 27.93 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1385 helix: 1.26 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.28 (0.42), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG t 66 TYR 0.016 0.001 TYR a 96 PHE 0.021 0.001 PHE t 98 TRP 0.010 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00314 (11144) covalent geometry : angle 0.75524 (15092) hydrogen bonds : bond 0.03936 ( 809) hydrogen bonds : angle 4.28279 ( 2427) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 395 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7507 (mtp-110) cc_final: 0.7300 (mtp-110) REVERT: a 83 GLN cc_start: 0.8799 (tp40) cc_final: 0.7475 (tm-30) REVERT: a 84 MET cc_start: 0.7338 (tmm) cc_final: 0.7012 (tmm) REVERT: c 57 GLU cc_start: 0.7942 (tt0) cc_final: 0.7563 (tp30) REVERT: d 82 MET cc_start: 0.8768 (tpp) cc_final: 0.8522 (tpp) REVERT: e 74 ASP cc_start: 0.8463 (t70) cc_final: 0.8033 (t70) REVERT: f 72 MET cc_start: 0.8993 (tpp) cc_final: 0.8669 (mmm) REVERT: f 77 LYS cc_start: 0.8017 (mttt) cc_final: 0.7589 (mmtt) REVERT: f 91 LYS cc_start: 0.8150 (ttpt) cc_final: 0.7734 (ttpp) REVERT: r 61 MET cc_start: 0.8596 (ptp) cc_final: 0.8327 (ptp) REVERT: r 177 SER cc_start: 0.8556 (m) cc_final: 0.8268 (m) REVERT: r 210 MET cc_start: 0.6896 (tmm) cc_final: 0.6664 (tmm) REVERT: r 224 MET cc_start: 0.7675 (tmm) cc_final: 0.7115 (ttt) REVERT: r 241 GLN cc_start: 0.8302 (tm-30) cc_final: 0.8037 (tm-30) REVERT: r 243 PHE cc_start: 0.7480 (t80) cc_final: 0.7187 (t80) REVERT: s 60 MET cc_start: 0.7955 (mmt) cc_final: 0.6439 (ttt) REVERT: s 61 MET cc_start: 0.7616 (ptp) cc_final: 0.7317 (ptp) REVERT: s 129 LYS cc_start: 0.7658 (mmmm) cc_final: 0.7408 (mmmm) REVERT: s 190 PHE cc_start: 0.8219 (OUTLIER) cc_final: 0.7907 (t80) REVERT: s 224 MET cc_start: 0.7005 (tpt) cc_final: 0.6796 (tpt) REVERT: t 36 GLN cc_start: 0.8217 (pm20) cc_final: 0.7722 (pm20) REVERT: t 107 LYS cc_start: 0.8230 (ttmm) cc_final: 0.7969 (ttmt) REVERT: t 168 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7719 (mtm110) REVERT: t 210 MET cc_start: 0.7859 (tmm) cc_final: 0.7501 (tmm) REVERT: t 224 MET cc_start: 0.7636 (ttt) cc_final: 0.7328 (ttm) REVERT: v 76 ASN cc_start: 0.8896 (t0) cc_final: 0.8331 (m110) REVERT: v 190 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8431 (t80) REVERT: v 195 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9091 (tp) outliers start: 46 outliers final: 37 residues processed: 413 average time/residue: 0.0891 time to fit residues: 53.6371 Evaluate side-chains 424 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 384 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 100 MET Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 88 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain c residue 49 GLN Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 209 MET Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 65 THR Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 44 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 103 GLN c 83 GLN f 87 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.128999 restraints weight = 18740.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132391 restraints weight = 8711.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.134498 restraints weight = 4886.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135816 restraints weight = 3170.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.136654 restraints weight = 2330.155| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11144 Z= 0.147 Angle : 0.779 13.896 15092 Z= 0.362 Chirality : 0.042 0.321 1816 Planarity : 0.004 0.049 1885 Dihedral : 4.370 22.198 1484 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 3.63 % Allowed : 28.19 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.24), residues: 1385 helix: 1.32 (0.16), residues: 1132 sheet: None (None), residues: 0 loop : -2.23 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 53 TYR 0.014 0.002 TYR c 96 PHE 0.020 0.001 PHE t 98 TRP 0.010 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00327 (11144) covalent geometry : angle 0.77889 (15092) hydrogen bonds : bond 0.03949 ( 809) hydrogen bonds : angle 4.29488 ( 2427) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 385 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 44 ARG cc_start: 0.7594 (mtp-110) cc_final: 0.7393 (mtp-110) REVERT: a 83 GLN cc_start: 0.8781 (tp40) cc_final: 0.7297 (tm-30) REVERT: a 84 MET cc_start: 0.7327 (tmm) cc_final: 0.6989 (tmm) REVERT: c 57 GLU cc_start: 0.7859 (tt0) cc_final: 0.7560 (tp30) REVERT: d 53 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7543 (tmm-80) REVERT: d 82 MET cc_start: 0.8760 (tpp) cc_final: 0.8509 (tpp) REVERT: e 74 ASP cc_start: 0.8462 (t70) cc_final: 0.8034 (t70) REVERT: f 77 LYS cc_start: 0.7995 (mttt) cc_final: 0.7577 (mmtt) REVERT: f 91 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7652 (ttpp) REVERT: f 98 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7807 (mp0) REVERT: r 61 MET cc_start: 0.8637 (ptp) cc_final: 0.8355 (ptp) REVERT: r 177 SER cc_start: 0.8660 (m) cc_final: 0.8363 (m) REVERT: r 210 MET cc_start: 0.6943 (tmm) cc_final: 0.6720 (tmm) REVERT: r 224 MET cc_start: 0.7687 (tmm) cc_final: 0.7121 (ttt) REVERT: r 235 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7781 (tt) REVERT: r 241 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8035 (tm-30) REVERT: r 243 PHE cc_start: 0.7505 (t80) cc_final: 0.7220 (t80) REVERT: s 60 MET cc_start: 0.7956 (mmt) cc_final: 0.6211 (ttt) REVERT: s 61 MET cc_start: 0.7461 (ptp) cc_final: 0.7149 (ptp) REVERT: s 129 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7310 (mmmm) REVERT: s 190 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7902 (t80) REVERT: s 224 MET cc_start: 0.7015 (tpt) cc_final: 0.6803 (tpt) REVERT: t 36 GLN cc_start: 0.8201 (pm20) cc_final: 0.7668 (pm20) REVERT: t 107 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7977 (ttmt) REVERT: t 168 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7726 (mtm110) REVERT: t 178 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7718 (mt-10) REVERT: t 210 MET cc_start: 0.7808 (tmm) cc_final: 0.7497 (tmm) REVERT: t 224 MET cc_start: 0.7637 (ttt) cc_final: 0.7375 (ttm) REVERT: u 224 MET cc_start: 0.7760 (ttt) cc_final: 0.7357 (ttp) REVERT: v 76 ASN cc_start: 0.8885 (t0) cc_final: 0.8336 (m110) REVERT: v 190 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.8445 (t80) REVERT: v 195 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9092 (tp) outliers start: 43 outliers final: 36 residues processed: 401 average time/residue: 0.0862 time to fit residues: 50.1892 Evaluate side-chains 425 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 385 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 61 LEU Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 100 MET Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 97 GLN Chi-restraints excluded: chain b residue 99 VAL Chi-restraints excluded: chain c residue 88 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 88 VAL Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 209 MET Chi-restraints excluded: chain r residue 227 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 61 MET Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 199 VAL Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 49 THR Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 0.0570 chunk 63 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.131104 restraints weight = 18936.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.134569 restraints weight = 8816.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136688 restraints weight = 4930.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138043 restraints weight = 3193.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138926 restraints weight = 2333.304| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11144 Z= 0.134 Angle : 0.805 20.789 15092 Z= 0.364 Chirality : 0.041 0.300 1816 Planarity : 0.004 0.049 1885 Dihedral : 4.289 20.626 1484 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 2.70 % Allowed : 29.37 % Favored : 67.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.24), residues: 1385 helix: 1.48 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.39 (0.43), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 53 TYR 0.016 0.001 TYR c 96 PHE 0.020 0.001 PHE t 98 TRP 0.010 0.001 TRP s 232 HIS 0.005 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00298 (11144) covalent geometry : angle 0.80469 (15092) hydrogen bonds : bond 0.03655 ( 809) hydrogen bonds : angle 4.19959 ( 2427) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2770 Ramachandran restraints generated. 1385 Oldfield, 0 Emsley, 1385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 397 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8613 (tp40) cc_final: 0.7107 (tm-30) REVERT: a 84 MET cc_start: 0.7222 (tmm) cc_final: 0.6882 (tmm) REVERT: c 57 GLU cc_start: 0.7829 (tt0) cc_final: 0.7532 (tp30) REVERT: d 53 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7638 (tmm-80) REVERT: f 77 LYS cc_start: 0.8012 (mttt) cc_final: 0.7536 (mmtt) REVERT: f 91 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7620 (ttpp) REVERT: f 98 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7762 (mp0) REVERT: r 61 MET cc_start: 0.8484 (ptp) cc_final: 0.8174 (ptp) REVERT: r 177 SER cc_start: 0.8725 (m) cc_final: 0.8395 (m) REVERT: r 210 MET cc_start: 0.6915 (tmm) cc_final: 0.6695 (tmm) REVERT: r 224 MET cc_start: 0.7686 (tmm) cc_final: 0.7120 (ttt) REVERT: r 241 GLN cc_start: 0.8278 (tm-30) cc_final: 0.8027 (tm-30) REVERT: r 243 PHE cc_start: 0.7418 (t80) cc_final: 0.7121 (t80) REVERT: s 60 MET cc_start: 0.7950 (mmt) cc_final: 0.6274 (ttt) REVERT: s 61 MET cc_start: 0.7489 (ptp) cc_final: 0.7232 (ptp) REVERT: s 190 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7973 (t80) REVERT: s 224 MET cc_start: 0.6942 (tpt) cc_final: 0.6730 (tpt) REVERT: t 36 GLN cc_start: 0.8205 (pm20) cc_final: 0.7671 (pm20) REVERT: t 107 LYS cc_start: 0.8213 (ttmm) cc_final: 0.7969 (ttpt) REVERT: t 127 LEU cc_start: 0.8693 (tp) cc_final: 0.8363 (tt) REVERT: t 138 MET cc_start: 0.7613 (mmt) cc_final: 0.7043 (mmt) REVERT: t 168 ARG cc_start: 0.8090 (mtm-85) cc_final: 0.7791 (mtm110) REVERT: t 178 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7602 (mt-10) REVERT: t 210 MET cc_start: 0.7749 (tmm) cc_final: 0.7445 (tmm) REVERT: t 224 MET cc_start: 0.7526 (ttt) cc_final: 0.7275 (ttm) REVERT: u 169 ILE cc_start: 0.8318 (mm) cc_final: 0.8029 (mp) REVERT: u 174 TYR cc_start: 0.8685 (t80) cc_final: 0.8372 (t80) REVERT: v 76 ASN cc_start: 0.8786 (t0) cc_final: 0.8263 (m110) REVERT: v 138 MET cc_start: 0.7981 (mtp) cc_final: 0.7702 (mtt) REVERT: v 190 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8443 (t80) REVERT: v 195 ILE cc_start: 0.9303 (OUTLIER) cc_final: 0.9091 (tp) outliers start: 32 outliers final: 24 residues processed: 409 average time/residue: 0.0911 time to fit residues: 54.0117 Evaluate side-chains 412 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 385 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 71 VAL Chi-restraints excluded: chain d residue 75 MET Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 105 ILE Chi-restraints excluded: chain r residue 106 ASP Chi-restraints excluded: chain r residue 110 VAL Chi-restraints excluded: chain r residue 235 LEU Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 190 PHE Chi-restraints excluded: chain s residue 191 ILE Chi-restraints excluded: chain s residue 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 190 PHE Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 112 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 85 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 49 GLN f 87 GLN v 141 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.146286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.130141 restraints weight = 18836.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.133607 restraints weight = 8687.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135750 restraints weight = 4837.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.137108 restraints weight = 3114.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137993 restraints weight = 2272.031| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11144 Z= 0.141 Angle : 0.811 18.182 15092 Z= 0.371 Chirality : 0.042 0.320 1816 Planarity : 0.005 0.067 1885 Dihedral : 4.299 22.412 1484 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 2.78 % Allowed : 29.79 % Favored : 67.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.24), residues: 1385 helix: 1.50 (0.16), residues: 1138 sheet: None (None), residues: 0 loop : -2.28 (0.43), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG v 143 TYR 0.014 0.001 TYR a 96 PHE 0.019 0.001 PHE t 98 TRP 0.007 0.001 TRP t 232 HIS 0.006 0.001 HIS e 39 Details of bonding type rmsd covalent geometry : bond 0.00318 (11144) covalent geometry : angle 0.81129 (15092) hydrogen bonds : bond 0.03745 ( 809) hydrogen bonds : angle 4.21424 ( 2427) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2090.97 seconds wall clock time: 36 minutes 37.12 seconds (2197.12 seconds total)