Starting phenix.real_space_refine on Tue Jul 29 00:16:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cg4_30350/07_2025/7cg4_30350.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cg4_30350/07_2025/7cg4_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_30350/07_2025/7cg4_30350.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cg4_30350/07_2025/7cg4_30350.map" model { file = "/net/cci-nas-00/data/ceres_data/7cg4_30350/07_2025/7cg4_30350.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cg4_30350/07_2025/7cg4_30350.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 9.27, per 1000 atoms: 0.85 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: 3.28 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.10 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: 3.47 Time building geometry restraints manager: 3.58 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: 64.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.140 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.250 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.013 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.017 0.001 PHE v 64 TYR 0.013 0.001 TYR s 244 ARG 0.002 0.000 ARG r 168 Details of bonding type rmsd hydrogen bonds : bond 0.12108 ( 809) hydrogen bonds : angle 5.57778 ( 2427) covalent geometry : bond 0.00328 (11144) covalent geometry : angle 0.69137 (15092) *********************** 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 : 1.376 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: 0.8319 (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: 0.2268 time to fit residues: 144.5979 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 : 1.261 ------------------------------------------------------------------------------- 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 116 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 58 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 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 d 49 GLN r 141 GLN t 43 GLN u 86 ASN u 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.127906 restraints weight = 18694.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.131302 restraints weight = 8634.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.133401 restraints weight = 4833.653| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11144 Z= 0.146 Angle : 0.721 9.760 15092 Z= 0.341 Chirality : 0.041 0.170 1816 Planarity : 0.005 0.065 1885 Dihedral : 5.336 59.733 1490 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 3.38 % Allowed : 18.57 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.23), residues: 1385 helix: 0.13 (0.16), residues: 1121 sheet: None (None), residues: 0 loop : -3.05 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP s 232 HIS 0.006 0.001 HIS e 39 PHE 0.017 0.001 PHE c 34 TYR 0.013 0.001 TYR t 244 ARG 0.007 0.001 ARG b 89 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 809) hydrogen bonds : angle 4.63994 ( 2427) covalent geometry : bond 0.00306 (11144) covalent geometry : angle 0.72084 (15092) *********************** 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 459 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 419 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 57 GLU cc_start: 0.8070 (tt0) cc_final: 0.7547 (tp30) REVERT: c 75 MET cc_start: 0.8162 (tmm) cc_final: 0.7870 (tpt) REVERT: e 74 ASP cc_start: 0.8388 (t70) cc_final: 0.8080 (t70) REVERT: e 83 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: e 84 MET cc_start: 0.7465 (tmm) cc_final: 0.6840 (tmm) REVERT: f 77 LYS cc_start: 0.8056 (mttt) cc_final: 0.7658 (mmtt) REVERT: f 91 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7804 (ttpp) REVERT: r 76 ASN cc_start: 0.9007 (t0) cc_final: 0.8732 (t0) REVERT: r 211 MET cc_start: 0.7130 (mmp) cc_final: 0.6775 (mmm) REVERT: r 241 GLN cc_start: 0.8311 (tm-30) cc_final: 0.8051 (tm-30) REVERT: s 60 MET cc_start: 0.8078 (mmt) cc_final: 0.6334 (ttt) REVERT: s 101 MET cc_start: 0.7665 (mmt) cc_final: 0.7266 (mmt) REVERT: s 211 MET cc_start: 0.8508 (pmm) cc_final: 0.8206 (pmm) REVERT: t 171 LEU cc_start: 0.8768 (tt) cc_final: 0.8565 (tp) REVERT: t 178 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7770 (mt-10) REVERT: u 178 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: v 123 MET cc_start: 0.5837 (tpt) cc_final: 0.5575 (tpt) REVERT: v 190 PHE cc_start: 0.8866 (OUTLIER) cc_final: 0.8440 (t80) REVERT: v 195 ILE cc_start: 0.9214 (tt) cc_final: 0.8977 (tp) outliers start: 40 outliers final: 25 residues processed: 432 average time/residue: 0.2120 time to fit residues: 130.7398 Evaluate side-chains 426 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 398 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain c residue 77 LYS Chi-restraints excluded: chain d residue 60 THR 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 37 SER 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 203 VAL Chi-restraints excluded: chain u residue 80 THR Chi-restraints excluded: chain u residue 178 GLU Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 37 SER 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 50 optimal weight: 0.8980 chunk 112 optimal weight: 0.0670 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.0040 chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 0.0370 chunk 118 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.1966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN ** r 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 36 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.147700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.131703 restraints weight = 18657.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135207 restraints weight = 8491.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137332 restraints weight = 4689.754| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2110 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= 0.127 Angle : 0.687 9.081 15092 Z= 0.320 Chirality : 0.039 0.190 1816 Planarity : 0.004 0.060 1885 Dihedral : 5.042 51.750 1490 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.87 % Rotamer: Outliers : 2.95 % Allowed : 22.28 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1385 helix: 0.80 (0.16), residues: 1126 sheet: None (None), residues: 0 loop : -2.68 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP t 232 HIS 0.003 0.001 HIS e 39 PHE 0.013 0.001 PHE t 226 TYR 0.019 0.001 TYR b 96 ARG 0.005 0.000 ARG d 53 Details of bonding type rmsd hydrogen bonds : bond 0.03867 ( 809) hydrogen bonds : angle 4.31458 ( 2427) covalent geometry : bond 0.00260 (11144) covalent geometry : angle 0.68709 (15092) *********************** 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 450 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 415 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 97 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8632 (mm-40) REVERT: c 57 GLU cc_start: 0.8021 (tt0) cc_final: 0.7524 (tp30) REVERT: c 74 ASP cc_start: 0.8780 (m-30) cc_final: 0.8543 (m-30) REVERT: d 82 MET cc_start: 0.8530 (tpp) cc_final: 0.8280 (tpp) REVERT: e 83 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.7255 (tm-30) REVERT: e 84 MET cc_start: 0.7548 (tmm) cc_final: 0.6773 (tmm) REVERT: f 72 MET cc_start: 0.8957 (tpp) cc_final: 0.8565 (mmm) REVERT: f 77 LYS cc_start: 0.8049 (mttt) cc_final: 0.7657 (mmtt) REVERT: f 91 LYS cc_start: 0.8105 (ttpt) cc_final: 0.7721 (ttpp) REVERT: f 100 MET cc_start: 0.7974 (tpp) cc_final: 0.7715 (tpp) REVERT: r 190 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7947 (t80) REVERT: r 210 MET cc_start: 0.7319 (tmm) cc_final: 0.6940 (tmm) REVERT: r 224 MET cc_start: 0.7532 (tmm) cc_final: 0.7055 (ttt) REVERT: r 241 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7944 (tm-30) REVERT: s 60 MET cc_start: 0.7954 (mmt) cc_final: 0.6403 (ttt) REVERT: s 61 MET cc_start: 0.7977 (ptp) cc_final: 0.7607 (ptp) REVERT: s 101 MET cc_start: 0.7459 (mmt) cc_final: 0.7245 (mmt) REVERT: s 190 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7931 (t80) REVERT: s 209 MET cc_start: 0.8333 (mpp) cc_final: 0.8119 (mpp) REVERT: t 127 LEU cc_start: 0.8592 (tp) cc_final: 0.8102 (tt) REVERT: t 168 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7911 (mtm110) REVERT: t 210 MET cc_start: 0.7947 (tmm) cc_final: 0.7269 (tmm) REVERT: t 224 MET cc_start: 0.7628 (ttt) cc_final: 0.7284 (ttm) REVERT: t 236 MET cc_start: 0.7548 (mtt) cc_final: 0.7321 (mtm) REVERT: u 209 MET cc_start: 0.8908 (tpp) cc_final: 0.8591 (tpp) REVERT: v 66 ARG cc_start: 0.7280 (ptp-170) cc_final: 0.6972 (ptm160) REVERT: v 76 ASN cc_start: 0.8988 (t0) cc_final: 0.8292 (m110) REVERT: v 111 ASP cc_start: 0.3807 (OUTLIER) cc_final: 0.3551 (m-30) REVERT: v 190 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8422 (t80) REVERT: v 195 ILE cc_start: 0.9145 (tt) cc_final: 0.8910 (tp) outliers start: 35 outliers final: 19 residues processed: 428 average time/residue: 0.2207 time to fit residues: 133.8922 Evaluate side-chains 418 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 394 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 b residue 97 GLN Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 83 GLN 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 190 PHE 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 227 VAL 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 191 ILE Chi-restraints excluded: chain v residue 64 PHE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 75 optimal weight: 0.0060 chunk 24 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN c 49 GLN s 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.147291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.131241 restraints weight = 18596.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.134781 restraints weight = 8551.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.136943 restraints weight = 4729.945| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2350 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= 0.124 Angle : 0.678 9.672 15092 Z= 0.318 Chirality : 0.040 0.258 1816 Planarity : 0.004 0.053 1885 Dihedral : 4.878 49.342 1490 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.98 % Favored : 94.95 % Rotamer: Outliers : 4.30 % Allowed : 23.21 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.24), residues: 1385 helix: 0.98 (0.16), residues: 1140 sheet: None (None), residues: 0 loop : -2.74 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP s 232 HIS 0.005 0.001 HIS e 39 PHE 0.012 0.001 PHE r 187 TYR 0.021 0.001 TYR b 96 ARG 0.005 0.000 ARG b 53 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 809) hydrogen bonds : angle 4.21157 ( 2427) covalent geometry : bond 0.00264 (11144) covalent geometry : angle 0.67827 (15092) *********************** 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 462 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 411 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 97 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8622 (mm-40) REVERT: c 57 GLU cc_start: 0.7987 (tt0) cc_final: 0.7571 (tp30) REVERT: c 84 MET cc_start: 0.7576 (tmm) cc_final: 0.7371 (tmm) REVERT: d 53 ARG cc_start: 0.7847 (tmm-80) cc_final: 0.7638 (ttp80) REVERT: d 57 GLU cc_start: 0.7306 (tp30) cc_final: 0.6915 (tp30) REVERT: e 83 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: e 84 MET cc_start: 0.7680 (tmm) cc_final: 0.6852 (tmm) REVERT: f 72 MET cc_start: 0.8954 (tpp) cc_final: 0.8582 (mmm) REVERT: f 77 LYS cc_start: 0.8090 (mttt) cc_final: 0.7683 (mmtt) REVERT: f 91 LYS cc_start: 0.8088 (ttpt) cc_final: 0.7709 (ttpp) REVERT: r 96 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8253 (mp) REVERT: r 190 PHE cc_start: 0.8203 (OUTLIER) cc_final: 0.7962 (t80) REVERT: r 210 MET cc_start: 0.7265 (tmm) cc_final: 0.7023 (tmm) REVERT: r 211 MET cc_start: 0.7665 (mmm) cc_final: 0.7387 (mmm) REVERT: r 224 MET cc_start: 0.7585 (tmm) cc_final: 0.7056 (ttt) REVERT: r 241 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7928 (tm-30) REVERT: s 60 MET cc_start: 0.7897 (mmt) cc_final: 0.6410 (ttt) REVERT: s 61 MET cc_start: 0.7859 (ptp) cc_final: 0.7509 (ptp) REVERT: s 75 ARG cc_start: 0.8480 (ttp80) cc_final: 0.8071 (ttm170) REVERT: s 101 MET cc_start: 0.7454 (mmt) cc_final: 0.7228 (mmt) REVERT: s 190 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7939 (t80) REVERT: t 107 LYS cc_start: 0.8242 (ttmm) cc_final: 0.7947 (ttpt) REVERT: t 127 LEU cc_start: 0.8624 (tp) cc_final: 0.8137 (tt) REVERT: t 138 MET cc_start: 0.7995 (mtt) cc_final: 0.7760 (mmt) REVERT: t 168 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7857 (mtm110) REVERT: t 224 MET cc_start: 0.7642 (ttt) cc_final: 0.7359 (ttm) REVERT: t 236 MET cc_start: 0.7653 (mtt) cc_final: 0.7283 (mtm) REVERT: u 150 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.7064 (t80) REVERT: v 66 ARG cc_start: 0.7405 (ptp-170) cc_final: 0.7155 (ptm160) REVERT: v 76 ASN cc_start: 0.8977 (t0) cc_final: 0.8302 (m110) REVERT: v 111 ASP cc_start: 0.3827 (OUTLIER) cc_final: 0.3624 (m-30) REVERT: v 190 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8429 (t80) REVERT: v 195 ILE cc_start: 0.9150 (tt) cc_final: 0.8916 (tp) outliers start: 51 outliers final: 32 residues processed: 430 average time/residue: 0.2530 time to fit residues: 155.0370 Evaluate side-chains 432 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 393 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 97 GLN Chi-restraints excluded: chain d residue 37 GLN Chi-restraints excluded: chain d residue 47 ASP Chi-restraints excluded: chain d residue 54 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 37 SER Chi-restraints excluded: chain r residue 65 THR Chi-restraints excluded: chain r residue 96 LEU 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 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 t residue 179 LEU Chi-restraints excluded: chain t residue 196 ILE 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 179 LEU Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 224 MET 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 71 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 133 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 chunk 16 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.148006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131956 restraints weight = 18664.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.135437 restraints weight = 8610.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.137596 restraints weight = 4784.695| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2609 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= 0.125 Angle : 0.696 10.862 15092 Z= 0.324 Chirality : 0.039 0.195 1816 Planarity : 0.004 0.051 1885 Dihedral : 4.744 49.122 1490 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 4.47 % Allowed : 24.47 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.24), residues: 1385 helix: 1.22 (0.16), residues: 1131 sheet: None (None), residues: 0 loop : -2.53 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.019 0.001 PHE c 34 TYR 0.015 0.001 TYR u 174 ARG 0.006 0.000 ARG b 53 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 809) hydrogen bonds : angle 4.14591 ( 2427) covalent geometry : bond 0.00269 (11144) covalent geometry : angle 0.69646 (15092) *********************** 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 454 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 401 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 97 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8592 (mm-40) REVERT: c 57 GLU cc_start: 0.7953 (tt0) cc_final: 0.7532 (tp30) REVERT: c 84 MET cc_start: 0.7610 (tmm) cc_final: 0.7374 (tmm) REVERT: d 53 ARG cc_start: 0.7855 (tmm-80) cc_final: 0.7627 (tmm-80) REVERT: d 57 GLU cc_start: 0.7212 (tp30) cc_final: 0.6888 (tp30) REVERT: e 83 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7141 (tm-30) REVERT: e 84 MET cc_start: 0.7703 (tmm) cc_final: 0.7454 (tmm) REVERT: f 72 MET cc_start: 0.9003 (tpp) cc_final: 0.8629 (mmm) REVERT: f 77 LYS cc_start: 0.8018 (mttt) cc_final: 0.7595 (mmtt) REVERT: f 91 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7789 (ttpp) REVERT: r 66 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8136 (ptm160) REVERT: r 190 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7860 (t80) REVERT: r 224 MET cc_start: 0.7595 (tmm) cc_final: 0.7045 (ttt) REVERT: r 241 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7903 (tm-30) REVERT: s 60 MET cc_start: 0.7900 (mmt) cc_final: 0.6539 (ttt) REVERT: s 61 MET cc_start: 0.7702 (ptp) cc_final: 0.7299 (ptp) REVERT: s 190 PHE cc_start: 0.8196 (OUTLIER) cc_final: 0.7894 (t80) REVERT: s 209 MET cc_start: 0.8349 (mpp) cc_final: 0.8112 (mpp) REVERT: s 224 MET cc_start: 0.6762 (tpp) cc_final: 0.6496 (tpt) REVERT: t 36 GLN cc_start: 0.8380 (pm20) cc_final: 0.7914 (pm20) REVERT: t 107 LYS cc_start: 0.8258 (ttmm) cc_final: 0.7999 (ttpt) REVERT: t 127 LEU cc_start: 0.8604 (tp) cc_final: 0.8126 (tt) REVERT: t 138 MET cc_start: 0.8039 (mtt) cc_final: 0.7762 (mtt) REVERT: t 168 ARG cc_start: 0.8233 (mtm-85) cc_final: 0.7843 (mtm110) REVERT: t 224 MET cc_start: 0.7607 (ttt) cc_final: 0.7283 (ttm) REVERT: t 232 TRP cc_start: 0.7950 (m-90) cc_final: 0.7492 (m-90) REVERT: t 236 MET cc_start: 0.7645 (mtt) cc_final: 0.7429 (mtm) REVERT: u 150 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7045 (t80) REVERT: v 76 ASN cc_start: 0.8927 (t0) cc_final: 0.8246 (m110) REVERT: v 144 GLU cc_start: 0.3149 (OUTLIER) cc_final: 0.2525 (pm20) REVERT: v 195 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8956 (tp) outliers start: 53 outliers final: 29 residues processed: 427 average time/residue: 0.3475 time to fit residues: 217.4199 Evaluate side-chains 424 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 388 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 d residue 37 GLN Chi-restraints excluded: chain d residue 47 ASP 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 37 SER Chi-restraints excluded: chain r residue 65 THR 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 189 ILE Chi-restraints excluded: chain r residue 190 PHE Chi-restraints excluded: chain r residue 209 MET 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 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 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 64 PHE Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 179 LEU Chi-restraints excluded: chain v residue 195 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 105 optimal weight: 0.0000 chunk 84 optimal weight: 0.7980 chunk 127 optimal weight: 0.5980 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 0.2980 chunk 128 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 114 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 49 GLN e 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.148096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131963 restraints weight = 18553.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.135476 restraints weight = 8508.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.137651 restraints weight = 4732.286| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11144 Z= 0.126 Angle : 0.719 13.076 15092 Z= 0.331 Chirality : 0.040 0.284 1816 Planarity : 0.004 0.051 1885 Dihedral : 4.640 48.246 1490 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 3.63 % Allowed : 26.24 % Favored : 70.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.24), residues: 1385 helix: 1.33 (0.16), residues: 1137 sheet: None (None), residues: 0 loop : -2.67 (0.40), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.014 0.001 PHE r 187 TYR 0.015 0.001 TYR a 96 ARG 0.007 0.001 ARG v 143 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 809) hydrogen bonds : angle 4.10983 ( 2427) covalent geometry : bond 0.00273 (11144) covalent geometry : angle 0.71871 (15092) *********************** 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 448 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 405 time to evaluate : 1.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8822 (tp40) cc_final: 0.7490 (tm-30) REVERT: c 57 GLU cc_start: 0.7972 (tt0) cc_final: 0.7545 (tp30) REVERT: c 84 MET cc_start: 0.7618 (tmm) cc_final: 0.7372 (tmm) REVERT: c 100 MET cc_start: 0.8791 (tpp) cc_final: 0.7906 (mtp) REVERT: d 53 ARG cc_start: 0.7858 (tmm-80) cc_final: 0.7605 (tmm-80) REVERT: d 57 GLU cc_start: 0.7186 (tp30) cc_final: 0.6956 (tp30) REVERT: f 72 MET cc_start: 0.9018 (tpp) cc_final: 0.8665 (mmm) REVERT: f 77 LYS cc_start: 0.8054 (mttt) cc_final: 0.7630 (mmtt) REVERT: f 91 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7759 (ttpp) REVERT: r 66 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8096 (ptm160) REVERT: r 224 MET cc_start: 0.7575 (tmm) cc_final: 0.7083 (ttt) REVERT: r 241 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7894 (tm-30) REVERT: s 60 MET cc_start: 0.8028 (mmt) cc_final: 0.6633 (ttt) REVERT: s 61 MET cc_start: 0.7601 (ptp) cc_final: 0.7166 (ptp) REVERT: s 101 MET cc_start: 0.7016 (mmt) cc_final: 0.6573 (mmt) REVERT: s 190 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7873 (t80) REVERT: s 224 MET cc_start: 0.6830 (tpp) cc_final: 0.6538 (tpt) REVERT: t 36 GLN cc_start: 0.8331 (pm20) cc_final: 0.7793 (pm20) REVERT: t 107 LYS cc_start: 0.8271 (ttmm) cc_final: 0.7943 (ttpt) REVERT: t 138 MET cc_start: 0.7937 (mtt) cc_final: 0.7657 (mtt) REVERT: t 168 ARG cc_start: 0.8141 (mtm-85) cc_final: 0.7725 (mtm110) REVERT: t 224 MET cc_start: 0.7654 (ttt) cc_final: 0.7293 (ttm) REVERT: t 232 TRP cc_start: 0.7634 (m-90) cc_final: 0.7391 (m-90) REVERT: t 236 MET cc_start: 0.7679 (mtt) cc_final: 0.7472 (mtm) REVERT: u 150 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.7111 (t80) REVERT: v 60 MET cc_start: 0.7952 (tpt) cc_final: 0.7616 (tpt) REVERT: v 76 ASN cc_start: 0.8946 (t0) cc_final: 0.8381 (m110) REVERT: v 144 GLU cc_start: 0.3112 (OUTLIER) cc_final: 0.2504 (pm20) REVERT: v 195 ILE cc_start: 0.9190 (tt) cc_final: 0.8965 (tp) outliers start: 43 outliers final: 34 residues processed: 424 average time/residue: 0.2668 time to fit residues: 160.8277 Evaluate side-chains 427 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 389 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 d residue 37 GLN 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 d residue 104 VAL 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 41 SER Chi-restraints excluded: chain r residue 65 THR 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 189 ILE 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 190 PHE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 225 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 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 194 LEU Chi-restraints excluded: chain u residue 224 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 144 GLU Chi-restraints excluded: chain v residue 179 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 87 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 75 optimal weight: 0.0000 chunk 16 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.147661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.131457 restraints weight = 18983.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.135007 restraints weight = 8753.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.137189 restraints weight = 4853.155| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2861 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= 0.130 Angle : 0.733 12.565 15092 Z= 0.336 Chirality : 0.040 0.252 1816 Planarity : 0.004 0.047 1885 Dihedral : 4.321 33.454 1487 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.69 % Favored : 95.23 % Rotamer: Outliers : 3.88 % Allowed : 27.00 % Favored : 69.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.24), residues: 1385 helix: 1.42 (0.16), residues: 1142 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.013 0.001 PHE r 187 TYR 0.011 0.001 TYR s 244 ARG 0.006 0.000 ARG b 53 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 809) hydrogen bonds : angle 4.08847 ( 2427) covalent geometry : bond 0.00285 (11144) covalent geometry : angle 0.73270 (15092) *********************** 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 435 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 389 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8783 (tp40) cc_final: 0.7483 (tm-30) REVERT: c 57 GLU cc_start: 0.7971 (tt0) cc_final: 0.7565 (tp30) REVERT: c 84 MET cc_start: 0.7615 (tmm) cc_final: 0.7370 (tmm) REVERT: c 100 MET cc_start: 0.8768 (tpp) cc_final: 0.7888 (mtp) REVERT: d 53 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7580 (tmm-80) REVERT: f 72 MET cc_start: 0.8949 (tpp) cc_final: 0.8603 (mmm) REVERT: f 77 LYS cc_start: 0.8041 (mttt) cc_final: 0.7618 (mmmt) REVERT: f 91 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7757 (ttpp) REVERT: r 66 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.7992 (ptm160) REVERT: r 101 MET cc_start: 0.7521 (mmp) cc_final: 0.7284 (mmm) REVERT: r 118 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.6915 (pp20) REVERT: r 224 MET cc_start: 0.7596 (tmm) cc_final: 0.7077 (ttt) REVERT: r 241 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7965 (tm-30) REVERT: s 60 MET cc_start: 0.8030 (mmt) cc_final: 0.6633 (ttt) REVERT: s 61 MET cc_start: 0.7530 (ptp) cc_final: 0.7088 (ptp) REVERT: s 101 MET cc_start: 0.7022 (mmt) cc_final: 0.6622 (mmt) REVERT: s 190 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7860 (t80) REVERT: s 224 MET cc_start: 0.6882 (tpp) cc_final: 0.6601 (tpt) REVERT: t 36 GLN cc_start: 0.8311 (pm20) cc_final: 0.7748 (pm20) REVERT: t 107 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7942 (ttmt) REVERT: t 138 MET cc_start: 0.7919 (mtt) cc_final: 0.7675 (mtt) REVERT: t 168 ARG cc_start: 0.8107 (mtm-85) cc_final: 0.7753 (mtm110) REVERT: t 210 MET cc_start: 0.7824 (tmm) cc_final: 0.7496 (tmm) REVERT: t 224 MET cc_start: 0.7662 (ttt) cc_final: 0.7347 (ttm) REVERT: t 236 MET cc_start: 0.7669 (mtt) cc_final: 0.7451 (mtm) REVERT: u 150 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.7137 (t80) REVERT: v 76 ASN cc_start: 0.8923 (t0) cc_final: 0.8298 (m110) REVERT: v 190 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.8410 (t80) REVERT: v 195 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9052 (tp) outliers start: 46 outliers final: 32 residues processed: 407 average time/residue: 0.2395 time to fit residues: 141.1650 Evaluate side-chains 418 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 380 time to evaluate : 1.205 ------------------------------------------------------------------------------- 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 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 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 118 GLU Chi-restraints excluded: chain r residue 189 ILE 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 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 43 GLN 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 150 PHE Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 194 LEU Chi-restraints excluded: chain u residue 224 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 179 LEU 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 36 optimal weight: 0.5980 chunk 104 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 0.8980 chunk 75 optimal weight: 0.0370 chunk 94 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.149121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.132861 restraints weight = 18596.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.136373 restraints weight = 8639.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.138522 restraints weight = 4826.790| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11144 Z= 0.126 Angle : 0.749 13.571 15092 Z= 0.342 Chirality : 0.040 0.276 1816 Planarity : 0.004 0.049 1885 Dihedral : 4.120 21.287 1484 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 3.54 % Allowed : 27.51 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.24), residues: 1385 helix: 1.55 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -2.33 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP t 232 HIS 0.004 0.001 HIS e 39 PHE 0.013 0.001 PHE t 150 TYR 0.010 0.001 TYR u 174 ARG 0.006 0.000 ARG b 53 Details of bonding type rmsd hydrogen bonds : bond 0.03392 ( 809) hydrogen bonds : angle 4.00822 ( 2427) covalent geometry : bond 0.00276 (11144) covalent geometry : angle 0.74922 (15092) *********************** 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 436 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 394 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8656 (tp40) cc_final: 0.7139 (tm-30) REVERT: c 57 GLU cc_start: 0.7949 (tt0) cc_final: 0.7544 (tp30) REVERT: c 84 MET cc_start: 0.7669 (tmm) cc_final: 0.7412 (tmm) REVERT: d 53 ARG cc_start: 0.7858 (tmm-80) cc_final: 0.7576 (tmm-80) REVERT: f 72 MET cc_start: 0.8915 (tpp) cc_final: 0.8579 (mmm) REVERT: f 77 LYS cc_start: 0.8038 (mttt) cc_final: 0.7600 (mmmt) REVERT: f 91 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7517 (ttpp) REVERT: f 103 GLN cc_start: 0.7473 (tm-30) cc_final: 0.7217 (tm-30) REVERT: r 66 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7943 (ptm160) REVERT: r 101 MET cc_start: 0.7584 (mmp) cc_final: 0.7302 (mmm) REVERT: r 118 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: r 120 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7577 (mtmm) REVERT: r 207 LEU cc_start: 0.8123 (tt) cc_final: 0.7919 (tt) REVERT: r 224 MET cc_start: 0.7661 (tmm) cc_final: 0.7170 (ttt) REVERT: s 60 MET cc_start: 0.8020 (mmt) cc_final: 0.6737 (ttt) REVERT: s 61 MET cc_start: 0.7467 (ptp) cc_final: 0.7016 (ptp) REVERT: s 75 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8020 (ttm170) REVERT: s 101 MET cc_start: 0.6971 (mmt) cc_final: 0.6568 (mmt) REVERT: s 129 LYS cc_start: 0.7559 (mmmm) cc_final: 0.7332 (mmmm) REVERT: s 190 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7917 (t80) REVERT: s 224 MET cc_start: 0.6851 (tpp) cc_final: 0.6621 (tpt) REVERT: t 36 GLN cc_start: 0.8300 (pm20) cc_final: 0.7687 (pm20) REVERT: t 107 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7937 (ttpt) REVERT: t 127 LEU cc_start: 0.8628 (tp) cc_final: 0.8320 (tt) REVERT: t 138 MET cc_start: 0.7860 (mtt) cc_final: 0.7586 (mtt) REVERT: t 168 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7762 (mtm110) REVERT: t 210 MET cc_start: 0.7793 (tmm) cc_final: 0.7469 (tmm) REVERT: t 224 MET cc_start: 0.7597 (ttt) cc_final: 0.7315 (ttm) REVERT: t 236 MET cc_start: 0.7723 (mtt) cc_final: 0.7445 (mtm) REVERT: u 169 ILE cc_start: 0.8274 (mm) cc_final: 0.8011 (mp) REVERT: v 60 MET cc_start: 0.7868 (tpt) cc_final: 0.7618 (tpp) REVERT: v 76 ASN cc_start: 0.8922 (t0) cc_final: 0.8354 (m110) REVERT: v 190 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8406 (t80) REVERT: v 195 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8930 (tp) outliers start: 42 outliers final: 28 residues processed: 411 average time/residue: 0.2510 time to fit residues: 148.5913 Evaluate side-chains 421 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 388 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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 b residue 102 MET 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 41 SER Chi-restraints excluded: chain r residue 65 THR 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 118 GLU Chi-restraints excluded: chain r residue 189 ILE 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 196 ILE Chi-restraints excluded: chain t residue 43 GLN Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 194 LEU Chi-restraints excluded: chain u residue 224 MET Chi-restraints excluded: chain v residue 51 LEU Chi-restraints excluded: chain v residue 70 VAL Chi-restraints excluded: chain v residue 179 LEU 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 89 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 86 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 0.0770 chunk 101 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 49 GLN e 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.148282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.131971 restraints weight = 18830.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135493 restraints weight = 8750.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.137714 restraints weight = 4877.367| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11144 Z= 0.134 Angle : 0.794 13.821 15092 Z= 0.359 Chirality : 0.041 0.264 1816 Planarity : 0.004 0.054 1885 Dihedral : 4.137 20.848 1484 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.95 % Allowed : 28.35 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.24), residues: 1385 helix: 1.58 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -2.31 (0.42), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.013 0.001 PHE u 150 TYR 0.017 0.001 TYR c 96 ARG 0.006 0.000 ARG b 53 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 809) hydrogen bonds : angle 4.03101 ( 2427) covalent geometry : bond 0.00301 (11144) covalent geometry : angle 0.79399 (15092) *********************** 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 430 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 395 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8615 (tp40) cc_final: 0.7089 (tm-30) REVERT: c 57 GLU cc_start: 0.7956 (tt0) cc_final: 0.7569 (tp30) REVERT: c 84 MET cc_start: 0.7609 (tmm) cc_final: 0.7372 (tmm) REVERT: d 53 ARG cc_start: 0.7868 (tmm-80) cc_final: 0.7588 (tmm-80) REVERT: f 72 MET cc_start: 0.8902 (tpp) cc_final: 0.8572 (mmm) REVERT: f 77 LYS cc_start: 0.7990 (mttt) cc_final: 0.7563 (mmtt) REVERT: f 91 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7599 (ttpp) REVERT: f 103 GLN cc_start: 0.7485 (tm-30) cc_final: 0.7236 (tm-30) REVERT: r 101 MET cc_start: 0.7601 (mmp) cc_final: 0.7264 (mmm) REVERT: r 118 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7041 (pp20) REVERT: r 120 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7586 (mtmm) REVERT: r 224 MET cc_start: 0.7694 (tmm) cc_final: 0.7192 (ttt) REVERT: s 60 MET cc_start: 0.8026 (mmt) cc_final: 0.6756 (ttt) REVERT: s 75 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8044 (ttm170) REVERT: s 190 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7919 (t80) REVERT: s 224 MET cc_start: 0.6875 (tpp) cc_final: 0.6570 (tpt) REVERT: t 127 LEU cc_start: 0.8627 (tp) cc_final: 0.8329 (tt) REVERT: t 138 MET cc_start: 0.7911 (mtt) cc_final: 0.7680 (mtt) REVERT: t 168 ARG cc_start: 0.8101 (mtm-85) cc_final: 0.7786 (mtm110) REVERT: t 210 MET cc_start: 0.7624 (tmm) cc_final: 0.7185 (tmm) REVERT: t 224 MET cc_start: 0.7624 (ttt) cc_final: 0.7345 (ttm) REVERT: t 236 MET cc_start: 0.7696 (mtt) cc_final: 0.7448 (mtm) REVERT: u 169 ILE cc_start: 0.8315 (mm) cc_final: 0.8034 (mp) REVERT: u 211 MET cc_start: 0.7602 (mmt) cc_final: 0.7328 (mpp) REVERT: v 76 ASN cc_start: 0.8953 (t0) cc_final: 0.8278 (m110) REVERT: v 190 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8411 (t80) REVERT: v 195 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8935 (tp) outliers start: 35 outliers final: 28 residues processed: 409 average time/residue: 0.3344 time to fit residues: 193.7102 Evaluate side-chains 418 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 386 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 60 THR 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 c residue 53 ARG 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 49 GLN Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 41 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 118 GLU 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 196 ILE Chi-restraints excluded: chain s residue 230 ASP Chi-restraints excluded: chain t residue 100 ILE Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 224 MET 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 73 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 64 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.148595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132358 restraints weight = 18673.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.135883 restraints weight = 8682.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.138062 restraints weight = 4833.120| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11144 Z= 0.136 Angle : 0.811 13.979 15092 Z= 0.367 Chirality : 0.042 0.339 1816 Planarity : 0.004 0.064 1885 Dihedral : 4.169 22.112 1484 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.48 % Favored : 95.45 % Rotamer: Outliers : 2.78 % Allowed : 28.78 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.24), residues: 1385 helix: 1.61 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -2.27 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP t 232 HIS 0.005 0.001 HIS e 39 PHE 0.011 0.001 PHE t 150 TYR 0.012 0.001 TYR c 96 ARG 0.007 0.001 ARG e 48 Details of bonding type rmsd hydrogen bonds : bond 0.03498 ( 809) hydrogen bonds : angle 4.04854 ( 2427) covalent geometry : bond 0.00307 (11144) covalent geometry : angle 0.81125 (15092) ********************** 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 422 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 389 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 83 GLN cc_start: 0.8619 (tp40) cc_final: 0.7095 (tm-30) REVERT: c 57 GLU cc_start: 0.7957 (tt0) cc_final: 0.7571 (tp30) REVERT: c 84 MET cc_start: 0.7617 (tmm) cc_final: 0.7372 (tmm) REVERT: d 53 ARG cc_start: 0.7869 (tmm-80) cc_final: 0.7591 (tmm-80) REVERT: f 72 MET cc_start: 0.8897 (tpp) cc_final: 0.8584 (mmm) REVERT: f 77 LYS cc_start: 0.7981 (mttt) cc_final: 0.7534 (mmmt) REVERT: f 91 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7595 (ttpp) REVERT: f 103 GLN cc_start: 0.7416 (tm-30) cc_final: 0.7173 (tm-30) REVERT: r 101 MET cc_start: 0.7625 (mmp) cc_final: 0.7317 (mmm) REVERT: r 118 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7039 (pp20) REVERT: r 120 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7575 (mtmm) REVERT: r 177 SER cc_start: 0.8774 (m) cc_final: 0.8451 (m) REVERT: r 224 MET cc_start: 0.7696 (tmm) cc_final: 0.7189 (ttt) REVERT: s 60 MET cc_start: 0.8013 (mmt) cc_final: 0.6734 (ttt) REVERT: s 61 MET cc_start: 0.7343 (ptp) cc_final: 0.7003 (ptp) REVERT: s 75 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8031 (ttm170) REVERT: s 129 LYS cc_start: 0.7577 (mmmm) cc_final: 0.7307 (mmmm) REVERT: s 190 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7910 (t80) REVERT: s 224 MET cc_start: 0.6832 (tpp) cc_final: 0.6542 (tpt) REVERT: t 36 GLN cc_start: 0.8183 (pm20) cc_final: 0.7249 (tp-100) REVERT: t 107 LYS cc_start: 0.8293 (ttmm) cc_final: 0.8016 (ttpt) REVERT: t 127 LEU cc_start: 0.8664 (tp) cc_final: 0.8303 (tt) REVERT: t 138 MET cc_start: 0.7923 (mtt) cc_final: 0.7683 (mtt) REVERT: t 150 PHE cc_start: 0.7061 (m-80) cc_final: 0.6817 (m-80) REVERT: t 168 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7793 (mtm110) REVERT: t 210 MET cc_start: 0.7693 (tmm) cc_final: 0.7484 (tmm) REVERT: t 224 MET cc_start: 0.7642 (ttt) cc_final: 0.7385 (ttm) REVERT: t 236 MET cc_start: 0.7666 (mtt) cc_final: 0.7418 (mtm) REVERT: u 169 ILE cc_start: 0.8304 (mm) cc_final: 0.8041 (mt) REVERT: v 76 ASN cc_start: 0.8851 (t0) cc_final: 0.8170 (m110) REVERT: v 190 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8428 (t80) REVERT: v 195 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8942 (tp) outliers start: 33 outliers final: 25 residues processed: 401 average time/residue: 0.2045 time to fit residues: 117.3362 Evaluate side-chains 412 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 383 time to evaluate : 1.174 ------------------------------------------------------------------------------- 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 49 GLN Chi-restraints excluded: chain e residue 60 THR Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain r residue 41 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 118 GLU 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 196 ILE Chi-restraints excluded: chain t residue 179 LEU Chi-restraints excluded: chain t residue 227 VAL Chi-restraints excluded: chain u residue 187 PHE Chi-restraints excluded: chain u residue 191 ILE Chi-restraints excluded: chain u residue 224 MET 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 88 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 46 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 98 optimal weight: 0.0020 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 overall best weight: 0.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.149506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.133246 restraints weight = 18477.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136808 restraints weight = 8586.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.138988 restraints weight = 4773.420| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11144 Z= 0.134 Angle : 0.834 21.506 15092 Z= 0.372 Chirality : 0.041 0.288 1816 Planarity : 0.005 0.067 1885 Dihedral : 4.167 21.305 1484 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.74 % Rotamer: Outliers : 2.87 % Allowed : 28.86 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1385 helix: 1.64 (0.16), residues: 1143 sheet: None (None), residues: 0 loop : -2.23 (0.43), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP t 232 HIS 0.004 0.001 HIS e 39 PHE 0.010 0.001 PHE v 150 TYR 0.010 0.001 TYR d 96 ARG 0.008 0.000 ARG v 143 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 809) hydrogen bonds : angle 4.04130 ( 2427) covalent geometry : bond 0.00299 (11144) covalent geometry : angle 0.83398 (15092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6462.93 seconds wall clock time: 120 minutes 12.26 seconds (7212.26 seconds total)