Starting phenix.real_space_refine on Wed Sep 17 16:24:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu9_63392/09_2025/9lu9_63392.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.036 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 52 5.16 5 C 6363 2.51 5 N 1619 2.21 5 O 1824 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9858 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1669 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 9, 'TRANS': 208} Chain: "B" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "C" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "D" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "F" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 372 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "G" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 288 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'AV0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.20 Number of scatterers: 9858 At special positions: 0 Unit cell: (91.52, 97.68, 117.92, 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 52 16.00 O 1824 8.00 N 1619 7.00 C 6363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 263.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2344 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 0 sheets defined 91.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 32 through 51 removed outlier: 3.950A pdb=" N GLY A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 58 through 67 Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.828A pdb=" N MET A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 94 No H-bonds generated for 'chain 'A' and resid 92 through 94' Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 120 through 171 removed outlier: 3.599A pdb=" N LEU A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.551A pdb=" N ILE A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 199 removed outlier: 3.901A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 231 Processing helix chain 'A' and resid 233 through 245 removed outlier: 3.653A pdb=" N TYR A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 26 through 31 removed outlier: 3.777A pdb=" N PHE B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.762A pdb=" N ILE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Proline residue: B 60 - end of helix Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.797A pdb=" N VAL B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 100 removed outlier: 3.620A pdb=" N LYS B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 Processing helix chain 'B' and resid 120 through 171 removed outlier: 3.599A pdb=" N LEU B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Proline residue: B 154 - end of helix removed outlier: 3.610A pdb=" N HIS B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 199 removed outlier: 3.828A pdb=" N ALA B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 231 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.500A pdb=" N VAL B 237 " --> pdb=" O ASN B 233 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 22 Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 32 through 51 Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.763A pdb=" N ILE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 60 - end of helix Processing helix chain 'C' and resid 73 through 92 Processing helix chain 'C' and resid 93 through 100 removed outlier: 4.027A pdb=" N GLU C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 120 through 171 removed outlier: 3.588A pdb=" N LEU C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE C 146 " --> pdb=" O TYR C 142 " (cutoff:3.500A) Proline residue: C 154 - end of helix Processing helix chain 'C' and resid 177 through 199 removed outlier: 3.873A pdb=" N SER C 181 " --> pdb=" O GLN C 177 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 231 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.943A pdb=" N TYR C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 32 through 51 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.730A pdb=" N ILE D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 73 through 92 removed outlier: 3.628A pdb=" N TRP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 removed outlier: 3.710A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 120 through 169 removed outlier: 3.613A pdb=" N LEU D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Proline residue: D 154 - end of helix Processing helix chain 'D' and resid 177 through 199 removed outlier: 3.532A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 231 Processing helix chain 'D' and resid 233 through 243 removed outlier: 3.567A pdb=" N THR D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 23 removed outlier: 3.572A pdb=" N GLU E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 32 through 51 Processing helix chain 'E' and resid 52 through 67 removed outlier: 3.741A pdb=" N ILE E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) Proline residue: E 60 - end of helix Processing helix chain 'E' and resid 72 through 91 removed outlier: 4.237A pdb=" N GLU E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 101 Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 120 through 171 removed outlier: 3.593A pdb=" N LEU E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE E 146 " --> pdb=" O TYR E 142 " (cutoff:3.500A) Proline residue: E 154 - end of helix Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 177 through 199 removed outlier: 4.904A pdb=" N VAL E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 231 Processing helix chain 'E' and resid 233 through 245 removed outlier: 3.930A pdb=" N TYR E 244 " --> pdb=" O LYS E 240 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE E 245 " --> pdb=" O LEU E 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 47 removed outlier: 3.747A pdb=" N ASP F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 64 removed outlier: 3.969A pdb=" N THR F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 53 removed outlier: 4.368A pdb=" N THR G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 44 " --> pdb=" O VAL G 40 " (cutoff:3.500A) 850 hydrogen bonds defined for protein. 2529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2104 1.33 - 1.46: 3092 1.46 - 1.59: 4718 1.59 - 1.72: 0 1.72 - 1.85: 104 Bond restraints: 10018 Sorted by residual: bond pdb=" C PHE B 200 " pdb=" O PHE B 200 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.16e-02 7.43e+03 9.93e+00 bond pdb=" CA ALA D 66 " pdb=" CB ALA D 66 " ideal model delta sigma weight residual 1.529 1.480 0.048 1.58e-02 4.01e+03 9.39e+00 bond pdb=" CA ALA C 153 " pdb=" CB ALA C 153 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.33e-02 5.65e+03 9.22e+00 bond pdb=" CA ALA E 153 " pdb=" CB ALA E 153 " ideal model delta sigma weight residual 1.531 1.495 0.036 1.33e-02 5.65e+03 7.41e+00 bond pdb=" CA ALA D 153 " pdb=" CB ALA D 153 " ideal model delta sigma weight residual 1.531 1.496 0.036 1.33e-02 5.65e+03 7.20e+00 ... (remaining 10013 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 12027 2.16 - 4.32: 1399 4.32 - 6.48: 141 6.48 - 8.64: 14 8.64 - 10.80: 2 Bond angle restraints: 13583 Sorted by residual: angle pdb=" N PRO A 104 " pdb=" CA PRO A 104 " pdb=" C PRO A 104 " ideal model delta sigma weight residual 113.53 102.73 10.80 1.39e+00 5.18e-01 6.04e+01 angle pdb=" CA ASP B 2 " pdb=" CB ASP B 2 " pdb=" CG ASP B 2 " ideal model delta sigma weight residual 112.60 119.45 -6.85 1.00e+00 1.00e+00 4.69e+01 angle pdb=" CA ASN C 197 " pdb=" CB ASN C 197 " pdb=" CG ASN C 197 " ideal model delta sigma weight residual 112.60 106.35 6.25 1.00e+00 1.00e+00 3.90e+01 angle pdb=" CA ASP E 133 " pdb=" CB ASP E 133 " pdb=" CG ASP E 133 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.00e+00 1.00e+00 3.15e+01 angle pdb=" CB GLU C 138 " pdb=" CG GLU C 138 " pdb=" CD GLU C 138 " ideal model delta sigma weight residual 112.60 121.05 -8.45 1.70e+00 3.46e-01 2.47e+01 ... (remaining 13578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 5799 34.92 - 69.84: 273 69.84 - 104.76: 26 104.76 - 139.68: 13 139.68 - 174.61: 1 Dihedral angle restraints: 6112 sinusoidal: 2463 harmonic: 3649 Sorted by residual: dihedral pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " pdb=" NH1 ARG C 71 " ideal model delta sinusoidal sigma weight residual 0.00 -72.34 72.34 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CD ARG B 109 " pdb=" NE ARG B 109 " pdb=" CZ ARG B 109 " pdb=" NH1 ARG B 109 " ideal model delta sinusoidal sigma weight residual 0.00 71.76 -71.76 1 1.00e+01 1.00e-02 6.60e+01 dihedral pdb=" CD ARG A 125 " pdb=" NE ARG A 125 " pdb=" CZ ARG A 125 " pdb=" NH1 ARG A 125 " ideal model delta sinusoidal sigma weight residual 0.00 65.59 -65.59 1 1.00e+01 1.00e-02 5.63e+01 ... (remaining 6109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.005: 1646 1.005 - 2.009: 0 2.009 - 3.014: 0 3.014 - 4.018: 0 4.018 - 5.023: 1 Chirality restraints: 1647 Sorted by residual: chirality pdb=" C2 AV0 G 401 " pdb=" C1 AV0 G 401 " pdb=" C3 AV0 G 401 " pdb=" O2 AV0 G 401 " both_signs ideal model delta sigma weight residual False -2.51 2.51 -5.02 2.00e-01 2.50e+01 6.31e+02 chirality pdb=" CA ASP E 133 " pdb=" N ASP E 133 " pdb=" C ASP E 133 " pdb=" CB ASP E 133 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.38e+00 chirality pdb=" CA ASN C 197 " pdb=" N ASN C 197 " pdb=" C ASN C 197 " pdb=" CB ASN C 197 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 ... (remaining 1644 not shown) Planarity restraints: 1702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 71 " -0.996 9.50e-02 1.11e+02 4.47e-01 1.24e+02 pdb=" NE ARG C 71 " 0.071 2.00e-02 2.50e+03 pdb=" CZ ARG C 71 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 71 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 71 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 109 " -0.955 9.50e-02 1.11e+02 4.29e-01 1.17e+02 pdb=" NE ARG B 109 " 0.073 2.00e-02 2.50e+03 pdb=" CZ ARG B 109 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG B 109 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 109 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 125 " -0.916 9.50e-02 1.11e+02 4.11e-01 1.06e+02 pdb=" NE ARG A 125 " 0.067 2.00e-02 2.50e+03 pdb=" CZ ARG A 125 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 125 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 125 " -0.012 2.00e-02 2.50e+03 ... (remaining 1699 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1901 2.79 - 3.32: 10622 3.32 - 3.85: 16074 3.85 - 4.37: 18180 4.37 - 4.90: 30994 Nonbonded interactions: 77771 Sorted by model distance: nonbonded pdb=" O SER F 59 " pdb=" OG1 THR F 62 " model vdw 2.265 3.040 nonbonded pdb=" OD1 ASN D 197 " pdb=" NH1 ARG G 23 " model vdw 2.463 3.120 nonbonded pdb=" C THR A 155 " pdb=" OG1 THR A 155 " model vdw 2.468 2.616 nonbonded pdb=" OAI AV0 G 401 " pdb=" OBY AV0 G 401 " model vdw 2.471 2.432 nonbonded pdb=" OG1 THR B 161 " pdb=" OD1 ASP F 30 " model vdw 2.502 3.040 ... (remaining 77766 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' selection = (chain 'B' and resid 29 through 246) selection = (chain 'C' and resid 29 through 246) selection = (chain 'D' and resid 29 through 246) selection = (chain 'E' and resid 29 through 246) } 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 individual isotropic 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: 1.510 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.720 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 0.009 0.058 10018 Z= 0.610 Angle : 1.430 10.799 13583 Z= 0.947 Chirality : 0.154 5.023 1647 Planarity : 0.027 0.447 1702 Dihedral : 19.981 174.605 3768 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 11.48 % Allowed : 8.23 % Favored : 80.29 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.21), residues: 1267 helix: 0.02 (0.14), residues: 1083 sheet: None (None), residues: 0 loop : -0.92 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.007 ARG B 109 TYR 0.058 0.011 TYR B 51 PHE 0.052 0.011 PHE C 40 TRP 0.036 0.008 TRP A 77 HIS 0.025 0.006 HIS C 139 Details of bonding type rmsd covalent geometry : bond 0.00940 (10018) covalent geometry : angle 1.43009 (13583) hydrogen bonds : bond 0.22822 ( 850) hydrogen bonds : angle 8.01649 ( 2529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 277 time to evaluate : 0.369 Fit side-chains REVERT: A 30 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6243 (tt) REVERT: A 68 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5924 (pttp) REVERT: A 70 ASN cc_start: 0.3630 (OUTLIER) cc_final: 0.3278 (p0) REVERT: A 84 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.6016 (mmm) REVERT: A 89 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6440 (mmm160) REVERT: A 99 LYS cc_start: 0.3994 (OUTLIER) cc_final: 0.3202 (mtpt) REVERT: A 239 LYS cc_start: 0.7023 (OUTLIER) cc_final: 0.6766 (tppt) REVERT: B 64 LYS cc_start: 0.8083 (mttt) cc_final: 0.7732 (tttt) REVERT: B 90 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.8200 (mtm-85) REVERT: B 91 GLU cc_start: 0.6823 (mp0) cc_final: 0.6463 (mp0) REVERT: B 99 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (mmtm) REVERT: B 109 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8431 (ttp80) REVERT: C 53 MET cc_start: 0.9017 (tpp) cc_final: 0.8617 (tpt) REVERT: C 70 ASN cc_start: 0.9144 (t0) cc_final: 0.8871 (t0) REVERT: C 117 ASP cc_start: 0.7917 (m-30) cc_final: 0.7590 (t0) REVERT: D 32 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8356 (tt0) REVERT: D 84 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.7967 (mtp) REVERT: D 98 GLN cc_start: 0.8179 (tm-30) cc_final: 0.7963 (mm-40) REVERT: D 120 ASP cc_start: 0.8364 (p0) cc_final: 0.8076 (t0) REVERT: E 26 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7794 (tt0) REVERT: E 70 ASN cc_start: 0.7632 (t0) cc_final: 0.7336 (m-40) REVERT: E 83 GLU cc_start: 0.7583 (tt0) cc_final: 0.7094 (tm-30) REVERT: E 109 ARG cc_start: 0.7037 (ttp80) cc_final: 0.6717 (mtm110) REVERT: E 171 HIS cc_start: 0.7979 (m90) cc_final: 0.7698 (m90) REVERT: E 232 ASP cc_start: 0.8138 (m-30) cc_final: 0.7854 (m-30) outliers start: 120 outliers final: 35 residues processed: 357 average time/residue: 0.1095 time to fit residues: 52.6626 Evaluate side-chains 248 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 71 ARG Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 99 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 128 MET Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 239 LYS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 181 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 161 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 54 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 0.0370 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN B 103 HIS B 197 ASN C 242 ASN D 121 GLN D 171 HIS ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 229 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126940 restraints weight = 12370.489| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.01 r_work: 0.3429 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10018 Z= 0.158 Angle : 0.622 8.673 13583 Z= 0.320 Chirality : 0.040 0.295 1647 Planarity : 0.005 0.047 1702 Dihedral : 12.263 168.112 1587 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.98 % Allowed : 14.74 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.36 (0.23), residues: 1267 helix: 1.98 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 57 TYR 0.015 0.001 TYR A 244 PHE 0.013 0.001 PHE A 107 TRP 0.034 0.001 TRP A 77 HIS 0.006 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00303 (10018) covalent geometry : angle 0.62187 (13583) hydrogen bonds : bond 0.05776 ( 850) hydrogen bonds : angle 4.66491 ( 2529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 222 time to evaluate : 0.378 Fit side-chains REVERT: A 73 GLU cc_start: 0.5749 (OUTLIER) cc_final: 0.4983 (tm-30) REVERT: A 84 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5770 (mmm) REVERT: A 86 MET cc_start: 0.5609 (tpt) cc_final: 0.4323 (ttt) REVERT: A 89 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6867 (mmm160) REVERT: A 167 GLN cc_start: 0.7189 (tm-30) cc_final: 0.6887 (tm-30) REVERT: A 219 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7830 (mt-10) REVERT: B 80 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8047 (t70) REVERT: B 90 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8157 (mtm-85) REVERT: B 91 GLU cc_start: 0.6777 (mp0) cc_final: 0.6449 (mp0) REVERT: B 99 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8213 (mmtm) REVERT: C 218 MET cc_start: 0.8708 (mtt) cc_final: 0.8416 (mtp) REVERT: C 230 ASN cc_start: 0.8777 (m-40) cc_final: 0.8504 (t0) REVERT: D 80 ASP cc_start: 0.8823 (m-30) cc_final: 0.8390 (m-30) REVERT: D 89 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6604 (ttp80) REVERT: D 98 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7822 (mp10) REVERT: E 26 GLN cc_start: 0.7354 (mm-40) cc_final: 0.7084 (tt0) REVERT: E 57 ARG cc_start: 0.8617 (mtt90) cc_final: 0.8100 (mmm-85) REVERT: E 83 GLU cc_start: 0.7836 (tt0) cc_final: 0.7134 (tm-30) REVERT: E 109 ARG cc_start: 0.6824 (ttp80) cc_final: 0.6623 (mtp180) REVERT: E 214 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7984 (mt-10) REVERT: F 65 GLN cc_start: 0.6717 (OUTLIER) cc_final: 0.5382 (tm-30) outliers start: 52 outliers final: 17 residues processed: 259 average time/residue: 0.1016 time to fit residues: 36.2003 Evaluate side-chains 218 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 65 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 86 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 26 GLN E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.160426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124151 restraints weight = 12407.432| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.97 r_work: 0.3382 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10018 Z= 0.147 Angle : 0.559 7.406 13583 Z= 0.287 Chirality : 0.038 0.163 1647 Planarity : 0.004 0.046 1702 Dihedral : 9.718 163.966 1518 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.02 % Allowed : 16.84 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.99 (0.23), residues: 1267 helix: 2.39 (0.15), residues: 1111 sheet: None (None), residues: 0 loop : -1.22 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 90 TYR 0.008 0.001 TYR A 51 PHE 0.018 0.001 PHE A 107 TRP 0.032 0.001 TRP A 77 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00312 (10018) covalent geometry : angle 0.55910 (13583) hydrogen bonds : bond 0.05398 ( 850) hydrogen bonds : angle 4.33449 ( 2529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 205 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.4929 (tm-30) REVERT: A 84 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.5700 (tpp) REVERT: A 86 MET cc_start: 0.5770 (tpt) cc_final: 0.4526 (ttt) REVERT: A 89 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6784 (mmm160) REVERT: A 218 MET cc_start: 0.7746 (mmt) cc_final: 0.7387 (mmt) REVERT: A 219 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7646 (mt-10) REVERT: B 22 TRP cc_start: 0.7664 (t60) cc_final: 0.6816 (t-100) REVERT: B 80 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8104 (t70) REVERT: B 90 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.8049 (mtm-85) REVERT: B 91 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6395 (mp0) REVERT: B 94 LEU cc_start: 0.7698 (pt) cc_final: 0.7370 (mt) REVERT: B 99 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8282 (mmtm) REVERT: B 227 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8260 (t) REVERT: C 117 ASP cc_start: 0.8040 (t0) cc_final: 0.7839 (t0) REVERT: C 218 MET cc_start: 0.8737 (mtt) cc_final: 0.8353 (mtp) REVERT: D 98 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7822 (mp10) REVERT: D 156 MET cc_start: 0.9269 (mmt) cc_final: 0.8743 (mmt) REVERT: E 26 GLN cc_start: 0.7321 (mm-40) cc_final: 0.6999 (tt0) REVERT: E 83 GLU cc_start: 0.7734 (tt0) cc_final: 0.7167 (tm-30) REVERT: F 64 PHE cc_start: 0.7407 (m-80) cc_final: 0.7177 (m-80) REVERT: F 65 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5241 (tm-30) outliers start: 42 outliers final: 22 residues processed: 236 average time/residue: 0.1031 time to fit residues: 33.1688 Evaluate side-chains 213 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 65 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.125785 restraints weight = 12444.622| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.96 r_work: 0.3419 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10018 Z= 0.132 Angle : 0.525 7.478 13583 Z= 0.268 Chirality : 0.036 0.140 1647 Planarity : 0.004 0.047 1702 Dihedral : 9.028 162.010 1511 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.16 % Allowed : 18.56 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.24), residues: 1267 helix: 2.56 (0.15), residues: 1110 sheet: None (None), residues: 0 loop : -1.03 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 90 TYR 0.007 0.001 TYR A 51 PHE 0.016 0.001 PHE A 107 TRP 0.033 0.001 TRP A 77 HIS 0.004 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00273 (10018) covalent geometry : angle 0.52537 (13583) hydrogen bonds : bond 0.04794 ( 850) hydrogen bonds : angle 4.12308 ( 2529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.329 Fit side-chains REVERT: A 73 GLU cc_start: 0.5677 (OUTLIER) cc_final: 0.4925 (tm-30) REVERT: A 86 MET cc_start: 0.5656 (tpt) cc_final: 0.4509 (ttt) REVERT: A 89 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.6643 (mmm160) REVERT: B 22 TRP cc_start: 0.7690 (t60) cc_final: 0.6735 (t-100) REVERT: B 80 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8158 (t70) REVERT: B 90 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7929 (mtm-85) REVERT: B 91 GLU cc_start: 0.6723 (mp0) cc_final: 0.6404 (mp0) REVERT: B 94 LEU cc_start: 0.7828 (pt) cc_final: 0.7472 (mp) REVERT: B 99 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8249 (mmtm) REVERT: B 227 SER cc_start: 0.8658 (OUTLIER) cc_final: 0.8227 (t) REVERT: C 117 ASP cc_start: 0.7962 (t0) cc_final: 0.7686 (t0) REVERT: C 218 MET cc_start: 0.8786 (mtt) cc_final: 0.8403 (mtp) REVERT: D 89 ARG cc_start: 0.7397 (ttm-80) cc_final: 0.6776 (ttp80) REVERT: D 98 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7759 (mp10) REVERT: E 26 GLN cc_start: 0.7235 (mm-40) cc_final: 0.6892 (tt0) REVERT: E 83 GLU cc_start: 0.7554 (tt0) cc_final: 0.7007 (tm-30) REVERT: E 191 TYR cc_start: 0.8861 (m-10) cc_final: 0.8484 (m-10) REVERT: F 64 PHE cc_start: 0.7270 (m-80) cc_final: 0.7061 (m-80) outliers start: 33 outliers final: 19 residues processed: 221 average time/residue: 0.0975 time to fit residues: 30.0721 Evaluate side-chains 212 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN C 197 ASN E 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.161688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.125955 restraints weight = 12536.277| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.96 r_work: 0.3445 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10018 Z= 0.129 Angle : 0.517 8.438 13583 Z= 0.262 Chirality : 0.036 0.129 1647 Planarity : 0.004 0.048 1702 Dihedral : 8.653 160.492 1503 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.35 % Allowed : 19.23 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.35 (0.24), residues: 1267 helix: 2.65 (0.16), residues: 1100 sheet: None (None), residues: 0 loop : -0.98 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.007 0.001 TYR A 51 PHE 0.022 0.001 PHE A 107 TRP 0.029 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00266 (10018) covalent geometry : angle 0.51669 (13583) hydrogen bonds : bond 0.04674 ( 850) hydrogen bonds : angle 4.05426 ( 2529) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.275 Fit side-chains REVERT: A 73 GLU cc_start: 0.5718 (OUTLIER) cc_final: 0.4908 (tm-30) REVERT: A 84 MET cc_start: 0.6783 (mtt) cc_final: 0.5742 (tpp) REVERT: A 86 MET cc_start: 0.5871 (tpt) cc_final: 0.4719 (ttt) REVERT: A 89 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6492 (mmm160) REVERT: B 22 TRP cc_start: 0.7705 (t60) cc_final: 0.6790 (t-100) REVERT: B 80 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8100 (t70) REVERT: B 90 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.8049 (mtm-85) REVERT: B 91 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6659 (mp0) REVERT: B 94 LEU cc_start: 0.7880 (pt) cc_final: 0.7537 (mp) REVERT: B 99 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8260 (mmtm) REVERT: B 113 GLN cc_start: 0.8272 (tp40) cc_final: 0.7813 (tm-30) REVERT: B 227 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8193 (t) REVERT: D 80 ASP cc_start: 0.8994 (m-30) cc_final: 0.8665 (t0) REVERT: D 89 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.6898 (ttp80) REVERT: D 98 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7767 (mp10) REVERT: E 26 GLN cc_start: 0.7247 (mm-40) cc_final: 0.6962 (tt0) REVERT: E 83 GLU cc_start: 0.7604 (tt0) cc_final: 0.7155 (tm-30) REVERT: E 191 TYR cc_start: 0.8876 (m-10) cc_final: 0.8546 (m-10) REVERT: F 64 PHE cc_start: 0.7386 (m-80) cc_final: 0.7159 (m-80) outliers start: 35 outliers final: 24 residues processed: 227 average time/residue: 0.0975 time to fit residues: 30.8677 Evaluate side-chains 229 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 198 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN C 197 ASN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.121107 restraints weight = 12622.055| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.25 r_work: 0.3293 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10018 Z= 0.126 Angle : 0.517 8.162 13583 Z= 0.261 Chirality : 0.036 0.128 1647 Planarity : 0.004 0.049 1702 Dihedral : 8.504 158.920 1503 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.35 % Allowed : 19.81 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.24), residues: 1267 helix: 2.72 (0.16), residues: 1104 sheet: None (None), residues: 0 loop : -1.20 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.007 0.001 TYR A 51 PHE 0.016 0.001 PHE A 107 TRP 0.027 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00262 (10018) covalent geometry : angle 0.51743 (13583) hydrogen bonds : bond 0.04542 ( 850) hydrogen bonds : angle 3.98896 ( 2529) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.264 Fit side-chains REVERT: A 73 GLU cc_start: 0.5393 (OUTLIER) cc_final: 0.4814 (tm-30) REVERT: A 86 MET cc_start: 0.5526 (tpt) cc_final: 0.4459 (ttt) REVERT: A 89 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6661 (mmm160) REVERT: B 22 TRP cc_start: 0.7403 (t60) cc_final: 0.6496 (t-100) REVERT: B 26 GLN cc_start: 0.7470 (tm-30) cc_final: 0.6217 (tm-30) REVERT: B 80 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7895 (t70) REVERT: B 90 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.7698 (mtm-85) REVERT: B 91 GLU cc_start: 0.6549 (mp0) cc_final: 0.6130 (mp0) REVERT: B 94 LEU cc_start: 0.7753 (pt) cc_final: 0.7471 (mp) REVERT: B 99 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8091 (mmtm) REVERT: B 113 GLN cc_start: 0.8079 (tp40) cc_final: 0.7514 (tm-30) REVERT: B 227 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7903 (t) REVERT: D 80 ASP cc_start: 0.8800 (m-30) cc_final: 0.8479 (t0) REVERT: D 98 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7600 (mp10) REVERT: E 26 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6584 (tt0) REVERT: E 83 GLU cc_start: 0.7237 (tt0) cc_final: 0.6685 (tm-30) REVERT: E 191 TYR cc_start: 0.8398 (m-10) cc_final: 0.7987 (m-10) REVERT: G 25 MET cc_start: 0.8018 (mtt) cc_final: 0.7614 (mtt) outliers start: 35 outliers final: 25 residues processed: 229 average time/residue: 0.0935 time to fit residues: 29.8140 Evaluate side-chains 223 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 0.0770 chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 39 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 81 optimal weight: 0.0870 chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.3434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.162598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125433 restraints weight = 12691.598| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.26 r_work: 0.3378 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10018 Z= 0.116 Angle : 0.505 8.781 13583 Z= 0.255 Chirality : 0.035 0.118 1647 Planarity : 0.004 0.048 1702 Dihedral : 8.351 158.905 1499 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.78 % Allowed : 20.96 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.54 (0.24), residues: 1267 helix: 2.77 (0.16), residues: 1101 sheet: None (None), residues: 0 loop : -0.92 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 57 TYR 0.009 0.001 TYR F 43 PHE 0.010 0.001 PHE A 107 TRP 0.025 0.001 TRP A 77 HIS 0.002 0.000 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00221 (10018) covalent geometry : angle 0.50471 (13583) hydrogen bonds : bond 0.04011 ( 850) hydrogen bonds : angle 3.82928 ( 2529) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 207 time to evaluate : 0.307 Fit side-chains REVERT: A 73 GLU cc_start: 0.5459 (OUTLIER) cc_final: 0.4871 (tm-30) REVERT: A 86 MET cc_start: 0.5545 (tpt) cc_final: 0.4554 (ttt) REVERT: A 89 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6757 (mmm160) REVERT: A 156 MET cc_start: 0.8579 (mmt) cc_final: 0.8364 (mmt) REVERT: B 22 TRP cc_start: 0.7325 (t60) cc_final: 0.6458 (t-100) REVERT: B 26 GLN cc_start: 0.7448 (tm-30) cc_final: 0.6220 (tm-30) REVERT: B 80 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7858 (t70) REVERT: B 90 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7809 (mtm-85) REVERT: B 91 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6051 (mp0) REVERT: B 94 LEU cc_start: 0.7794 (pt) cc_final: 0.7431 (mp) REVERT: B 99 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.8134 (mmtm) REVERT: B 113 GLN cc_start: 0.8043 (tp40) cc_final: 0.7481 (tm-30) REVERT: B 227 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7812 (t) REVERT: D 80 ASP cc_start: 0.8793 (m-30) cc_final: 0.8451 (t0) REVERT: D 98 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7592 (mp10) REVERT: E 26 GLN cc_start: 0.6982 (mm-40) cc_final: 0.6493 (tt0) REVERT: E 83 GLU cc_start: 0.7109 (tt0) cc_final: 0.6619 (tm-30) REVERT: E 191 TYR cc_start: 0.8369 (m-10) cc_final: 0.7978 (m-10) REVERT: F 64 PHE cc_start: 0.6755 (m-80) cc_final: 0.6508 (m-80) outliers start: 29 outliers final: 15 residues processed: 224 average time/residue: 0.0988 time to fit residues: 30.6769 Evaluate side-chains 211 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 189 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN ** C 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.159024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.120952 restraints weight = 12733.906| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.27 r_work: 0.3294 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10018 Z= 0.130 Angle : 0.535 8.897 13583 Z= 0.267 Chirality : 0.036 0.144 1647 Planarity : 0.004 0.050 1702 Dihedral : 8.129 157.033 1496 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.68 % Allowed : 22.39 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.52 (0.24), residues: 1267 helix: 2.78 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 57 TYR 0.011 0.001 TYR D 191 PHE 0.026 0.001 PHE A 107 TRP 0.021 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00280 (10018) covalent geometry : angle 0.53547 (13583) hydrogen bonds : bond 0.04390 ( 850) hydrogen bonds : angle 3.93535 ( 2529) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5372 (OUTLIER) cc_final: 0.4736 (tm-30) REVERT: A 86 MET cc_start: 0.5338 (tpt) cc_final: 0.4410 (ttt) REVERT: A 89 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6669 (mmm160) REVERT: B 22 TRP cc_start: 0.7267 (t60) cc_final: 0.6434 (t-100) REVERT: B 26 GLN cc_start: 0.7471 (tm-30) cc_final: 0.6233 (tm-30) REVERT: B 80 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7931 (t70) REVERT: B 90 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7738 (mtm-85) REVERT: B 91 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6152 (mp0) REVERT: B 94 LEU cc_start: 0.7846 (pt) cc_final: 0.7567 (mp) REVERT: B 99 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8176 (mmtm) REVERT: B 113 GLN cc_start: 0.8007 (tp40) cc_final: 0.7487 (tm-30) REVERT: B 227 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7835 (t) REVERT: C 167 GLN cc_start: 0.8234 (tm-30) cc_final: 0.7898 (tm-30) REVERT: C 226 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6776 (mp) REVERT: D 53 MET cc_start: 0.7094 (tpt) cc_final: 0.6671 (tpt) REVERT: D 80 ASP cc_start: 0.8773 (m-30) cc_final: 0.8444 (t0) REVERT: D 98 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7580 (mp10) REVERT: E 26 GLN cc_start: 0.7073 (mm-40) cc_final: 0.6605 (tt0) REVERT: E 83 GLU cc_start: 0.7112 (tt0) cc_final: 0.6540 (tm-30) REVERT: E 191 TYR cc_start: 0.8367 (m-10) cc_final: 0.7992 (m-10) REVERT: F 64 PHE cc_start: 0.6787 (m-80) cc_final: 0.6556 (m-80) outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.0969 time to fit residues: 29.4127 Evaluate side-chains 219 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 98 optimal weight: 0.0980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN D 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.155204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116924 restraints weight = 12694.339| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.25 r_work: 0.3231 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10018 Z= 0.156 Angle : 0.579 11.096 13583 Z= 0.290 Chirality : 0.037 0.141 1647 Planarity : 0.004 0.053 1702 Dihedral : 8.165 155.683 1496 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.06 % Allowed : 21.91 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.36 (0.24), residues: 1267 helix: 2.67 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.26 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.008 0.001 TYR F 43 PHE 0.025 0.001 PHE A 107 TRP 0.022 0.001 TRP A 77 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00359 (10018) covalent geometry : angle 0.57937 (13583) hydrogen bonds : bond 0.05024 ( 850) hydrogen bonds : angle 4.10663 ( 2529) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 202 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5474 (OUTLIER) cc_final: 0.4846 (tm-30) REVERT: A 86 MET cc_start: 0.5226 (tpt) cc_final: 0.4304 (ttt) REVERT: A 89 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.6649 (mmm160) REVERT: B 22 TRP cc_start: 0.7309 (t60) cc_final: 0.6494 (t-100) REVERT: B 26 GLN cc_start: 0.7493 (tm-30) cc_final: 0.6219 (tm-30) REVERT: B 80 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7904 (t70) REVERT: B 90 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7805 (mtm-85) REVERT: B 91 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6064 (mp0) REVERT: B 94 LEU cc_start: 0.7875 (pt) cc_final: 0.7617 (mp) REVERT: B 99 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8178 (mmtm) REVERT: B 113 GLN cc_start: 0.7957 (tp40) cc_final: 0.7427 (tm-30) REVERT: B 117 ASP cc_start: 0.8079 (t0) cc_final: 0.7857 (t0) REVERT: B 227 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.7991 (t) REVERT: D 80 ASP cc_start: 0.8775 (m-30) cc_final: 0.8201 (m-30) REVERT: D 98 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7574 (mp10) REVERT: D 167 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8057 (tp40) REVERT: E 26 GLN cc_start: 0.7364 (mm-40) cc_final: 0.6898 (tt0) REVERT: E 83 GLU cc_start: 0.7214 (tt0) cc_final: 0.6675 (tm-30) REVERT: E 191 TYR cc_start: 0.8433 (m-10) cc_final: 0.8040 (m-10) REVERT: F 64 PHE cc_start: 0.6855 (m-80) cc_final: 0.6616 (m-80) outliers start: 32 outliers final: 21 residues processed: 220 average time/residue: 0.0898 time to fit residues: 27.7314 Evaluate side-chains 224 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 167 GLN Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 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 197 ASN C 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.158443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120802 restraints weight = 12574.134| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.25 r_work: 0.3263 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10018 Z= 0.127 Angle : 0.541 8.534 13583 Z= 0.273 Chirality : 0.037 0.134 1647 Planarity : 0.004 0.052 1702 Dihedral : 8.099 156.533 1496 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.78 % Allowed : 22.78 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.44 (0.24), residues: 1267 helix: 2.73 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -1.28 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.008 0.001 TYR D 191 PHE 0.015 0.001 PHE A 107 TRP 0.022 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00262 (10018) covalent geometry : angle 0.54093 (13583) hydrogen bonds : bond 0.04492 ( 850) hydrogen bonds : angle 3.95777 ( 2529) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 203 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5434 (OUTLIER) cc_final: 0.4819 (tm-30) REVERT: A 86 MET cc_start: 0.5464 (tpt) cc_final: 0.4587 (ttt) REVERT: A 89 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6691 (mmm160) REVERT: B 22 TRP cc_start: 0.7270 (t60) cc_final: 0.6475 (t-100) REVERT: B 26 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6229 (tm-30) REVERT: B 80 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.7918 (t70) REVERT: B 90 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7766 (mtm-85) REVERT: B 91 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6182 (mp0) REVERT: B 94 LEU cc_start: 0.7894 (pt) cc_final: 0.7635 (mp) REVERT: B 99 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8128 (mmtm) REVERT: B 113 GLN cc_start: 0.8021 (tp40) cc_final: 0.7549 (tm-30) REVERT: B 117 ASP cc_start: 0.8046 (t0) cc_final: 0.7826 (t0) REVERT: C 226 LEU cc_start: 0.7005 (OUTLIER) cc_final: 0.6723 (mp) REVERT: D 80 ASP cc_start: 0.8782 (m-30) cc_final: 0.8451 (t0) REVERT: D 98 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7553 (mp10) REVERT: D 167 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8028 (tp40) REVERT: E 26 GLN cc_start: 0.7282 (mm-40) cc_final: 0.6806 (tt0) REVERT: E 83 GLU cc_start: 0.7166 (tt0) cc_final: 0.6663 (tm-30) REVERT: E 191 TYR cc_start: 0.8376 (m-10) cc_final: 0.7996 (m-10) outliers start: 29 outliers final: 20 residues processed: 221 average time/residue: 0.0946 time to fit residues: 29.5608 Evaluate side-chains 225 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 198 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 144 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain B residue 91 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 0.0370 chunk 65 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN D 242 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.166766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.131498 restraints weight = 12491.724| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.95 r_work: 0.3454 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10018 Z= 0.122 Angle : 0.539 9.221 13583 Z= 0.269 Chirality : 0.036 0.190 1647 Planarity : 0.004 0.052 1702 Dihedral : 8.083 155.901 1496 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.97 % Allowed : 22.49 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.49 (0.24), residues: 1267 helix: 2.78 (0.16), residues: 1099 sheet: None (None), residues: 0 loop : -1.21 (0.43), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 57 TYR 0.009 0.001 TYR F 43 PHE 0.012 0.001 PHE A 107 TRP 0.021 0.001 TRP A 77 HIS 0.003 0.000 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00250 (10018) covalent geometry : angle 0.53869 (13583) hydrogen bonds : bond 0.04238 ( 850) hydrogen bonds : angle 3.90539 ( 2529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2241.88 seconds wall clock time: 39 minutes 4.84 seconds (2344.84 seconds total)