Starting phenix.real_space_refine on Wed Apr 30 16:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lu9_63392/04_2025/9lu9_63392.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lu9_63392/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9lu9_63392/04_2025/9lu9_63392.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lu9_63392/04_2025/9lu9_63392.map" model { file = "/net/cci-nas-00/data/ceres_data/9lu9_63392/04_2025/9lu9_63392.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lu9_63392/04_2025/9lu9_63392.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.99, per 1000 atoms: 0.61 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: 2.44 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.80 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: 2.64 Time building geometry restraints manager: 2.85 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: 0.670 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.790 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.220 ------------------------------------------------------------------------------- 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 : 8.31 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (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 TRP 0.036 0.008 TRP A 77 HIS 0.025 0.006 HIS C 139 PHE 0.052 0.011 PHE C 40 TYR 0.058 0.011 TYR B 51 ARG 0.043 0.007 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.22822 ( 850) hydrogen bonds : angle 8.01649 ( 2529) covalent geometry : bond 0.00940 (10018) covalent geometry : angle 1.43009 (13583) *********************** 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 : 1.022 Fit side-chains REVERT: A 30 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6244 (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: 0.3279 (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: 0.6441 (mmm160) REVERT: A 99 LYS cc_start: 0.3994 (OUTLIER) cc_final: 0.3203 (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: 0.7589 (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: 0.7964 (mm-40) REVERT: D 120 ASP cc_start: 0.8364 (p0) cc_final: 0.8077 (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: 0.6718 (mtm110) REVERT: E 171 HIS cc_start: 0.7979 (m90) cc_final: 0.7702 (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: 0.2388 time to fit residues: 114.2636 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 : 1.063 ------------------------------------------------------------------------------- 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 104 optimal weight: 0.4980 chunk 93 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3984 r_free = 0.3984 target = 0.162177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.125968 restraints weight = 12219.475| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.98 r_work: 0.3419 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3313 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= 0.157 Angle : 0.628 8.709 13583 Z= 0.323 Chirality : 0.041 0.277 1647 Planarity : 0.005 0.048 1702 Dihedral : 12.329 165.004 1587 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 4.88 % Allowed : 14.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.23), residues: 1267 helix: 1.96 (0.15), residues: 1107 sheet: None (None), residues: 0 loop : -1.31 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 77 HIS 0.006 0.001 HIS D 54 PHE 0.014 0.001 PHE A 107 TYR 0.014 0.001 TYR A 244 ARG 0.008 0.001 ARG E 57 Details of bonding type rmsd hydrogen bonds : bond 0.05898 ( 850) hydrogen bonds : angle 4.69528 ( 2529) covalent geometry : bond 0.00309 (10018) covalent geometry : angle 0.62833 (13583) *********************** 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 270 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 1.091 Fit side-chains REVERT: A 73 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5020 (tm-30) REVERT: A 84 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5747 (mmm) REVERT: A 86 MET cc_start: 0.5746 (tpt) cc_final: 0.4486 (ttt) REVERT: A 89 ARG cc_start: 0.7261 (OUTLIER) cc_final: 0.6865 (mmm160) REVERT: A 133 ASP cc_start: 0.7953 (m-30) cc_final: 0.7738 (m-30) REVERT: A 167 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6928 (tm-30) REVERT: A 219 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7859 (mt-10) REVERT: B 80 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8047 (t70) REVERT: B 90 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.8193 (mtm-85) REVERT: B 91 GLU cc_start: 0.6791 (mp0) cc_final: 0.6440 (mp0) REVERT: B 99 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: C 218 MET cc_start: 0.8723 (mtt) cc_final: 0.8428 (mtp) REVERT: C 230 ASN cc_start: 0.8787 (m-40) cc_final: 0.8509 (t0) REVERT: D 80 ASP cc_start: 0.8832 (m-30) cc_final: 0.8403 (m-30) REVERT: D 98 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7848 (mp10) REVERT: E 26 GLN cc_start: 0.7400 (mm-40) cc_final: 0.7147 (tt0) REVERT: E 57 ARG cc_start: 0.8576 (mtt90) cc_final: 0.8194 (mmm-85) REVERT: E 83 GLU cc_start: 0.7839 (tt0) cc_final: 0.7112 (tm-30) REVERT: E 109 ARG cc_start: 0.6845 (ttp80) cc_final: 0.6644 (mtp180) REVERT: E 214 GLU cc_start: 0.8361 (mm-30) cc_final: 0.8028 (mt-10) REVERT: F 65 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.5429 (tm-30) REVERT: G 45 MET cc_start: 0.8315 (tpp) cc_final: 0.7955 (mmm) outliers start: 51 outliers final: 15 residues processed: 255 average time/residue: 0.2245 time to fit residues: 78.8126 Evaluate side-chains 217 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 1.003 ------------------------------------------------------------------------------- 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 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 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 28 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 E 177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.154930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118447 restraints weight = 12741.531| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.97 r_work: 0.3339 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10018 Z= 0.204 Angle : 0.620 7.673 13583 Z= 0.322 Chirality : 0.040 0.179 1647 Planarity : 0.004 0.048 1702 Dihedral : 10.033 162.550 1517 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 4.69 % Allowed : 16.94 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.23), residues: 1267 helix: 2.18 (0.15), residues: 1105 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 77 HIS 0.005 0.001 HIS B 54 PHE 0.020 0.002 PHE A 107 TYR 0.010 0.001 TYR A 51 ARG 0.005 0.001 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.06237 ( 850) hydrogen bonds : angle 4.62573 ( 2529) covalent geometry : bond 0.00482 (10018) covalent geometry : angle 0.62041 (13583) *********************** 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 243 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 194 time to evaluate : 1.004 Fit side-chains REVERT: A 73 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.4898 (tm-30) REVERT: A 84 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5528 (tpp) REVERT: A 86 MET cc_start: 0.5949 (tpt) cc_final: 0.4746 (ttt) REVERT: A 89 ARG cc_start: 0.7371 (OUTLIER) cc_final: 0.6684 (mmm160) REVERT: A 219 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 22 TRP cc_start: 0.7822 (t60) cc_final: 0.6999 (t-100) REVERT: B 80 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8152 (t70) REVERT: B 90 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.8220 (mtm-85) REVERT: B 91 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: B 94 LEU cc_start: 0.7714 (pt) cc_final: 0.7398 (mp) REVERT: B 99 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8265 (mmtm) REVERT: B 227 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8431 (t) REVERT: C 86 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8350 (ptp) REVERT: D 89 ARG cc_start: 0.7405 (ttm-80) cc_final: 0.6832 (ttp80) REVERT: D 98 GLN cc_start: 0.8053 (tm-30) cc_final: 0.7812 (mp10) REVERT: E 26 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7351 (tt0) REVERT: E 83 GLU cc_start: 0.7818 (tt0) cc_final: 0.7319 (tm-30) REVERT: E 181 SER cc_start: 0.8459 (m) cc_final: 0.8257 (m) REVERT: F 64 PHE cc_start: 0.7637 (m-80) cc_final: 0.7407 (m-80) REVERT: F 65 GLN cc_start: 0.6877 (OUTLIER) cc_final: 0.5597 (tm-30) REVERT: G 45 MET cc_start: 0.8376 (tpp) cc_final: 0.7909 (tpp) outliers start: 49 outliers final: 27 residues processed: 228 average time/residue: 0.2341 time to fit residues: 72.9174 Evaluate side-chains 221 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 14 VAL 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 117 ASP 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 86 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 34 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 124 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 50 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3958 r_free = 0.3958 target = 0.159354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123382 restraints weight = 12561.633| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.97 r_work: 0.3404 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4223 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= 0.140 Angle : 0.536 7.532 13583 Z= 0.275 Chirality : 0.037 0.141 1647 Planarity : 0.004 0.047 1702 Dihedral : 9.333 161.815 1516 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.64 % Allowed : 18.18 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.24), residues: 1267 helix: 2.48 (0.15), residues: 1106 sheet: None (None), residues: 0 loop : -1.14 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 77 HIS 0.004 0.001 HIS D 54 PHE 0.017 0.001 PHE A 107 TYR 0.007 0.001 TYR A 51 ARG 0.005 0.000 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.05075 ( 850) hydrogen bonds : angle 4.23481 ( 2529) covalent geometry : bond 0.00295 (10018) covalent geometry : angle 0.53559 (13583) *********************** 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 242 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 204 time to evaluate : 1.018 Fit side-chains REVERT: A 73 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.4626 (tm-30) REVERT: A 84 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.5826 (tpp) REVERT: A 86 MET cc_start: 0.5678 (tpt) cc_final: 0.4520 (ttt) REVERT: A 89 ARG cc_start: 0.7440 (OUTLIER) cc_final: 0.6729 (mmm160) REVERT: A 219 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7751 (mt-10) REVERT: B 22 TRP cc_start: 0.7775 (t60) cc_final: 0.6873 (t-100) REVERT: B 80 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8212 (t70) REVERT: B 90 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8106 (mtm-85) REVERT: B 91 GLU cc_start: 0.6810 (mp0) cc_final: 0.6494 (mp0) REVERT: B 94 LEU cc_start: 0.7836 (pt) cc_final: 0.7478 (mp) REVERT: B 99 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8268 (mmtm) REVERT: B 227 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8301 (t) REVERT: D 53 MET cc_start: 0.7889 (tpt) cc_final: 0.7516 (tpt) REVERT: D 89 ARG cc_start: 0.7343 (ttm-80) cc_final: 0.6845 (ttp80) REVERT: D 98 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7775 (mp10) REVERT: E 26 GLN cc_start: 0.7376 (mm-40) cc_final: 0.7120 (tt0) REVERT: E 83 GLU cc_start: 0.7781 (tt0) cc_final: 0.7223 (tm-30) REVERT: E 89 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.5581 (ttp-110) REVERT: E 181 SER cc_start: 0.8289 (m) cc_final: 0.8073 (m) REVERT: E 191 TYR cc_start: 0.8880 (m-10) cc_final: 0.8616 (m-10) REVERT: F 64 PHE cc_start: 0.7441 (m-80) cc_final: 0.7217 (m-80) outliers start: 38 outliers final: 22 residues processed: 227 average time/residue: 0.2296 time to fit residues: 71.8322 Evaluate side-chains 220 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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 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 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 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 72 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 195 SER 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 89 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 35 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.9980 chunk 62 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.159572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.124430 restraints weight = 12669.730| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.90 r_work: 0.3413 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10018 Z= 0.148 Angle : 0.537 7.666 13583 Z= 0.276 Chirality : 0.037 0.134 1647 Planarity : 0.004 0.049 1702 Dihedral : 8.886 159.811 1511 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.73 % Allowed : 19.33 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.24), residues: 1267 helix: 2.50 (0.15), residues: 1101 sheet: None (None), residues: 0 loop : -1.29 (0.43), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 77 HIS 0.004 0.001 HIS D 54 PHE 0.015 0.001 PHE A 107 TYR 0.008 0.001 TYR A 51 ARG 0.006 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.05142 ( 850) hydrogen bonds : angle 4.20489 ( 2529) covalent geometry : bond 0.00326 (10018) covalent geometry : angle 0.53749 (13583) *********************** 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: 39 poor density : 200 time to evaluate : 1.324 Fit side-chains REVERT: A 73 GLU cc_start: 0.5545 (OUTLIER) cc_final: 0.4835 (tm-30) REVERT: A 86 MET cc_start: 0.5886 (tpt) cc_final: 0.4806 (ttt) REVERT: A 89 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.6688 (mmm160) REVERT: A 219 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7802 (mt-10) REVERT: B 22 TRP cc_start: 0.7804 (t60) cc_final: 0.6882 (t-100) REVERT: B 26 GLN cc_start: 0.8056 (tm-30) cc_final: 0.7039 (tm-30) REVERT: B 80 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8164 (t70) REVERT: B 90 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8037 (mtm-85) REVERT: B 91 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6624 (mp0) REVERT: B 94 LEU cc_start: 0.7905 (pt) cc_final: 0.7591 (mp) REVERT: B 99 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8285 (mmtm) REVERT: B 113 GLN cc_start: 0.8293 (tp40) cc_final: 0.7787 (tm-30) REVERT: B 227 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8248 (t) REVERT: D 53 MET cc_start: 0.7982 (tpt) cc_final: 0.7623 (tpt) REVERT: D 80 ASP cc_start: 0.8965 (m-30) cc_final: 0.8608 (t0) REVERT: D 98 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7792 (mp10) REVERT: E 26 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7140 (tt0) REVERT: E 83 GLU cc_start: 0.7753 (tt0) cc_final: 0.7295 (tm-30) REVERT: E 89 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6155 (ttp-110) REVERT: E 181 SER cc_start: 0.8253 (m) cc_final: 0.8040 (m) REVERT: E 191 TYR cc_start: 0.8883 (m-10) cc_final: 0.8551 (m-10) REVERT: E 236 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7460 (tp) REVERT: F 64 PHE cc_start: 0.7403 (m-80) cc_final: 0.7143 (m-80) REVERT: G 48 LEU cc_start: 0.8533 (tp) cc_final: 0.8137 (mt) outliers start: 39 outliers final: 23 residues processed: 227 average time/residue: 0.2235 time to fit residues: 70.5297 Evaluate side-chains 219 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 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 106 ILE Chi-restraints excluded: chain C residue 195 SER 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 89 ARG Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 243 THR 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 117 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 95 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN B 197 ASN C 197 ASN D 197 ASN E 197 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.166383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.129397 restraints weight = 12477.822| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.95 r_work: 0.3451 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4841 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= 0.121 Angle : 0.513 8.697 13583 Z= 0.258 Chirality : 0.036 0.129 1647 Planarity : 0.004 0.048 1702 Dihedral : 8.509 157.696 1503 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.58 % Allowed : 21.34 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.41 (0.24), residues: 1267 helix: 2.68 (0.16), residues: 1107 sheet: None (None), residues: 0 loop : -1.09 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 77 HIS 0.002 0.000 HIS D 54 PHE 0.017 0.001 PHE A 107 TYR 0.006 0.001 TYR D 191 ARG 0.007 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04317 ( 850) hydrogen bonds : angle 3.94699 ( 2529) covalent geometry : bond 0.00240 (10018) covalent geometry : angle 0.51259 (13583) *********************** 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 242 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 1.121 Fit side-chains REVERT: A 73 GLU cc_start: 0.5530 (OUTLIER) cc_final: 0.4884 (tm-30) REVERT: A 86 MET cc_start: 0.5834 (tpt) cc_final: 0.4747 (ttt) REVERT: A 89 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6732 (mmm160) REVERT: A 219 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7684 (mt-10) REVERT: B 22 TRP cc_start: 0.7689 (t60) cc_final: 0.6766 (t-100) REVERT: B 26 GLN cc_start: 0.8033 (tm-30) cc_final: 0.6896 (tm-30) REVERT: B 80 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (t70) REVERT: B 90 ARG cc_start: 0.8275 (tpt-90) cc_final: 0.7980 (mtm-85) REVERT: B 91 GLU cc_start: 0.6856 (mp0) cc_final: 0.6607 (mp0) REVERT: B 94 LEU cc_start: 0.7875 (pt) cc_final: 0.7556 (mp) REVERT: B 99 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8237 (mmtm) REVERT: B 113 GLN cc_start: 0.8270 (tp40) cc_final: 0.7766 (tm-30) REVERT: B 227 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8148 (t) REVERT: D 80 ASP cc_start: 0.8981 (m-30) cc_final: 0.8635 (t0) REVERT: D 98 GLN cc_start: 0.8090 (tm-30) cc_final: 0.7745 (mp10) REVERT: E 26 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6896 (tt0) REVERT: E 82 VAL cc_start: 0.8218 (p) cc_final: 0.8015 (p) REVERT: E 83 GLU cc_start: 0.7513 (tt0) cc_final: 0.6930 (tm-30) REVERT: E 191 TYR cc_start: 0.8862 (m-10) cc_final: 0.8546 (m-10) outliers start: 27 outliers final: 17 residues processed: 232 average time/residue: 0.2306 time to fit residues: 73.4375 Evaluate side-chains 223 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 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 72 SER Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain D residue 28 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 71 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 116 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 102 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.125802 restraints weight = 12635.238| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.99 r_work: 0.3432 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10018 Z= 0.122 Angle : 0.516 8.535 13583 Z= 0.259 Chirality : 0.036 0.126 1647 Planarity : 0.004 0.049 1702 Dihedral : 8.345 157.358 1499 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.78 % Allowed : 21.63 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.24), residues: 1267 helix: 2.71 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -1.20 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 PHE 0.019 0.001 PHE A 107 TYR 0.007 0.001 TYR F 43 ARG 0.005 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 850) hydrogen bonds : angle 3.92066 ( 2529) covalent geometry : bond 0.00245 (10018) covalent geometry : angle 0.51603 (13583) *********************** 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 228 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5635 (OUTLIER) cc_final: 0.4917 (tm-30) REVERT: A 77 TRP cc_start: 0.6098 (p-90) cc_final: 0.5718 (p-90) REVERT: A 86 MET cc_start: 0.5778 (tpt) cc_final: 0.4768 (ttt) REVERT: A 89 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.6586 (mmm160) REVERT: A 219 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7677 (mt-10) REVERT: B 22 TRP cc_start: 0.7638 (t60) cc_final: 0.6765 (t-100) REVERT: B 26 GLN cc_start: 0.8011 (tm-30) cc_final: 0.6881 (tm-30) REVERT: B 91 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6558 (mp0) REVERT: B 94 LEU cc_start: 0.7918 (pt) cc_final: 0.7610 (mp) REVERT: B 99 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8240 (mmtm) REVERT: B 113 GLN cc_start: 0.8218 (tp40) cc_final: 0.7751 (tm-30) REVERT: B 227 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8138 (t) REVERT: D 80 ASP cc_start: 0.8995 (m-30) cc_final: 0.8631 (t0) REVERT: D 98 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7748 (mp10) REVERT: E 26 GLN cc_start: 0.7274 (mm-40) cc_final: 0.6983 (tt0) REVERT: E 83 GLU cc_start: 0.7450 (tt0) cc_final: 0.7044 (tm-30) REVERT: E 191 TYR cc_start: 0.8841 (m-10) cc_final: 0.8553 (m-10) REVERT: E 236 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7501 (tp) outliers start: 29 outliers final: 17 residues processed: 220 average time/residue: 0.2481 time to fit residues: 76.2721 Evaluate side-chains 216 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.004 ------------------------------------------------------------------------------- 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 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 91 GLU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 205 SER 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 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 E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain F residue 25 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126879 restraints weight = 12704.950| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 1.88 r_work: 0.3430 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4934 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= 0.133 Angle : 0.533 8.424 13583 Z= 0.267 Chirality : 0.036 0.129 1647 Planarity : 0.004 0.051 1702 Dihedral : 8.263 156.180 1497 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.68 % Allowed : 21.44 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.24), residues: 1267 helix: 2.71 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -1.27 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 77 HIS 0.004 0.001 HIS D 54 PHE 0.021 0.001 PHE A 107 TYR 0.012 0.001 TYR D 191 ARG 0.005 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04559 ( 850) hydrogen bonds : angle 3.97213 ( 2529) covalent geometry : bond 0.00289 (10018) covalent geometry : angle 0.53322 (13583) *********************** 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 228 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 200 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.4983 (tm-30) REVERT: A 86 MET cc_start: 0.5719 (tpt) cc_final: 0.4744 (ttt) REVERT: A 89 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6533 (mmm160) REVERT: A 219 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7661 (mt-10) REVERT: B 22 TRP cc_start: 0.7586 (t60) cc_final: 0.6721 (t-100) REVERT: B 26 GLN cc_start: 0.7978 (tm-30) cc_final: 0.6858 (tm-30) REVERT: B 80 ASP cc_start: 0.8417 (t70) cc_final: 0.8144 (t70) REVERT: B 94 LEU cc_start: 0.7928 (pt) cc_final: 0.7635 (mp) REVERT: B 99 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8226 (mmtm) REVERT: B 113 GLN cc_start: 0.8182 (tp40) cc_final: 0.7760 (tm-30) REVERT: B 227 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8225 (t) REVERT: D 53 MET cc_start: 0.7748 (tpt) cc_final: 0.7363 (tpt) REVERT: D 80 ASP cc_start: 0.8968 (m-30) cc_final: 0.8614 (t0) REVERT: D 98 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7751 (mp10) REVERT: E 26 GLN cc_start: 0.7392 (mm-40) cc_final: 0.7077 (tt0) REVERT: E 83 GLU cc_start: 0.7484 (tt0) cc_final: 0.6966 (tm-30) REVERT: E 191 TYR cc_start: 0.8849 (m-10) cc_final: 0.8544 (m-10) REVERT: E 236 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7480 (tp) REVERT: F 64 PHE cc_start: 0.7298 (m-80) cc_final: 0.7009 (m-80) REVERT: G 45 MET cc_start: 0.8427 (tpp) cc_final: 0.8194 (tpp) outliers start: 28 outliers final: 22 residues processed: 217 average time/residue: 0.2172 time to fit residues: 65.4651 Evaluate side-chains 223 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.117 ------------------------------------------------------------------------------- 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 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 78 LEU Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 205 SER 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 D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 SER 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 236 LEU 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 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 76 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.170127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135633 restraints weight = 12545.505| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 1.90 r_work: 0.3504 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5308 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= 0.113 Angle : 0.512 8.194 13583 Z= 0.254 Chirality : 0.036 0.165 1647 Planarity : 0.004 0.051 1702 Dihedral : 8.170 157.079 1497 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.68 % Allowed : 21.44 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.63 (0.24), residues: 1267 helix: 2.82 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 77 HIS 0.002 0.000 HIS C 54 PHE 0.013 0.001 PHE A 107 TYR 0.009 0.001 TYR D 191 ARG 0.004 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03877 ( 850) hydrogen bonds : angle 3.77810 ( 2529) covalent geometry : bond 0.00217 (10018) covalent geometry : angle 0.51229 (13583) *********************** 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 238 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 210 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.4906 (tm-30) REVERT: A 84 MET cc_start: 0.6623 (mtt) cc_final: 0.6143 (mpp) REVERT: A 86 MET cc_start: 0.5757 (tpt) cc_final: 0.4722 (ttt) REVERT: A 89 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.6580 (mmm160) REVERT: B 22 TRP cc_start: 0.7571 (t60) cc_final: 0.6740 (t-100) REVERT: B 26 GLN cc_start: 0.7948 (tm-30) cc_final: 0.6823 (tm-30) REVERT: B 80 ASP cc_start: 0.8429 (t70) cc_final: 0.8161 (t70) REVERT: B 94 LEU cc_start: 0.7906 (pt) cc_final: 0.7682 (mp) REVERT: B 99 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8216 (mmtm) REVERT: B 113 GLN cc_start: 0.8226 (tp40) cc_final: 0.7849 (tm-30) REVERT: B 117 ASP cc_start: 0.8313 (t0) cc_final: 0.8096 (t0) REVERT: B 227 SER cc_start: 0.8577 (OUTLIER) cc_final: 0.8135 (t) REVERT: C 167 GLN cc_start: 0.8843 (tm-30) cc_final: 0.8545 (tm-30) REVERT: D 53 MET cc_start: 0.7508 (tpt) cc_final: 0.7112 (tpt) REVERT: D 80 ASP cc_start: 0.8980 (m-30) cc_final: 0.8610 (t0) REVERT: D 98 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7703 (mp10) REVERT: E 26 GLN cc_start: 0.7221 (mm-40) cc_final: 0.6959 (tt0) REVERT: E 83 GLU cc_start: 0.7467 (tt0) cc_final: 0.6958 (tm-30) REVERT: E 167 GLN cc_start: 0.8433 (tp40) cc_final: 0.8213 (tp-100) REVERT: E 191 TYR cc_start: 0.8820 (m-10) cc_final: 0.8577 (m-10) REVERT: E 236 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7497 (tp) outliers start: 28 outliers final: 21 residues processed: 227 average time/residue: 0.2135 time to fit residues: 67.7022 Evaluate side-chains 225 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain A residue 187 ILE 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 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 205 SER 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 191 TYR Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 236 LEU 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 29 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3944 r_free = 0.3944 target = 0.160031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.122558 restraints weight = 12732.337| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.19 r_work: 0.3352 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10018 Z= 0.124 Angle : 0.534 8.935 13583 Z= 0.266 Chirality : 0.036 0.128 1647 Planarity : 0.004 0.053 1702 Dihedral : 8.131 154.691 1497 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.58 % Allowed : 22.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.57 (0.24), residues: 1267 helix: 2.80 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 PHE 0.016 0.001 PHE A 107 TYR 0.012 0.001 TYR D 191 ARG 0.004 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 850) hydrogen bonds : angle 3.86865 ( 2529) covalent geometry : bond 0.00264 (10018) covalent geometry : angle 0.53410 (13583) ********************** 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 228 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.4786 (tm-30) REVERT: A 84 MET cc_start: 0.6422 (mtt) cc_final: 0.5776 (mpp) REVERT: A 86 MET cc_start: 0.5464 (tpt) cc_final: 0.4557 (ttt) REVERT: A 89 ARG cc_start: 0.7410 (OUTLIER) cc_final: 0.6653 (mmm160) REVERT: B 22 TRP cc_start: 0.7270 (t60) cc_final: 0.6443 (t-100) REVERT: B 26 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6153 (tm-30) REVERT: B 80 ASP cc_start: 0.8327 (t70) cc_final: 0.8042 (t70) REVERT: B 94 LEU cc_start: 0.7884 (pt) cc_final: 0.7682 (mp) REVERT: B 99 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8016 (mmtm) REVERT: B 113 GLN cc_start: 0.8087 (tp40) cc_final: 0.7604 (tm-30) REVERT: B 117 ASP cc_start: 0.8153 (t0) cc_final: 0.7939 (t0) REVERT: B 227 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.7882 (t) REVERT: C 167 GLN cc_start: 0.8391 (tm-30) cc_final: 0.8008 (tm-30) REVERT: D 53 MET cc_start: 0.7255 (tpt) cc_final: 0.6865 (tpt) REVERT: D 80 ASP cc_start: 0.8839 (m-30) cc_final: 0.8499 (t0) REVERT: D 98 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7470 (mp10) REVERT: E 26 GLN cc_start: 0.7202 (mm-40) cc_final: 0.6765 (tt0) REVERT: E 83 GLU cc_start: 0.7072 (tt0) cc_final: 0.6643 (tm-30) REVERT: E 167 GLN cc_start: 0.7695 (tp40) cc_final: 0.7477 (tp-100) REVERT: E 191 TYR cc_start: 0.8523 (m-10) cc_final: 0.8252 (m-10) REVERT: E 236 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6752 (tp) outliers start: 27 outliers final: 19 residues processed: 219 average time/residue: 0.2105 time to fit residues: 64.4172 Evaluate side-chains 221 residues out of total 1045 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 197 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 97 GLU Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 205 SER 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 D residue 28 THR Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 195 SER Chi-restraints excluded: chain E residue 236 LEU 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 17 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.160015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.122249 restraints weight = 12775.220| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.20 r_work: 0.3343 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.5326 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= 0.124 Angle : 0.530 8.606 13583 Z= 0.265 Chirality : 0.036 0.157 1647 Planarity : 0.004 0.052 1702 Dihedral : 8.079 154.654 1497 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.30 % Allowed : 22.58 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.59 (0.24), residues: 1267 helix: 2.81 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -1.30 (0.47), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 77 HIS 0.003 0.001 HIS D 54 PHE 0.016 0.001 PHE A 107 TYR 0.013 0.001 TYR C 142 ARG 0.004 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 850) hydrogen bonds : angle 3.86718 ( 2529) covalent geometry : bond 0.00261 (10018) covalent geometry : angle 0.53011 (13583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5505.37 seconds wall clock time: 95 minutes 38.17 seconds (5738.17 seconds total)