Starting phenix.real_space_refine on Wed Sep 17 15:09:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ddn_46777/09_2025/9ddn_46777.map" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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 38 5.16 5 C 6147 2.51 5 N 1617 2.21 5 O 1668 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9470 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1743 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 216} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1713 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "C" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "D" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1714 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 5, 'TRANS': 212} Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1735 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain: "F" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 245 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "Y" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Chain: "Z" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 191 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Time building chain proxies: 2.72, per 1000 atoms: 0.29 Number of scatterers: 9470 At special positions: 0 Unit cell: (93.79, 86.32, 114.54, 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 38 16.00 O 1668 8.00 N 1617 7.00 C 6147 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: 1.03 Conformation dependent library (CDL) restraints added in 359.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 89.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 4.305A pdb=" N LYS A 12 " --> pdb=" O LEU A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 58 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.729A pdb=" N LEU A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.942A pdb=" N LEU A 76 " --> pdb=" O ARG A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 96 removed outlier: 3.735A pdb=" N ALA A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 125 removed outlier: 4.242A pdb=" N VAL A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 155 removed outlier: 3.878A pdb=" N LEU A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 135 " --> pdb=" O GLY A 131 " (cutoff:3.500A) Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 163 through 166 Processing helix chain 'A' and resid 167 through 221 removed outlier: 3.526A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Proline residue: A 187 - end of helix Processing helix chain 'B' and resid 8 through 12 removed outlier: 3.524A pdb=" N LYS B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 8 through 12' Processing helix chain 'B' and resid 14 through 58 removed outlier: 3.510A pdb=" N ASP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 100 through 124 removed outlier: 3.578A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 157 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 163 through 184 Proline residue: B 169 - end of helix removed outlier: 3.562A pdb=" N THR B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 222 removed outlier: 4.723A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 13 Processing helix chain 'C' and resid 14 through 57 Processing helix chain 'C' and resid 61 through 71 removed outlier: 4.253A pdb=" N GLN C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER C 69 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY C 71 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 95 removed outlier: 4.090A pdb=" N ARG C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 117 removed outlier: 4.091A pdb=" N SER C 115 " --> pdb=" O ALA C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 157 removed outlier: 3.723A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 163 through 223 Proline residue: C 169 - end of helix removed outlier: 3.663A pdb=" N ILE C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Proline residue: C 187 - end of helix Processing helix chain 'D' and resid 7 through 11 Processing helix chain 'D' and resid 14 through 58 removed outlier: 3.532A pdb=" N LYS D 18 " --> pdb=" O SER D 14 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN D 43 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS D 55 " --> pdb=" O ALA D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 71 removed outlier: 4.411A pdb=" N GLY D 71 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 removed outlier: 7.190A pdb=" N THR D 77 " --> pdb=" O ASP D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 95 Processing helix chain 'D' and resid 103 through 125 removed outlier: 4.019A pdb=" N GLY D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 157 removed outlier: 3.561A pdb=" N LEU D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) Proline residue: D 138 - end of helix Processing helix chain 'D' and resid 163 through 207 removed outlier: 3.862A pdb=" N VAL D 167 " --> pdb=" O THR D 163 " (cutoff:3.500A) Proline residue: D 169 - end of helix Proline residue: D 187 - end of helix removed outlier: 3.862A pdb=" N ASN D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 223 Processing helix chain 'E' and resid 6 through 11 Processing helix chain 'E' and resid 14 through 58 removed outlier: 3.648A pdb=" N LEU E 42 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS E 55 " --> pdb=" O ALA E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 70 through 73 Processing helix chain 'E' and resid 77 through 96 Processing helix chain 'E' and resid 100 through 124 removed outlier: 3.698A pdb=" N SER E 115 " --> pdb=" O ALA E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 157 removed outlier: 3.929A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Proline residue: E 138 - end of helix Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 167 through 224 removed outlier: 4.299A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 179 " --> pdb=" O LEU E 175 " (cutoff:3.500A) Proline residue: E 187 - end of helix removed outlier: 3.823A pdb=" N VAL E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 32 removed outlier: 3.572A pdb=" N SER F 32 " --> pdb=" O ALA F 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 33 removed outlier: 3.930A pdb=" N ASP G 9 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 36 removed outlier: 3.549A pdb=" N LEU Y 25 " --> pdb=" O LEU Y 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 19 through 34 removed outlier: 4.215A pdb=" N ASP Z 23 " --> pdb=" O VAL Z 19 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE Z 32 " --> pdb=" O LEU Z 28 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) 806 hydrogen bonds defined for protein. 2397 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.32 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: 1872 1.33 - 1.45: 2196 1.45 - 1.57: 5507 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9651 Sorted by residual: bond pdb=" N ASN A 75 " pdb=" CA ASN A 75 " ideal model delta sigma weight residual 1.458 1.500 -0.041 1.14e-02 7.69e+03 1.31e+01 bond pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.17e-02 7.31e+03 1.11e+01 bond pdb=" N HIS D 94 " pdb=" CA HIS D 94 " ideal model delta sigma weight residual 1.454 1.498 -0.043 1.31e-02 5.83e+03 1.09e+01 bond pdb=" N ILE Z 16 " pdb=" CA ILE Z 16 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ASN C 75 " pdb=" CA ASN C 75 " ideal model delta sigma weight residual 1.458 1.497 -0.040 1.25e-02 6.40e+03 1.01e+01 ... (remaining 9646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 8680 1.51 - 3.02: 3484 3.02 - 4.53: 812 4.53 - 6.04: 68 6.04 - 7.55: 10 Bond angle restraints: 13054 Sorted by residual: angle pdb=" N ARG C 64 " pdb=" CA ARG C 64 " pdb=" C ARG C 64 " ideal model delta sigma weight residual 113.88 107.18 6.70 1.23e+00 6.61e-01 2.97e+01 angle pdb=" N THR E 39 " pdb=" CA THR E 39 " pdb=" C THR E 39 " ideal model delta sigma weight residual 113.12 106.44 6.68 1.25e+00 6.40e-01 2.85e+01 angle pdb=" N TYR C 66 " pdb=" CA TYR C 66 " pdb=" CB TYR C 66 " ideal model delta sigma weight residual 109.94 102.39 7.55 1.49e+00 4.50e-01 2.57e+01 angle pdb=" N PHE D 27 " pdb=" CA PHE D 27 " pdb=" C PHE D 27 " ideal model delta sigma weight residual 111.40 106.12 5.28 1.22e+00 6.72e-01 1.87e+01 angle pdb=" CA GLN B 67 " pdb=" C GLN B 67 " pdb=" O GLN B 67 " ideal model delta sigma weight residual 120.42 116.19 4.23 1.06e+00 8.90e-01 1.59e+01 ... (remaining 13049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 5263 17.63 - 35.25: 401 35.25 - 52.88: 60 52.88 - 70.50: 23 70.50 - 88.13: 4 Dihedral angle restraints: 5751 sinusoidal: 2257 harmonic: 3494 Sorted by residual: dihedral pdb=" CA GLU C 119 " pdb=" C GLU C 119 " pdb=" N LEU C 120 " pdb=" CA LEU C 120 " ideal model delta harmonic sigma weight residual 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA ASN C 122 " pdb=" C ASN C 122 " pdb=" N LEU C 123 " pdb=" CA LEU C 123 " ideal model delta harmonic sigma weight residual 180.00 150.89 29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ARG C 118 " pdb=" C ARG C 118 " pdb=" N GLU C 119 " pdb=" CA GLU C 119 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 5748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 848 0.063 - 0.126: 451 0.126 - 0.188: 178 0.188 - 0.251: 33 0.251 - 0.314: 9 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA ARG C 118 " pdb=" N ARG C 118 " pdb=" C ARG C 118 " pdb=" CB ARG C 118 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA SER E 98 " pdb=" N SER E 98 " pdb=" C SER E 98 " pdb=" CB SER E 98 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA LYS C 18 " pdb=" N LYS C 18 " pdb=" C LYS C 18 " pdb=" CB LYS C 18 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1516 not shown) Planarity restraints: 1644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 84 " -0.088 2.00e-02 2.50e+03 5.01e-02 5.01e+01 pdb=" CG TYR E 84 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR E 84 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR E 84 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR E 84 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR E 84 " 0.027 2.00e-02 2.50e+03 pdb=" CZ TYR E 84 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 84 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 57 " -0.083 2.00e-02 2.50e+03 4.16e-02 4.33e+01 pdb=" CG TRP C 57 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP C 57 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP C 57 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP C 57 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP C 57 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 57 " 0.058 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 57 " -0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 57 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP C 57 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 209 " -0.080 2.00e-02 2.50e+03 4.88e-02 4.17e+01 pdb=" CG PHE A 209 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 209 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 PHE A 209 " 0.040 2.00e-02 2.50e+03 pdb=" CE1 PHE A 209 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 209 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 209 " -0.049 2.00e-02 2.50e+03 ... (remaining 1641 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 13 2.59 - 3.17: 8148 3.17 - 3.75: 15446 3.75 - 4.32: 19144 4.32 - 4.90: 32313 Nonbonded interactions: 75064 Sorted by model distance: nonbonded pdb=" O ASN C 75 " pdb=" OD1 ASN C 75 " model vdw 2.015 3.040 nonbonded pdb=" O SER C 69 " pdb=" N LYS C 72 " model vdw 2.435 3.120 nonbonded pdb=" N ASP Z 23 " pdb=" OD1 ASP Z 23 " model vdw 2.472 3.120 nonbonded pdb=" CG ARG D 113 " pdb=" NH1 ARG D 113 " model vdw 2.489 3.520 nonbonded pdb=" O LYS D 55 " pdb=" OG SER D 58 " model vdw 2.503 3.040 ... (remaining 75059 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 223) selection = (chain 'B' and resid 7 through 223) selection = (chain 'C' and resid 7 through 223) selection = (chain 'D' and resid 7 through 223) selection = (chain 'E' and resid 7 through 223) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 6 through 32) } ncs_group { reference = (chain 'Y' and resid 13 through 37) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.800 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 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 : 0.012 0.043 9651 Z= 0.729 Angle : 1.624 7.554 13054 Z= 1.121 Chirality : 0.086 0.314 1519 Planarity : 0.014 0.123 1644 Dihedral : 13.461 88.128 3479 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.71 % Allowed : 6.82 % Favored : 92.46 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.22), residues: 1188 helix: -0.63 (0.14), residues: 1020 sheet: None (None), residues: 0 loop : 0.08 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 110 TYR 0.088 0.014 TYR E 84 PHE 0.080 0.011 PHE A 209 TRP 0.083 0.018 TRP B 147 HIS 0.009 0.002 HIS G 22 Details of bonding type rmsd covalent geometry : bond 0.01186 ( 9651) covalent geometry : angle 1.62400 (13054) hydrogen bonds : bond 0.17802 ( 806) hydrogen bonds : angle 7.39423 ( 2397) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 388 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 GLN cc_start: 0.9490 (mt0) cc_final: 0.9170 (mt0) REVERT: A 121 GLU cc_start: 0.8991 (tt0) cc_final: 0.8739 (tm-30) REVERT: A 173 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8455 (tp30) REVERT: B 21 MET cc_start: 0.8825 (tpp) cc_final: 0.8623 (mmp) REVERT: B 48 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8190 (tm-30) REVERT: B 72 LYS cc_start: 0.9002 (tppt) cc_final: 0.8292 (tptp) REVERT: B 76 LEU cc_start: 0.8255 (tp) cc_final: 0.7933 (mt) REVERT: B 80 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8476 (tp30) REVERT: B 81 GLN cc_start: 0.8586 (tp40) cc_final: 0.8165 (tm-30) REVERT: B 201 LYS cc_start: 0.9458 (ttpp) cc_final: 0.9145 (ttmm) REVERT: C 18 LYS cc_start: 0.8868 (pttt) cc_final: 0.8525 (pttm) REVERT: C 67 GLN cc_start: 0.9589 (mt0) cc_final: 0.9389 (mt0) REVERT: C 76 LEU cc_start: 0.8381 (mt) cc_final: 0.8029 (mp) REVERT: C 117 ASN cc_start: 0.9171 (m-40) cc_final: 0.8725 (m-40) REVERT: C 139 TYR cc_start: 0.9168 (m-10) cc_final: 0.8754 (m-10) REVERT: C 150 MET cc_start: 0.8846 (mmm) cc_final: 0.8573 (mmm) REVERT: C 210 MET cc_start: 0.8530 (ppp) cc_final: 0.8278 (ttp) REVERT: D 114 ILE cc_start: 0.8678 (tp) cc_final: 0.8461 (tp) REVERT: D 116 MET cc_start: 0.8896 (tpp) cc_final: 0.8679 (tpt) REVERT: D 167 VAL cc_start: 0.9591 (t) cc_final: 0.9355 (p) REVERT: E 76 LEU cc_start: 0.9182 (mt) cc_final: 0.8915 (mt) REVERT: E 77 THR cc_start: 0.8957 (p) cc_final: 0.8751 (p) REVERT: E 79 SER cc_start: 0.9249 (m) cc_final: 0.8988 (p) REVERT: E 106 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8627 (tm-30) REVERT: E 121 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8677 (tm-30) REVERT: E 122 ASN cc_start: 0.9171 (t0) cc_final: 0.8921 (t0) REVERT: E 210 MET cc_start: 0.9138 (ttt) cc_final: 0.8928 (ttm) REVERT: G 12 LYS cc_start: 0.8929 (mmtt) cc_final: 0.8635 (mptt) REVERT: G 25 LEU cc_start: 0.9340 (tt) cc_final: 0.9028 (tt) REVERT: G 31 TRP cc_start: 0.8677 (t-100) cc_final: 0.8359 (t60) REVERT: Z 17 ASN cc_start: 0.9168 (t0) cc_final: 0.8176 (t0) outliers start: 7 outliers final: 1 residues processed: 389 average time/residue: 0.1300 time to fit residues: 65.9120 Evaluate side-chains 277 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 276 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 64 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 193 ASN B 43 ASN B 122 ASN B 205 ASN C 97 ASN D 94 HIS D 99 HIS D 151 HIS D 218 HIS E 205 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.099375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.069721 restraints weight = 21106.316| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 3.57 r_work: 0.2956 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 9651 Z= 0.190 Angle : 0.725 9.886 13054 Z= 0.384 Chirality : 0.042 0.226 1519 Planarity : 0.005 0.066 1644 Dihedral : 5.104 45.791 1293 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.65 % Allowed : 16.29 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.24), residues: 1188 helix: 1.26 (0.16), residues: 1029 sheet: None (None), residues: 0 loop : 0.16 (0.51), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 64 TYR 0.032 0.002 TYR D 66 PHE 0.016 0.002 PHE C 87 TRP 0.009 0.001 TRP E 57 HIS 0.008 0.001 HIS B 99 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 9651) covalent geometry : angle 0.72463 (13054) hydrogen bonds : bond 0.05928 ( 806) hydrogen bonds : angle 4.41876 ( 2397) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 GLU cc_start: 0.9021 (tt0) cc_final: 0.8778 (tm-30) REVERT: B 73 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7345 (tpp80) REVERT: B 76 LEU cc_start: 0.8392 (tp) cc_final: 0.8029 (mt) REVERT: B 124 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 201 LYS cc_start: 0.9492 (ttpp) cc_final: 0.9257 (ttmm) REVERT: C 117 ASN cc_start: 0.8869 (m-40) cc_final: 0.8652 (m-40) REVERT: C 139 TYR cc_start: 0.9161 (m-10) cc_final: 0.8930 (m-10) REVERT: C 150 MET cc_start: 0.8873 (mmm) cc_final: 0.8606 (mmm) REVERT: D 116 MET cc_start: 0.8966 (tpp) cc_final: 0.8693 (tpt) REVERT: E 121 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8708 (tm-30) REVERT: E 122 ASN cc_start: 0.9161 (t0) cc_final: 0.8932 (t0) REVERT: F 13 ARG cc_start: 0.7377 (mmt180) cc_final: 0.7156 (mmt180) REVERT: G 7 GLN cc_start: 0.9146 (mp10) cc_final: 0.8712 (mp10) REVERT: G 12 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8530 (mptt) REVERT: G 31 TRP cc_start: 0.8684 (t-100) cc_final: 0.8404 (t60) REVERT: Z 17 ASN cc_start: 0.9138 (t0) cc_final: 0.8247 (t0) outliers start: 26 outliers final: 12 residues processed: 296 average time/residue: 0.1147 time to fit residues: 45.6666 Evaluate side-chains 262 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 249 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 26 PHE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 23 VAL Chi-restraints excluded: chain Y residue 16 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 50 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 97 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.100689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.070959 restraints weight = 21064.139| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.49 r_work: 0.3022 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9651 Z= 0.155 Angle : 0.666 11.734 13054 Z= 0.342 Chirality : 0.040 0.171 1519 Planarity : 0.004 0.068 1644 Dihedral : 4.520 33.925 1289 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 2.65 % Allowed : 19.55 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.30 (0.25), residues: 1188 helix: 1.78 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : 0.09 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 64 TYR 0.048 0.003 TYR C 66 PHE 0.013 0.001 PHE G 26 TRP 0.008 0.001 TRP D 57 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9651) covalent geometry : angle 0.66585 (13054) hydrogen bonds : bond 0.04942 ( 806) hydrogen bonds : angle 4.09521 ( 2397) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 293 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8347 (tm-30) REVERT: A 57 TRP cc_start: 0.9000 (m100) cc_final: 0.8228 (m100) REVERT: A 106 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8158 (mt-10) REVERT: A 121 GLU cc_start: 0.9048 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 210 MET cc_start: 0.9174 (tpp) cc_final: 0.8460 (tpt) REVERT: A 211 GLU cc_start: 0.8968 (tp30) cc_final: 0.8710 (tp30) REVERT: A 212 GLU cc_start: 0.9372 (mm-30) cc_final: 0.8939 (mm-30) REVERT: B 50 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8942 (pt0) REVERT: B 84 TYR cc_start: 0.9029 (t80) cc_final: 0.8752 (t80) REVERT: B 122 ASN cc_start: 0.9146 (t0) cc_final: 0.8922 (t0) REVERT: C 18 LYS cc_start: 0.8996 (pttt) cc_final: 0.8668 (pttm) REVERT: C 84 TYR cc_start: 0.8674 (t80) cc_final: 0.8328 (t80) REVERT: C 116 MET cc_start: 0.8946 (tpp) cc_final: 0.8383 (tpt) REVERT: C 150 MET cc_start: 0.8883 (mmm) cc_final: 0.8601 (mmm) REVERT: D 116 MET cc_start: 0.9002 (tpp) cc_final: 0.8768 (tpt) REVERT: E 121 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8666 (tm-30) REVERT: E 210 MET cc_start: 0.9100 (ttm) cc_final: 0.8350 (tpt) REVERT: F 13 ARG cc_start: 0.7312 (mmt180) cc_final: 0.7105 (mmt180) REVERT: G 7 GLN cc_start: 0.9169 (mp10) cc_final: 0.8581 (mp10) REVERT: G 12 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8513 (mptt) REVERT: G 31 TRP cc_start: 0.8618 (t-100) cc_final: 0.8286 (t60) REVERT: Z 17 ASN cc_start: 0.9088 (t0) cc_final: 0.8743 (t0) outliers start: 26 outliers final: 18 residues processed: 303 average time/residue: 0.1013 time to fit residues: 42.5187 Evaluate side-chains 278 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain F residue 26 PHE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain Y residue 16 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 87 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 220 GLN D 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.100239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070782 restraints weight = 21237.776| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.50 r_work: 0.3013 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9651 Z= 0.157 Angle : 0.669 12.502 13054 Z= 0.341 Chirality : 0.040 0.173 1519 Planarity : 0.004 0.059 1644 Dihedral : 4.361 32.775 1289 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.46 % Allowed : 21.18 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.57 (0.25), residues: 1188 helix: 1.97 (0.16), residues: 1027 sheet: None (None), residues: 0 loop : 0.13 (0.51), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 73 TYR 0.040 0.003 TYR D 66 PHE 0.012 0.001 PHE G 26 TRP 0.007 0.001 TRP F 31 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 9651) covalent geometry : angle 0.66901 (13054) hydrogen bonds : bond 0.04657 ( 806) hydrogen bonds : angle 4.01093 ( 2397) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8301 (tm-30) REVERT: A 57 TRP cc_start: 0.9015 (m100) cc_final: 0.8394 (m100) REVERT: A 70 GLN cc_start: 0.9351 (mt0) cc_final: 0.9050 (mm-40) REVERT: A 80 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8964 (tp30) REVERT: A 121 GLU cc_start: 0.9048 (tt0) cc_final: 0.8722 (tm-30) REVERT: A 210 MET cc_start: 0.9138 (tpp) cc_final: 0.8414 (tpt) REVERT: B 50 GLU cc_start: 0.9165 (mm-30) cc_final: 0.8924 (pt0) REVERT: B 67 GLN cc_start: 0.9524 (mt0) cc_final: 0.9293 (mp10) REVERT: B 121 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8338 (mt-10) REVERT: B 122 ASN cc_start: 0.9093 (t0) cc_final: 0.8849 (t0) REVERT: C 18 LYS cc_start: 0.9028 (pttt) cc_final: 0.8683 (pttm) REVERT: C 112 MET cc_start: 0.6955 (mtt) cc_final: 0.6743 (mtt) REVERT: C 116 MET cc_start: 0.8904 (tpp) cc_final: 0.8368 (tpt) REVERT: C 150 MET cc_start: 0.8858 (mmm) cc_final: 0.8592 (mmm) REVERT: D 116 MET cc_start: 0.9004 (tpp) cc_final: 0.8639 (tpt) REVERT: E 121 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8703 (tm-30) REVERT: F 13 ARG cc_start: 0.7305 (mmt180) cc_final: 0.7094 (mmt180) REVERT: G 7 GLN cc_start: 0.9046 (mp10) cc_final: 0.8666 (mp10) REVERT: G 12 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8505 (mptt) REVERT: G 31 TRP cc_start: 0.8610 (t-100) cc_final: 0.8295 (t60) REVERT: Z 17 ASN cc_start: 0.9060 (t0) cc_final: 0.8778 (t0) outliers start: 34 outliers final: 24 residues processed: 287 average time/residue: 0.1071 time to fit residues: 42.1177 Evaluate side-chains 281 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 256 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain F residue 26 PHE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 2.9990 chunk 15 optimal weight: 0.0050 chunk 95 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN D 70 GLN E 67 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.100146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.070504 restraints weight = 21439.405| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 3.53 r_work: 0.2991 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9651 Z= 0.178 Angle : 0.674 12.398 13054 Z= 0.342 Chirality : 0.040 0.181 1519 Planarity : 0.004 0.042 1644 Dihedral : 4.237 31.881 1289 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 5.09 % Allowed : 20.88 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.25), residues: 1188 helix: 2.08 (0.16), residues: 1025 sheet: None (None), residues: 0 loop : 0.26 (0.52), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 113 TYR 0.041 0.003 TYR C 66 PHE 0.018 0.001 PHE C 87 TRP 0.007 0.001 TRP D 57 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9651) covalent geometry : angle 0.67396 (13054) hydrogen bonds : bond 0.04512 ( 806) hydrogen bonds : angle 3.97643 ( 2397) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 269 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8969 (tp30) REVERT: A 88 LYS cc_start: 0.9160 (tptt) cc_final: 0.8909 (tppt) REVERT: A 121 GLU cc_start: 0.9056 (tt0) cc_final: 0.8755 (tm-30) REVERT: A 210 MET cc_start: 0.9108 (tpp) cc_final: 0.8567 (tpt) REVERT: B 50 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8945 (pt0) REVERT: B 121 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8375 (mt-10) REVERT: B 122 ASN cc_start: 0.9084 (t0) cc_final: 0.8839 (t0) REVERT: C 18 LYS cc_start: 0.9001 (pttt) cc_final: 0.8655 (pttm) REVERT: C 112 MET cc_start: 0.6839 (mtt) cc_final: 0.6256 (mtt) REVERT: C 116 MET cc_start: 0.8911 (tpp) cc_final: 0.8359 (tpt) REVERT: C 124 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 150 MET cc_start: 0.8879 (mmm) cc_final: 0.8597 (mmm) REVERT: C 214 THR cc_start: 0.8935 (p) cc_final: 0.8675 (p) REVERT: D 80 GLU cc_start: 0.9328 (tt0) cc_final: 0.8538 (tt0) REVERT: D 116 MET cc_start: 0.8904 (tpp) cc_final: 0.8503 (tpt) REVERT: D 166 MET cc_start: 0.9124 (pmm) cc_final: 0.8911 (pmm) REVERT: E 106 GLU cc_start: 0.9139 (pp20) cc_final: 0.8886 (pp20) REVERT: E 121 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8714 (tm-30) REVERT: E 210 MET cc_start: 0.9097 (ttm) cc_final: 0.8211 (tpt) REVERT: F 13 ARG cc_start: 0.7281 (mmt180) cc_final: 0.7038 (mmt180) REVERT: G 7 GLN cc_start: 0.9084 (mp10) cc_final: 0.8659 (mp10) REVERT: G 12 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8459 (mptt) REVERT: G 31 TRP cc_start: 0.8609 (t-100) cc_final: 0.8291 (t60) REVERT: Z 17 ASN cc_start: 0.9088 (t0) cc_final: 0.8844 (t0) outliers start: 50 outliers final: 37 residues processed: 286 average time/residue: 0.1097 time to fit residues: 42.7942 Evaluate side-chains 293 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 99 HIS Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 19 LEU Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain F residue 26 PHE Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 86 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 34 optimal weight: 0.1980 chunk 61 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 GLN B 208 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.102350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.072996 restraints weight = 20888.495| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.49 r_work: 0.3032 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.4251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9651 Z= 0.144 Angle : 0.666 12.945 13054 Z= 0.336 Chirality : 0.039 0.189 1519 Planarity : 0.003 0.031 1644 Dihedral : 4.215 31.370 1289 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.36 % Allowed : 23.22 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.25), residues: 1188 helix: 2.15 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : 0.21 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.042 0.002 TYR C 66 PHE 0.015 0.001 PHE C 87 TRP 0.007 0.001 TRP B 32 HIS 0.002 0.000 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 9651) covalent geometry : angle 0.66649 (13054) hydrogen bonds : bond 0.04340 ( 806) hydrogen bonds : angle 3.92916 ( 2397) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 277 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9246 (OUTLIER) cc_final: 0.8953 (tp30) REVERT: A 88 LYS cc_start: 0.9121 (tptt) cc_final: 0.8916 (tppt) REVERT: A 116 MET cc_start: 0.9141 (ttm) cc_final: 0.8931 (ttm) REVERT: A 121 GLU cc_start: 0.9021 (tt0) cc_final: 0.8713 (tm-30) REVERT: B 50 GLU cc_start: 0.9181 (mm-30) cc_final: 0.8924 (pt0) REVERT: B 121 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8328 (mt-10) REVERT: B 122 ASN cc_start: 0.9029 (t0) cc_final: 0.8801 (t0) REVERT: C 18 LYS cc_start: 0.8964 (pttt) cc_final: 0.8637 (pttm) REVERT: C 80 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8835 (pp20) REVERT: C 116 MET cc_start: 0.8896 (tpp) cc_final: 0.8203 (tpt) REVERT: C 124 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8657 (tm-30) REVERT: C 150 MET cc_start: 0.8850 (mmm) cc_final: 0.8526 (mmm) REVERT: C 211 GLU cc_start: 0.9148 (tt0) cc_final: 0.8453 (tm-30) REVERT: D 80 GLU cc_start: 0.9329 (tt0) cc_final: 0.8708 (tp30) REVERT: D 116 MET cc_start: 0.8829 (tpp) cc_final: 0.8482 (tpt) REVERT: E 99 HIS cc_start: 0.8132 (m90) cc_final: 0.7352 (m-70) REVERT: E 106 GLU cc_start: 0.9165 (pp20) cc_final: 0.8927 (pp20) REVERT: E 121 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8664 (tm-30) REVERT: E 210 MET cc_start: 0.8990 (ttm) cc_final: 0.8157 (tpt) REVERT: F 13 ARG cc_start: 0.7279 (mmt180) cc_final: 0.7074 (mmt180) REVERT: G 7 GLN cc_start: 0.9117 (mp10) cc_final: 0.8686 (mp10) REVERT: G 12 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8414 (mptt) REVERT: G 31 TRP cc_start: 0.8584 (t-100) cc_final: 0.8255 (t60) REVERT: Z 17 ASN cc_start: 0.9051 (t0) cc_final: 0.8784 (t0) outliers start: 33 outliers final: 19 residues processed: 288 average time/residue: 0.1008 time to fit residues: 40.3247 Evaluate side-chains 282 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 261 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.101421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071780 restraints weight = 21194.857| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.57 r_work: 0.3017 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9651 Z= 0.155 Angle : 0.672 12.909 13054 Z= 0.340 Chirality : 0.040 0.209 1519 Planarity : 0.003 0.032 1644 Dihedral : 4.176 30.982 1289 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.36 % Allowed : 23.22 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.25), residues: 1188 helix: 2.23 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : 0.02 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.059 0.002 TYR B 66 PHE 0.053 0.001 PHE C 87 TRP 0.006 0.001 TRP D 57 HIS 0.002 0.000 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9651) covalent geometry : angle 0.67196 (13054) hydrogen bonds : bond 0.04242 ( 806) hydrogen bonds : angle 3.94171 ( 2397) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 266 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8981 (tp30) REVERT: A 106 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8392 (mm-30) REVERT: A 121 GLU cc_start: 0.9047 (tt0) cc_final: 0.8729 (tm-30) REVERT: A 210 MET cc_start: 0.8910 (tpp) cc_final: 0.8565 (tpt) REVERT: B 15 LEU cc_start: 0.8983 (tp) cc_final: 0.8748 (tp) REVERT: B 50 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8927 (pt0) REVERT: B 104 VAL cc_start: 0.7949 (OUTLIER) cc_final: 0.7668 (t) REVERT: B 121 GLU cc_start: 0.8753 (mm-30) cc_final: 0.8343 (mt-10) REVERT: B 122 ASN cc_start: 0.9033 (t0) cc_final: 0.8802 (t0) REVERT: C 18 LYS cc_start: 0.8964 (pttt) cc_final: 0.8642 (pttm) REVERT: C 112 MET cc_start: 0.6778 (mtt) cc_final: 0.6088 (mtm) REVERT: C 116 MET cc_start: 0.8862 (tpp) cc_final: 0.8293 (tpt) REVERT: C 124 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8648 (tm-30) REVERT: C 150 MET cc_start: 0.8871 (mmm) cc_final: 0.8548 (mmm) REVERT: D 80 GLU cc_start: 0.9324 (tt0) cc_final: 0.8740 (tp30) REVERT: D 116 MET cc_start: 0.8828 (tpp) cc_final: 0.8486 (tpt) REVERT: E 99 HIS cc_start: 0.8137 (m90) cc_final: 0.7378 (m-70) REVERT: E 106 GLU cc_start: 0.9178 (pp20) cc_final: 0.8940 (pp20) REVERT: E 121 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8655 (tm-30) REVERT: E 210 MET cc_start: 0.9020 (ttm) cc_final: 0.8180 (tpt) REVERT: F 13 ARG cc_start: 0.7268 (mmt180) cc_final: 0.6963 (mmt180) REVERT: G 7 GLN cc_start: 0.9125 (mp10) cc_final: 0.8688 (mp10) REVERT: G 12 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8405 (mptt) REVERT: G 31 TRP cc_start: 0.8555 (t-100) cc_final: 0.8226 (t60) REVERT: Z 17 ASN cc_start: 0.9024 (t0) cc_final: 0.8762 (t0) outliers start: 33 outliers final: 25 residues processed: 277 average time/residue: 0.1047 time to fit residues: 39.9148 Evaluate side-chains 283 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain Y residue 16 ILE Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 56 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 97 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.102115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.072648 restraints weight = 21144.355| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 3.56 r_work: 0.3029 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9651 Z= 0.149 Angle : 0.679 13.365 13054 Z= 0.342 Chirality : 0.039 0.196 1519 Planarity : 0.003 0.041 1644 Dihedral : 4.142 30.402 1289 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.67 % Allowed : 23.83 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.84 (0.25), residues: 1188 helix: 2.20 (0.16), residues: 1021 sheet: None (None), residues: 0 loop : -0.10 (0.49), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 73 TYR 0.045 0.002 TYR B 66 PHE 0.021 0.001 PHE C 87 TRP 0.008 0.001 TRP F 31 HIS 0.002 0.000 HIS B 218 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 9651) covalent geometry : angle 0.67948 (13054) hydrogen bonds : bond 0.04175 ( 806) hydrogen bonds : angle 3.92184 ( 2397) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 268 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8981 (tp30) REVERT: A 106 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 121 GLU cc_start: 0.9037 (tt0) cc_final: 0.8708 (tm-30) REVERT: A 210 MET cc_start: 0.8919 (tpp) cc_final: 0.8679 (tpt) REVERT: B 15 LEU cc_start: 0.8958 (tp) cc_final: 0.8730 (tp) REVERT: B 50 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8919 (pt0) REVERT: B 121 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8308 (mt-10) REVERT: B 122 ASN cc_start: 0.9031 (t0) cc_final: 0.8809 (t0) REVERT: C 18 LYS cc_start: 0.9021 (pttt) cc_final: 0.8728 (pttm) REVERT: C 124 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8662 (tm-30) REVERT: C 150 MET cc_start: 0.8853 (mmm) cc_final: 0.8590 (mmm) REVERT: C 211 GLU cc_start: 0.8681 (tp30) cc_final: 0.7606 (tp30) REVERT: D 75 ASN cc_start: 0.9005 (p0) cc_final: 0.8792 (p0) REVERT: D 80 GLU cc_start: 0.9298 (tt0) cc_final: 0.8575 (tt0) REVERT: D 116 MET cc_start: 0.8840 (tpp) cc_final: 0.8460 (tpt) REVERT: E 99 HIS cc_start: 0.8158 (m90) cc_final: 0.7447 (m-70) REVERT: E 106 GLU cc_start: 0.9181 (pp20) cc_final: 0.8949 (pp20) REVERT: E 121 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8635 (tm-30) REVERT: F 13 ARG cc_start: 0.7296 (mmt180) cc_final: 0.7027 (mmt180) REVERT: G 7 GLN cc_start: 0.9105 (mp10) cc_final: 0.8620 (mp10) REVERT: G 12 LYS cc_start: 0.8675 (mmtt) cc_final: 0.8393 (mptt) REVERT: G 31 TRP cc_start: 0.8544 (t-100) cc_final: 0.8224 (t60) REVERT: Z 17 ASN cc_start: 0.8970 (t0) cc_final: 0.8693 (t0) outliers start: 36 outliers final: 24 residues processed: 279 average time/residue: 0.1047 time to fit residues: 40.3356 Evaluate side-chains 286 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 261 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 112 MET Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain G residue 9 ASP Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 87 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 58 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 114 optimal weight: 0.1980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.102145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.073975 restraints weight = 21118.294| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 3.50 r_work: 0.3053 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9651 Z= 0.149 Angle : 0.712 16.496 13054 Z= 0.356 Chirality : 0.040 0.213 1519 Planarity : 0.003 0.031 1644 Dihedral : 4.139 29.862 1289 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.55 % Allowed : 24.95 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.25), residues: 1188 helix: 2.18 (0.16), residues: 1020 sheet: None (None), residues: 0 loop : -0.18 (0.49), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 113 TYR 0.042 0.002 TYR B 66 PHE 0.022 0.001 PHE C 87 TRP 0.008 0.001 TRP D 57 HIS 0.003 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9651) covalent geometry : angle 0.71177 (13054) hydrogen bonds : bond 0.04114 ( 806) hydrogen bonds : angle 3.89354 ( 2397) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8974 (tp30) REVERT: A 106 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 121 GLU cc_start: 0.8980 (tt0) cc_final: 0.8651 (tm-30) REVERT: A 210 MET cc_start: 0.8944 (tpp) cc_final: 0.8546 (tpt) REVERT: B 50 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8929 (pt0) REVERT: B 110 ARG cc_start: 0.8771 (tpp80) cc_final: 0.8531 (tpp80) REVERT: B 121 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8282 (mt-10) REVERT: B 122 ASN cc_start: 0.8989 (t0) cc_final: 0.8787 (t0) REVERT: C 18 LYS cc_start: 0.9019 (pttt) cc_final: 0.8753 (pttm) REVERT: C 124 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8626 (tm-30) REVERT: C 150 MET cc_start: 0.8824 (mmm) cc_final: 0.8556 (mmm) REVERT: C 211 GLU cc_start: 0.8466 (tp30) cc_final: 0.7864 (tp30) REVERT: D 75 ASN cc_start: 0.8972 (p0) cc_final: 0.8765 (p0) REVERT: D 80 GLU cc_start: 0.9270 (tt0) cc_final: 0.8492 (tt0) REVERT: D 116 MET cc_start: 0.8810 (tpp) cc_final: 0.8419 (tpt) REVERT: E 99 HIS cc_start: 0.8157 (m90) cc_final: 0.7440 (m-70) REVERT: E 106 GLU cc_start: 0.9185 (pp20) cc_final: 0.8952 (pp20) REVERT: E 121 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8622 (tm-30) REVERT: E 210 MET cc_start: 0.8925 (ttm) cc_final: 0.8273 (tpt) REVERT: F 13 ARG cc_start: 0.7256 (mmt180) cc_final: 0.6966 (mmt180) REVERT: G 7 GLN cc_start: 0.9046 (mp10) cc_final: 0.8632 (mp10) REVERT: G 12 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8322 (mptt) REVERT: G 31 TRP cc_start: 0.8530 (t-100) cc_final: 0.8199 (t60) outliers start: 25 outliers final: 20 residues processed: 276 average time/residue: 0.1038 time to fit residues: 39.6650 Evaluate side-chains 288 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 208 ASN Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain G residue 24 ILE Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 75 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 15 optimal weight: 0.0270 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.102464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.074363 restraints weight = 20974.102| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.49 r_work: 0.3066 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9651 Z= 0.149 Angle : 0.739 16.848 13054 Z= 0.367 Chirality : 0.040 0.276 1519 Planarity : 0.003 0.031 1644 Dihedral : 4.141 29.506 1289 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.44 % Allowed : 25.46 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.74 (0.25), residues: 1188 helix: 2.15 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -0.32 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 113 TYR 0.039 0.002 TYR D 139 PHE 0.056 0.001 PHE C 87 TRP 0.009 0.001 TRP D 57 HIS 0.002 0.000 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9651) covalent geometry : angle 0.73947 (13054) hydrogen bonds : bond 0.04075 ( 806) hydrogen bonds : angle 3.88970 ( 2397) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 275 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.9284 (OUTLIER) cc_final: 0.9003 (tp30) REVERT: A 106 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8489 (mm-30) REVERT: A 121 GLU cc_start: 0.8998 (tt0) cc_final: 0.8671 (tm-30) REVERT: A 210 MET cc_start: 0.8796 (tpp) cc_final: 0.8564 (tpt) REVERT: B 50 GLU cc_start: 0.9221 (mm-30) cc_final: 0.9019 (pt0) REVERT: B 53 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8606 (mt-10) REVERT: B 80 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8571 (tp30) REVERT: B 110 ARG cc_start: 0.8765 (tpp80) cc_final: 0.8533 (tpp80) REVERT: B 121 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8301 (mt-10) REVERT: B 173 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8200 (mt-10) REVERT: C 18 LYS cc_start: 0.9036 (pttt) cc_final: 0.8786 (pttm) REVERT: C 76 LEU cc_start: 0.8503 (mp) cc_final: 0.8088 (mp) REVERT: C 150 MET cc_start: 0.8847 (mmm) cc_final: 0.8544 (mmm) REVERT: D 116 MET cc_start: 0.8809 (tpp) cc_final: 0.8403 (tpt) REVERT: E 99 HIS cc_start: 0.8120 (m90) cc_final: 0.7450 (m-70) REVERT: E 106 GLU cc_start: 0.9157 (pp20) cc_final: 0.8932 (pp20) REVERT: E 121 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8616 (tm-30) REVERT: E 210 MET cc_start: 0.9000 (ttm) cc_final: 0.8771 (tpp) REVERT: F 13 ARG cc_start: 0.7331 (mmt180) cc_final: 0.7032 (mmt180) REVERT: G 7 GLN cc_start: 0.9086 (mp10) cc_final: 0.8630 (mp10) REVERT: G 12 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8341 (mptt) REVERT: G 31 TRP cc_start: 0.8525 (t-100) cc_final: 0.8196 (t60) outliers start: 24 outliers final: 18 residues processed: 283 average time/residue: 0.1023 time to fit residues: 39.6700 Evaluate side-chains 276 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 257 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 80 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 67 GLN Chi-restraints excluded: chain E residue 61 GLU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 208 ASN Chi-restraints excluded: chain E residue 218 HIS Chi-restraints excluded: chain F residue 26 PHE Chi-restraints excluded: chain Z residue 31 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 73 optimal weight: 0.0270 chunk 9 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.103710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.073785 restraints weight = 20849.644| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.68 r_work: 0.2989 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9651 Z= 0.153 Angle : 0.762 17.814 13054 Z= 0.377 Chirality : 0.040 0.275 1519 Planarity : 0.003 0.031 1644 Dihedral : 4.134 29.085 1289 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.14 % Allowed : 26.48 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.72 (0.25), residues: 1188 helix: 2.14 (0.17), residues: 1019 sheet: None (None), residues: 0 loop : -0.23 (0.49), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 113 TYR 0.050 0.002 TYR B 66 PHE 0.038 0.001 PHE C 87 TRP 0.008 0.001 TRP D 57 HIS 0.002 0.000 HIS D 218 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9651) covalent geometry : angle 0.76180 (13054) hydrogen bonds : bond 0.04056 ( 806) hydrogen bonds : angle 3.90918 ( 2397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2434.97 seconds wall clock time: 42 minutes 27.97 seconds (2547.97 seconds total)