Starting phenix.real_space_refine on Wed Apr 30 21:34:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.map" model { file = "/net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lub_63393/04_2025/9lub_63393.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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 53 5.16 5 C 6523 2.51 5 N 1670 2.21 5 O 1867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10113 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "B" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "C" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "D" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "E" Number of atoms: 1865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1865 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 9, 'TRANS': 236} Chain: "F" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 389 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "G" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 399 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Time building chain proxies: 6.05, per 1000 atoms: 0.60 Number of scatterers: 10113 At special positions: 0 Unit cell: (90.64, 89.76, 111.76, 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 53 16.00 O 1867 8.00 N 1670 7.00 C 6523 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.2 seconds 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 0 sheets defined 91.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.556A pdb=" N PHE A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 31 removed outlier: 3.657A pdb=" N LEU A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 51 Processing helix chain 'A' and resid 52 through 57 removed outlier: 3.658A pdb=" N ILE A 56 " --> pdb=" O PRO A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 68 removed outlier: 3.618A pdb=" N GLY A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 101 removed outlier: 4.328A pdb=" N GLU A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG A 90 " --> pdb=" O MET A 86 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL A 93 " --> pdb=" O ARG A 89 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LEU A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N GLU A 97 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLN A 98 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.572A pdb=" N VAL A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 171 removed outlier: 4.127A pdb=" N LEU A 145 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 146 " --> pdb=" O TYR A 142 " (cutoff:3.500A) Proline residue: A 154 - end of helix removed outlier: 3.552A pdb=" N HIS A 171 " --> pdb=" O GLN A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 186 removed outlier: 4.138A pdb=" N VAL A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.523A pdb=" N LEU A 190 " --> pdb=" O PHE A 186 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASN A 197 " --> pdb=" O VAL A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 230 removed outlier: 4.055A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'B' and resid 2 through 23 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 32 through 51 Processing helix chain 'B' and resid 52 through 68 removed outlier: 3.760A pdb=" N ILE B 56 " --> pdb=" O PRO B 52 " (cutoff:3.500A) Proline residue: B 60 - end of helix removed outlier: 3.699A pdb=" N LYS B 64 " --> pdb=" O PRO B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 92 removed outlier: 3.551A pdb=" N TRP B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 removed outlier: 4.460A pdb=" N LEU B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN B 98 " --> pdb=" O LEU B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 117 Processing helix chain 'B' and resid 120 through 171 removed outlier: 3.627A pdb=" N LEU B 145 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE B 146 " --> pdb=" O TYR B 142 " (cutoff:3.500A) Proline residue: B 154 - end of helix Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 177 through 199 removed outlier: 4.246A pdb=" N SER B 181 " --> pdb=" O GLN B 177 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 231 removed outlier: 3.684A pdb=" N GLU B 214 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 243 removed outlier: 3.580A pdb=" N THR B 243 " --> pdb=" O LYS B 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 23 removed outlier: 4.125A pdb=" N GLU C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.841A pdb=" N LEU C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 51 removed outlier: 3.511A pdb=" N ALA C 36 " --> pdb=" O GLN C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 67 removed outlier: 3.757A pdb=" N ILE C 56 " --> pdb=" O PRO C 52 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 59 " --> pdb=" O ARG C 55 " (cutoff:3.500A) Proline residue: C 60 - end of helix Processing helix chain 'C' and resid 73 through 92 removed outlier: 3.738A pdb=" N ARG C 89 " --> pdb=" O SER C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 101 removed outlier: 3.666A pdb=" N GLU C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 117 Processing helix chain 'C' and resid 120 through 169 removed outlier: 3.661A pdb=" N LEU C 145 " --> pdb=" O ASN C 141 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 146 " --> pdb=" O TYR C 142 " (cutoff:3.500A) Proline residue: C 154 - end of helix Processing helix chain 'C' and resid 170 through 172 No H-bonds generated for 'chain 'C' and resid 170 through 172' Processing helix chain 'C' and resid 177 through 199 removed outlier: 3.899A pdb=" N ALA C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N THR C 189 " --> pdb=" O ALA C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 231 Processing helix chain 'C' and resid 233 through 245 removed outlier: 3.977A pdb=" N TYR C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 24 Processing helix chain 'D' and resid 26 through 30 Processing helix chain 'D' and resid 32 through 51 Processing helix chain 'D' and resid 52 through 68 removed outlier: 3.722A pdb=" N ILE D 56 " --> pdb=" O PRO D 52 " (cutoff:3.500A) Proline residue: D 60 - end of helix removed outlier: 3.701A pdb=" N LYS D 64 " --> pdb=" O PRO D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 92 removed outlier: 3.556A pdb=" N TRP D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 100 removed outlier: 4.180A pdb=" N LEU D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU D 97 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 117 Processing helix chain 'D' and resid 120 through 171 removed outlier: 3.650A pdb=" N LEU D 145 " --> pdb=" O ASN D 141 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE D 146 " --> pdb=" O TYR D 142 " (cutoff:3.500A) Proline residue: D 154 - end of helix Processing helix chain 'D' and resid 177 through 197 removed outlier: 3.659A pdb=" N SER D 181 " --> pdb=" O GLN D 177 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA D 188 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR D 189 " --> pdb=" O ALA D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 231 removed outlier: 3.698A pdb=" N ILE D 203 " --> pdb=" O ILE D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 243 removed outlier: 3.588A pdb=" N THR D 243 " --> pdb=" O LYS D 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 24 Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 32 through 51 Processing helix chain 'E' and resid 52 through 67 removed outlier: 3.735A pdb=" N ILE E 56 " --> pdb=" O PRO E 52 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU E 59 " --> pdb=" O ARG E 55 " (cutoff:3.500A) Proline residue: E 60 - end of helix Processing helix chain 'E' and resid 73 through 91 Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.929A pdb=" N LEU E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 117 Processing helix chain 'E' and resid 120 through 171 removed outlier: 3.524A pdb=" N ASP E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 145 " --> pdb=" O ASN E 141 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE E 146 " --> pdb=" O TYR E 142 " (cutoff:3.500A) Proline residue: E 154 - end of helix removed outlier: 3.599A pdb=" N HIS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 199 removed outlier: 3.565A pdb=" N LEU E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 179 " --> pdb=" O PRO E 175 " (cutoff:3.500A) Proline residue: E 180 - end of helix removed outlier: 3.662A pdb=" N VAL E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 231 Processing helix chain 'E' and resid 233 through 243 Processing helix chain 'F' and resid 18 through 37 removed outlier: 3.778A pdb=" N ASP F 24 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU F 28 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 40 No H-bonds generated for 'chain 'F' and resid 38 through 40' Processing helix chain 'F' and resid 43 through 58 removed outlier: 3.712A pdb=" N TYR F 47 " --> pdb=" O ASP F 43 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 16 No H-bonds generated for 'chain 'G' and resid 14 through 16' Processing helix chain 'G' and resid 17 through 37 removed outlier: 4.248A pdb=" N THR G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 59 removed outlier: 3.836A pdb=" N SER G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR G 56 " --> pdb=" O SER G 52 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 2.88 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: 2003 1.33 - 1.46: 2892 1.46 - 1.59: 5275 1.59 - 1.72: 0 1.72 - 1.84: 106 Bond restraints: 10276 Sorted by residual: bond pdb=" CA ALA C 153 " pdb=" CB ALA C 153 " ideal model delta sigma weight residual 1.531 1.484 0.047 1.33e-02 5.65e+03 1.25e+01 bond pdb=" CA ALA B 153 " pdb=" CB ALA B 153 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.30e-02 5.92e+03 1.00e+01 bond pdb=" C SER B 195 " pdb=" O SER B 195 " ideal model delta sigma weight residual 1.236 1.200 0.036 1.18e-02 7.18e+03 9.40e+00 bond pdb=" CA ALA A 153 " pdb=" CB ALA A 153 " ideal model delta sigma weight residual 1.531 1.491 0.040 1.33e-02 5.65e+03 9.06e+00 bond pdb=" C PHE F 58 " pdb=" O PHE F 58 " ideal model delta sigma weight residual 1.236 1.197 0.039 1.29e-02 6.01e+03 9.01e+00 ... (remaining 10271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11879 1.94 - 3.89: 1846 3.89 - 5.83: 184 5.83 - 7.78: 20 7.78 - 9.72: 6 Bond angle restraints: 13935 Sorted by residual: angle pdb=" CA ASP B 2 " pdb=" CB ASP B 2 " pdb=" CG ASP B 2 " ideal model delta sigma weight residual 112.60 119.31 -6.71 1.00e+00 1.00e+00 4.50e+01 angle pdb=" CA ASP A 2 " pdb=" CB ASP A 2 " pdb=" CG ASP A 2 " ideal model delta sigma weight residual 112.60 118.97 -6.37 1.00e+00 1.00e+00 4.06e+01 angle pdb=" O PHE F 58 " pdb=" C PHE F 58 " pdb=" N GLN F 59 " ideal model delta sigma weight residual 122.46 114.57 7.89 1.38e+00 5.25e-01 3.27e+01 angle pdb=" CA ASN E 197 " pdb=" C ASN E 197 " pdb=" O ASN E 197 " ideal model delta sigma weight residual 120.55 114.80 5.75 1.07e+00 8.73e-01 2.89e+01 angle pdb=" C ASP E 133 " pdb=" CA ASP E 133 " pdb=" CB ASP E 133 " ideal model delta sigma weight residual 110.67 120.39 -9.72 1.92e+00 2.71e-01 2.56e+01 ... (remaining 13930 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5410 17.88 - 35.75: 509 35.75 - 53.63: 190 53.63 - 71.50: 46 71.50 - 89.38: 17 Dihedral angle restraints: 6172 sinusoidal: 2402 harmonic: 3770 Sorted by residual: dihedral pdb=" CD ARG G 41 " pdb=" NE ARG G 41 " pdb=" CZ ARG G 41 " pdb=" NH1 ARG G 41 " ideal model delta sinusoidal sigma weight residual 0.00 70.22 -70.22 1 1.00e+01 1.00e-02 6.35e+01 dihedral pdb=" CD ARG D 208 " pdb=" NE ARG D 208 " pdb=" CZ ARG D 208 " pdb=" NH1 ARG D 208 " ideal model delta sinusoidal sigma weight residual 0.00 68.64 -68.64 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CD ARG F 41 " pdb=" NE ARG F 41 " pdb=" CZ ARG F 41 " pdb=" NH1 ARG F 41 " ideal model delta sinusoidal sigma weight residual 0.00 -63.26 63.26 1 1.00e+01 1.00e-02 5.28e+01 ... (remaining 6169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 1406 0.119 - 0.238: 257 0.238 - 0.356: 17 0.356 - 0.475: 1 0.475 - 0.594: 1 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ASP E 133 " pdb=" N ASP E 133 " pdb=" C ASP E 133 " pdb=" CB ASP E 133 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.82e+00 chirality pdb=" CA ASN C 197 " pdb=" N ASN C 197 " pdb=" C ASN C 197 " pdb=" CB ASN C 197 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CA ASN E 197 " pdb=" N ASN E 197 " pdb=" C ASN E 197 " pdb=" CB ASN E 197 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 1679 not shown) Planarity restraints: 1759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 41 " 1.086 9.50e-02 1.11e+02 4.88e-01 1.59e+02 pdb=" NE ARG F 41 " -0.042 2.00e-02 2.50e+03 pdb=" CZ ARG F 41 " -0.082 2.00e-02 2.50e+03 pdb=" NH1 ARG F 41 " 0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG F 41 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 208 " 1.088 9.50e-02 1.11e+02 4.88e-01 1.52e+02 pdb=" NE ARG D 208 " -0.050 2.00e-02 2.50e+03 pdb=" CZ ARG D 208 " -0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG D 208 " 0.025 2.00e-02 2.50e+03 pdb=" NH2 ARG D 208 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 41 " 0.993 9.50e-02 1.11e+02 4.46e-01 1.23e+02 pdb=" NE ARG G 41 " -0.071 2.00e-02 2.50e+03 pdb=" CZ ARG G 41 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG G 41 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG G 41 " 0.012 2.00e-02 2.50e+03 ... (remaining 1756 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 140 2.68 - 3.23: 10362 3.23 - 3.79: 15812 3.79 - 4.34: 20905 4.34 - 4.90: 33510 Nonbonded interactions: 80729 Sorted by model distance: nonbonded pdb=" OD1 ASN D 197 " pdb=" NH2 ARG F 17 " model vdw 2.121 3.120 nonbonded pdb=" O TYR G 47 " pdb=" N VAL G 50 " model vdw 2.387 3.120 nonbonded pdb=" OD1 ASN B 197 " pdb=" NH1 ARG G 17 " model vdw 2.387 3.120 nonbonded pdb=" O ASP G 24 " pdb=" OG1 THR G 27 " model vdw 2.408 3.040 nonbonded pdb=" OE1 GLN B 167 " pdb=" OG SER B 181 " model vdw 2.429 3.040 ... (remaining 80724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 14 through 60) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.660 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 10276 Z= 0.614 Angle : 1.409 9.719 13935 Z= 0.944 Chirality : 0.088 0.594 1682 Planarity : 0.027 0.488 1759 Dihedral : 17.478 89.379 3752 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 10.75 % Allowed : 8.43 % Favored : 80.82 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.20), residues: 1312 helix: -0.45 (0.13), residues: 1104 sheet: None (None), residues: 0 loop : -0.33 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.007 TRP F 18 HIS 0.017 0.006 HIS A 54 PHE 0.048 0.009 PHE C 40 TYR 0.067 0.012 TYR D 51 ARG 0.069 0.007 ARG F 41 Details of bonding type rmsd hydrogen bonds : bond 0.23375 ( 844) hydrogen bonds : angle 8.25889 ( 2508) covalent geometry : bond 0.00940 (10276) covalent geometry : angle 1.40858 (13935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 269 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8611 (m) cc_final: 0.8251 (p) REVERT: A 169 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 172 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7369 (tp) REVERT: B 27 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7675 (tt) REVERT: B 31 PHE cc_start: 0.6971 (t80) cc_final: 0.6338 (m-80) REVERT: B 71 ARG cc_start: 0.7184 (ptp-110) cc_final: 0.6897 (ptp90) REVERT: B 76 GLU cc_start: 0.8607 (mt-10) cc_final: 0.7903 (tp30) REVERT: B 113 GLN cc_start: 0.8103 (tp40) cc_final: 0.7680 (tp-100) REVERT: C 113 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.8010 (mm-40) REVERT: C 117 ASP cc_start: 0.8166 (m-30) cc_final: 0.7935 (m-30) REVERT: D 98 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7864 (mp10) REVERT: D 117 ASP cc_start: 0.8575 (m-30) cc_final: 0.8332 (m-30) REVERT: D 131 ASP cc_start: 0.9129 (t0) cc_final: 0.8880 (t0) REVERT: D 201 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9018 (mt) REVERT: D 213 GLU cc_start: 0.9328 (OUTLIER) cc_final: 0.9102 (mt-10) REVERT: E 64 LYS cc_start: 0.8645 (tptt) cc_final: 0.8266 (tppt) REVERT: E 86 MET cc_start: 0.8572 (tpp) cc_final: 0.8164 (mmp) REVERT: E 89 ARG cc_start: 0.7931 (mmm160) cc_final: 0.6921 (ttp-170) REVERT: E 195 SER cc_start: 0.9039 (p) cc_final: 0.8838 (p) REVERT: E 220 MET cc_start: 0.8702 (ttp) cc_final: 0.8421 (ttm) REVERT: E 233 ASN cc_start: 0.7815 (p0) cc_final: 0.7596 (p0) REVERT: G 39 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.5445 (ptt) outliers start: 116 outliers final: 43 residues processed: 349 average time/residue: 0.2228 time to fit residues: 107.7567 Evaluate side-chains 248 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 198 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain C residue 113 GLN Chi-restraints excluded: chain C residue 148 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain E residue 27 ILE Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 32 GLN Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 20 ILE Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 29 LEU Chi-restraints excluded: chain F residue 39 MET Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain G residue 42 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS B 229 GLN C 197 ASN C 230 ASN D 121 GLN D 230 ASN E 229 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.107943 restraints weight = 13943.712| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.37 r_work: 0.3228 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10276 Z= 0.159 Angle : 0.598 8.380 13935 Z= 0.315 Chirality : 0.041 0.157 1682 Planarity : 0.005 0.043 1759 Dihedral : 9.985 103.844 1495 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 6.02 % Allowed : 13.25 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.23), residues: 1312 helix: 1.95 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.15 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 18 HIS 0.004 0.001 HIS D 54 PHE 0.020 0.002 PHE F 58 TYR 0.013 0.002 TYR E 191 ARG 0.008 0.001 ARG D 71 Details of bonding type rmsd hydrogen bonds : bond 0.05974 ( 844) hydrogen bonds : angle 4.66391 ( 2508) covalent geometry : bond 0.00316 (10276) covalent geometry : angle 0.59770 (13935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 233 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8660 (tt) cc_final: 0.8432 (tt) REVERT: B 26 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6849 (mm110) REVERT: B 31 PHE cc_start: 0.6165 (t80) cc_final: 0.5904 (m-80) REVERT: B 76 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7397 (tp30) REVERT: B 80 ASP cc_start: 0.8283 (m-30) cc_final: 0.7835 (m-30) REVERT: B 109 ARG cc_start: 0.7966 (ttm-80) cc_final: 0.7519 (ttp80) REVERT: C 177 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: C 197 ASN cc_start: 0.8675 (m-40) cc_final: 0.8439 (m-40) REVERT: D 64 LYS cc_start: 0.7776 (mttt) cc_final: 0.7292 (mmtt) REVERT: D 90 ARG cc_start: 0.6730 (mtm110) cc_final: 0.6114 (ttp-170) REVERT: D 117 ASP cc_start: 0.8198 (m-30) cc_final: 0.7949 (m-30) REVERT: E 64 LYS cc_start: 0.8381 (tptt) cc_final: 0.7586 (mptt) REVERT: E 89 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7314 (ttp-170) REVERT: E 165 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8656 (tt) REVERT: F 41 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.5959 (ttp-110) outliers start: 65 outliers final: 28 residues processed: 280 average time/residue: 0.2101 time to fit residues: 82.7594 Evaluate side-chains 225 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN D 197 ASN G 15 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.148475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117772 restraints weight = 13380.257| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.09 r_work: 0.3339 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10276 Z= 0.137 Angle : 0.537 9.758 13935 Z= 0.278 Chirality : 0.038 0.123 1682 Planarity : 0.004 0.037 1759 Dihedral : 5.821 74.699 1432 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.52 % Allowed : 16.77 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.23), residues: 1312 helix: 2.41 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -0.22 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 22 HIS 0.005 0.001 HIS G 15 PHE 0.026 0.001 PHE G 32 TYR 0.010 0.001 TYR G 22 ARG 0.004 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.05111 ( 844) hydrogen bonds : angle 4.26726 ( 2508) covalent geometry : bond 0.00273 (10276) covalent geometry : angle 0.53727 (13935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 226 time to evaluate : 1.135 Fit side-chains REVERT: A 113 GLN cc_start: 0.8159 (tp40) cc_final: 0.7760 (mm-40) REVERT: B 31 PHE cc_start: 0.6554 (t80) cc_final: 0.6169 (m-80) REVERT: B 73 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: B 76 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7581 (mm-30) REVERT: B 80 ASP cc_start: 0.8409 (m-30) cc_final: 0.8146 (m-30) REVERT: B 109 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7586 (ttp80) REVERT: B 113 GLN cc_start: 0.7863 (tp-100) cc_final: 0.7361 (mm-40) REVERT: C 177 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.7112 (pm20) REVERT: C 230 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (m110) REVERT: D 64 LYS cc_start: 0.8171 (mttt) cc_final: 0.7647 (mmtt) REVERT: D 90 ARG cc_start: 0.6683 (mtm110) cc_final: 0.6440 (ttp-170) REVERT: D 131 ASP cc_start: 0.8852 (t0) cc_final: 0.8639 (t0) REVERT: E 64 LYS cc_start: 0.8747 (tptt) cc_final: 0.8092 (mptt) REVERT: E 86 MET cc_start: 0.8791 (tpp) cc_final: 0.8474 (mmp) REVERT: E 89 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7449 (ttp-170) REVERT: E 178 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7439 (tt) REVERT: F 41 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.5726 (ttp-110) REVERT: G 39 MET cc_start: 0.5676 (mmm) cc_final: 0.4769 (ptt) REVERT: G 43 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.5999 (m-30) outliers start: 38 outliers final: 19 residues processed: 252 average time/residue: 0.2314 time to fit residues: 80.3487 Evaluate side-chains 232 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 207 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 73 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 SER Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 58 PHE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 84 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 125 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.148753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117904 restraints weight = 13194.628| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.11 r_work: 0.3339 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10276 Z= 0.130 Angle : 0.511 5.669 13935 Z= 0.265 Chirality : 0.038 0.149 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.810 59.960 1414 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.24 % Allowed : 16.96 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.23), residues: 1312 helix: 2.54 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.18 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 77 HIS 0.010 0.001 HIS G 15 PHE 0.015 0.001 PHE G 32 TYR 0.021 0.001 TYR F 22 ARG 0.004 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 844) hydrogen bonds : angle 4.11572 ( 2508) covalent geometry : bond 0.00265 (10276) covalent geometry : angle 0.51145 (13935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 216 time to evaluate : 1.542 Fit side-chains REVERT: A 84 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8248 (mtm) REVERT: A 113 GLN cc_start: 0.8062 (tp40) cc_final: 0.7664 (mm-40) REVERT: B 31 PHE cc_start: 0.6397 (t80) cc_final: 0.6020 (m-80) REVERT: B 76 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7512 (mm-30) REVERT: B 80 ASP cc_start: 0.8429 (m-30) cc_final: 0.8132 (m-30) REVERT: B 109 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7579 (ttp80) REVERT: B 113 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7298 (mm-40) REVERT: C 177 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7123 (mp10) REVERT: C 197 ASN cc_start: 0.8877 (m-40) cc_final: 0.8543 (m-40) REVERT: C 230 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7582 (m110) REVERT: D 64 LYS cc_start: 0.8088 (mttt) cc_final: 0.7475 (mmtt) REVERT: D 77 TRP cc_start: 0.8878 (m-10) cc_final: 0.8668 (m-10) REVERT: D 131 ASP cc_start: 0.8819 (t0) cc_final: 0.8603 (t0) REVERT: E 64 LYS cc_start: 0.8569 (tptt) cc_final: 0.7894 (mptt) REVERT: E 86 MET cc_start: 0.8681 (tpp) cc_final: 0.8316 (mmp) REVERT: E 89 ARG cc_start: 0.7973 (mmm160) cc_final: 0.7281 (ttp-170) REVERT: F 30 LEU cc_start: 0.8344 (tp) cc_final: 0.8090 (tp) REVERT: F 41 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.5545 (ttp-110) REVERT: G 39 MET cc_start: 0.5338 (mmm) cc_final: 0.4608 (ptt) REVERT: G 43 ASP cc_start: 0.7054 (OUTLIER) cc_final: 0.6028 (m-30) outliers start: 35 outliers final: 21 residues processed: 244 average time/residue: 0.2604 time to fit residues: 87.1826 Evaluate side-chains 231 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 205 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 178 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 82 optimal weight: 0.0370 overall best weight: 0.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 230 ASN B 121 GLN B 167 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.150701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119839 restraints weight = 13275.643| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.12 r_work: 0.3362 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10276 Z= 0.125 Angle : 0.502 6.590 13935 Z= 0.259 Chirality : 0.037 0.147 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.449 58.813 1409 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.06 % Allowed : 18.16 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.23), residues: 1312 helix: 2.64 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.37 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 22 HIS 0.004 0.001 HIS G 15 PHE 0.014 0.001 PHE G 32 TYR 0.007 0.001 TYR G 22 ARG 0.004 0.000 ARG E 71 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 844) hydrogen bonds : angle 3.98948 ( 2508) covalent geometry : bond 0.00256 (10276) covalent geometry : angle 0.50247 (13935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 213 time to evaluate : 1.502 Fit side-chains REVERT: A 84 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8239 (mtm) REVERT: A 113 GLN cc_start: 0.8139 (tp40) cc_final: 0.7461 (mm-40) REVERT: A 163 MET cc_start: 0.8602 (mtp) cc_final: 0.8316 (mtp) REVERT: B 31 PHE cc_start: 0.6483 (t80) cc_final: 0.6013 (m-80) REVERT: B 76 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7531 (mm-30) REVERT: B 80 ASP cc_start: 0.8457 (m-30) cc_final: 0.8160 (m-30) REVERT: B 113 GLN cc_start: 0.7894 (tp-100) cc_final: 0.7468 (mm-40) REVERT: C 147 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.8379 (mt-10) REVERT: C 177 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6900 (pm20) REVERT: C 197 ASN cc_start: 0.8943 (m-40) cc_final: 0.8576 (m-40) REVERT: D 64 LYS cc_start: 0.8058 (mttt) cc_final: 0.7448 (mmtt) REVERT: D 131 ASP cc_start: 0.8819 (t0) cc_final: 0.8594 (t0) REVERT: E 64 LYS cc_start: 0.8609 (tptt) cc_final: 0.7998 (mptt) REVERT: E 71 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7633 (mmm160) REVERT: E 86 MET cc_start: 0.8700 (tpp) cc_final: 0.8298 (mmp) REVERT: E 89 ARG cc_start: 0.7922 (mmm160) cc_final: 0.7279 (ttp-170) REVERT: F 30 LEU cc_start: 0.8419 (tp) cc_final: 0.8169 (tp) REVERT: F 37 TYR cc_start: 0.8437 (t80) cc_final: 0.8185 (t80) REVERT: F 41 ARG cc_start: 0.7417 (OUTLIER) cc_final: 0.5568 (ttp-110) REVERT: G 39 MET cc_start: 0.4976 (mmm) cc_final: 0.4532 (ptt) REVERT: G 43 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6098 (m-30) outliers start: 33 outliers final: 18 residues processed: 237 average time/residue: 0.2701 time to fit residues: 89.3383 Evaluate side-chains 224 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 75 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 230 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN E 197 ASN G 15 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.157812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.125553 restraints weight = 14333.914| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 2.28 r_work: 0.3513 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10276 Z= 0.134 Angle : 0.515 6.621 13935 Z= 0.265 Chirality : 0.038 0.183 1682 Planarity : 0.004 0.040 1759 Dihedral : 4.169 58.060 1407 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.52 % Allowed : 18.16 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.23), residues: 1312 helix: 2.61 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.49 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 77 HIS 0.004 0.001 HIS B 54 PHE 0.014 0.001 PHE F 58 TYR 0.019 0.001 TYR F 22 ARG 0.006 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04679 ( 844) hydrogen bonds : angle 3.99684 ( 2508) covalent geometry : bond 0.00294 (10276) covalent geometry : angle 0.51453 (13935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 1.236 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8162 (tp40) cc_final: 0.7494 (mm-40) REVERT: A 235 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7217 (mm) REVERT: B 31 PHE cc_start: 0.6498 (t80) cc_final: 0.5955 (m-80) REVERT: B 76 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7560 (mm-30) REVERT: B 80 ASP cc_start: 0.8468 (m-30) cc_final: 0.8157 (m-30) REVERT: B 113 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7475 (mm-40) REVERT: B 131 ASP cc_start: 0.9051 (t0) cc_final: 0.8824 (t0) REVERT: C 177 GLN cc_start: 0.7106 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: C 197 ASN cc_start: 0.8955 (m-40) cc_final: 0.8595 (m-40) REVERT: D 64 LYS cc_start: 0.8063 (mttt) cc_final: 0.7506 (mmtt) REVERT: D 97 GLU cc_start: 0.7062 (tp30) cc_final: 0.6759 (mt-10) REVERT: D 131 ASP cc_start: 0.8901 (t0) cc_final: 0.8665 (t0) REVERT: D 168 VAL cc_start: 0.8816 (p) cc_final: 0.8573 (p) REVERT: E 64 LYS cc_start: 0.8601 (tptt) cc_final: 0.8006 (mptt) REVERT: E 71 ARG cc_start: 0.7898 (mmm-85) cc_final: 0.7674 (mmm160) REVERT: E 89 ARG cc_start: 0.7938 (mmm160) cc_final: 0.7343 (ttp-170) REVERT: F 30 LEU cc_start: 0.8482 (tp) cc_final: 0.8195 (tp) REVERT: G 13 SER cc_start: 0.4669 (OUTLIER) cc_final: 0.4448 (m) REVERT: G 39 MET cc_start: 0.4954 (mmm) cc_final: 0.4577 (ptt) REVERT: G 43 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6864 (m-30) outliers start: 38 outliers final: 25 residues processed: 237 average time/residue: 0.2286 time to fit residues: 74.6489 Evaluate side-chains 229 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 230 ASN Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 123 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.158007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.124330 restraints weight = 14294.690| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.42 r_work: 0.3530 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10276 Z= 0.122 Angle : 0.512 8.037 13935 Z= 0.261 Chirality : 0.037 0.199 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.112 57.842 1407 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 3.61 % Allowed : 18.44 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.23), residues: 1312 helix: 2.67 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.48 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 77 HIS 0.004 0.001 HIS G 15 PHE 0.014 0.001 PHE F 58 TYR 0.014 0.001 TYR F 37 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04383 ( 844) hydrogen bonds : angle 3.90750 ( 2508) covalent geometry : bond 0.00251 (10276) covalent geometry : angle 0.51243 (13935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.056 Fit side-chains REVERT: A 113 GLN cc_start: 0.8001 (tp40) cc_final: 0.7453 (mt0) REVERT: A 235 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7110 (mm) REVERT: B 31 PHE cc_start: 0.6324 (t80) cc_final: 0.5893 (m-80) REVERT: B 76 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7398 (mm-30) REVERT: B 80 ASP cc_start: 0.8400 (m-30) cc_final: 0.8054 (m-30) REVERT: B 113 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7406 (mm-40) REVERT: B 131 ASP cc_start: 0.8907 (t0) cc_final: 0.8698 (t0) REVERT: C 147 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: C 177 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6591 (pm20) REVERT: C 197 ASN cc_start: 0.8919 (m-40) cc_final: 0.8576 (m-40) REVERT: D 64 LYS cc_start: 0.7896 (mttt) cc_final: 0.7323 (mmtt) REVERT: D 97 GLU cc_start: 0.7030 (tp30) cc_final: 0.6653 (mt-10) REVERT: E 64 LYS cc_start: 0.8432 (tptt) cc_final: 0.7851 (mptt) REVERT: E 71 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7792 (mmm160) REVERT: E 89 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7333 (ttp-170) REVERT: E 128 MET cc_start: 0.8158 (mmm) cc_final: 0.7797 (mtt) REVERT: F 30 LEU cc_start: 0.8288 (tp) cc_final: 0.8059 (tp) REVERT: F 41 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.5650 (ttp-110) REVERT: G 13 SER cc_start: 0.4755 (OUTLIER) cc_final: 0.4529 (m) REVERT: G 39 MET cc_start: 0.4690 (mmm) cc_final: 0.4472 (ptt) REVERT: G 43 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6198 (m-30) outliers start: 39 outliers final: 24 residues processed: 236 average time/residue: 0.2474 time to fit residues: 81.9196 Evaluate side-chains 230 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 166 ILE Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 58 optimal weight: 0.0470 chunk 39 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 109 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.9280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 229 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.159866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.127511 restraints weight = 14318.386| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.30 r_work: 0.3492 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10276 Z= 0.127 Angle : 0.520 8.818 13935 Z= 0.263 Chirality : 0.038 0.227 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.085 57.598 1407 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.34 % Allowed : 18.91 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.39 (0.23), residues: 1312 helix: 2.69 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.54 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 77 HIS 0.003 0.001 HIS G 15 PHE 0.022 0.001 PHE F 32 TYR 0.025 0.001 TYR G 37 ARG 0.007 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 844) hydrogen bonds : angle 3.89888 ( 2508) covalent geometry : bond 0.00269 (10276) covalent geometry : angle 0.51996 (13935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 1.104 Fit side-chains REVERT: A 113 GLN cc_start: 0.8021 (tp40) cc_final: 0.7466 (mt0) REVERT: A 128 MET cc_start: 0.8409 (mmm) cc_final: 0.7779 (mtt) REVERT: A 235 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7105 (mm) REVERT: B 31 PHE cc_start: 0.6298 (t80) cc_final: 0.5859 (m-80) REVERT: B 76 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7343 (mm-30) REVERT: B 80 ASP cc_start: 0.8365 (m-30) cc_final: 0.8040 (m-30) REVERT: B 113 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7449 (mm-40) REVERT: B 131 ASP cc_start: 0.8909 (t0) cc_final: 0.8708 (t0) REVERT: C 147 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: C 177 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6629 (pm20) REVERT: C 197 ASN cc_start: 0.8956 (m-40) cc_final: 0.8653 (m-40) REVERT: D 64 LYS cc_start: 0.7914 (mttt) cc_final: 0.7344 (mmtt) REVERT: D 86 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8172 (mmp) REVERT: D 97 GLU cc_start: 0.6958 (tp30) cc_final: 0.6608 (mt-10) REVERT: D 171 HIS cc_start: 0.6003 (OUTLIER) cc_final: 0.5651 (m90) REVERT: E 64 LYS cc_start: 0.8436 (tptt) cc_final: 0.7872 (mptt) REVERT: E 89 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7347 (ttp-170) REVERT: F 41 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.5711 (ttp-110) REVERT: G 13 SER cc_start: 0.4928 (OUTLIER) cc_final: 0.4717 (m) REVERT: G 36 MET cc_start: 0.7353 (tpp) cc_final: 0.6936 (tpt) REVERT: G 39 MET cc_start: 0.4642 (mmm) cc_final: 0.4401 (ptt) REVERT: G 43 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6209 (m-30) outliers start: 36 outliers final: 25 residues processed: 231 average time/residue: 0.2234 time to fit residues: 71.7806 Evaluate side-chains 234 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 171 HIS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 198 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 19 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 119 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.124562 restraints weight = 14189.086| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.43 r_work: 0.3525 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10276 Z= 0.125 Angle : 0.518 8.891 13935 Z= 0.262 Chirality : 0.038 0.248 1682 Planarity : 0.004 0.040 1759 Dihedral : 4.046 57.806 1407 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.34 % Allowed : 19.28 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.23), residues: 1312 helix: 2.72 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.57 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 77 HIS 0.003 0.001 HIS G 15 PHE 0.019 0.001 PHE F 32 TYR 0.009 0.001 TYR F 22 ARG 0.006 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 844) hydrogen bonds : angle 3.86378 ( 2508) covalent geometry : bond 0.00264 (10276) covalent geometry : angle 0.51772 (13935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.198 Fit side-chains REVERT: A 113 GLN cc_start: 0.8044 (tp40) cc_final: 0.7492 (mt0) REVERT: A 128 MET cc_start: 0.8418 (mmm) cc_final: 0.7950 (mtt) REVERT: A 235 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7109 (mm) REVERT: B 31 PHE cc_start: 0.6264 (t80) cc_final: 0.5804 (m-80) REVERT: B 76 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7335 (mm-30) REVERT: B 80 ASP cc_start: 0.8371 (m-30) cc_final: 0.8041 (m-30) REVERT: B 113 GLN cc_start: 0.7919 (tp-100) cc_final: 0.7458 (mm-40) REVERT: C 147 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: C 177 GLN cc_start: 0.6875 (OUTLIER) cc_final: 0.6620 (pm20) REVERT: C 197 ASN cc_start: 0.8975 (m-40) cc_final: 0.8671 (m-40) REVERT: D 64 LYS cc_start: 0.7899 (mttt) cc_final: 0.7318 (mmtt) REVERT: D 86 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8155 (mmp) REVERT: D 97 GLU cc_start: 0.6961 (tp30) cc_final: 0.6490 (tt0) REVERT: D 171 HIS cc_start: 0.5934 (OUTLIER) cc_final: 0.5580 (m90) REVERT: E 64 LYS cc_start: 0.8413 (tptt) cc_final: 0.7809 (mptt) REVERT: E 89 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7366 (ttp-170) REVERT: F 37 TYR cc_start: 0.7758 (t80) cc_final: 0.7492 (t80) REVERT: F 41 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.5669 (ttp-110) REVERT: G 43 ASP cc_start: 0.7206 (OUTLIER) cc_final: 0.6217 (m-30) outliers start: 36 outliers final: 23 residues processed: 233 average time/residue: 0.2211 time to fit residues: 71.9936 Evaluate side-chains 232 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 177 GLN Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 242 ASN Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 94 LEU Chi-restraints excluded: chain D residue 171 HIS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 4.9990 chunk 117 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 chunk 91 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 229 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.159022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125243 restraints weight = 14249.975| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.43 r_work: 0.3535 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10276 Z= 0.121 Angle : 0.530 9.790 13935 Z= 0.265 Chirality : 0.038 0.235 1682 Planarity : 0.004 0.039 1759 Dihedral : 3.947 57.783 1406 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.59 % Allowed : 19.74 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.23), residues: 1312 helix: 2.76 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.56 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 77 HIS 0.003 0.001 HIS G 15 PHE 0.018 0.001 PHE F 32 TYR 0.022 0.001 TYR F 22 ARG 0.005 0.000 ARG B 109 Details of bonding type rmsd hydrogen bonds : bond 0.04245 ( 844) hydrogen bonds : angle 3.83487 ( 2508) covalent geometry : bond 0.00248 (10276) covalent geometry : angle 0.52954 (13935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2624 Ramachandran restraints generated. 1312 Oldfield, 0 Emsley, 1312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8060 (tp40) cc_final: 0.7493 (mt0) REVERT: A 128 MET cc_start: 0.8341 (mmm) cc_final: 0.7952 (mtt) REVERT: A 235 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7094 (mm) REVERT: B 31 PHE cc_start: 0.6226 (t80) cc_final: 0.5715 (m-80) REVERT: B 76 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7323 (mm-30) REVERT: B 80 ASP cc_start: 0.8389 (m-30) cc_final: 0.8090 (m-30) REVERT: B 113 GLN cc_start: 0.7916 (tp-100) cc_final: 0.7468 (mm-40) REVERT: C 147 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8101 (mt-10) REVERT: C 197 ASN cc_start: 0.8947 (m-40) cc_final: 0.8635 (m-40) REVERT: D 64 LYS cc_start: 0.7910 (mttt) cc_final: 0.7308 (mmtt) REVERT: D 86 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8145 (tpt) REVERT: D 97 GLU cc_start: 0.6930 (tp30) cc_final: 0.6469 (tt0) REVERT: D 171 HIS cc_start: 0.5870 (OUTLIER) cc_final: 0.5577 (m90) REVERT: E 64 LYS cc_start: 0.8427 (tptt) cc_final: 0.7831 (mptt) REVERT: E 86 MET cc_start: 0.8082 (mmp) cc_final: 0.7868 (tpp) REVERT: E 89 ARG cc_start: 0.7916 (mmm160) cc_final: 0.7475 (ttp-170) REVERT: F 37 TYR cc_start: 0.7816 (t80) cc_final: 0.7492 (t80) REVERT: F 41 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.5955 (ttp-110) REVERT: F 46 LYS cc_start: 0.6820 (mppt) cc_final: 0.6362 (tmtt) outliers start: 28 outliers final: 21 residues processed: 229 average time/residue: 0.2254 time to fit residues: 71.8247 Evaluate side-chains 230 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 204 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 233 ASN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 195 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 86 MET Chi-restraints excluded: chain D residue 171 HIS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 41 ARG Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 43 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 0.2980 chunk 56 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 197 ASN A 229 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.163344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.130836 restraints weight = 14297.803| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.31 r_work: 0.3567 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10276 Z= 0.122 Angle : 0.546 10.267 13935 Z= 0.275 Chirality : 0.037 0.194 1682 Planarity : 0.004 0.039 1759 Dihedral : 3.926 57.541 1406 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.41 % Allowed : 20.11 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.23), residues: 1312 helix: 2.74 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : -0.57 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 77 HIS 0.003 0.001 HIS G 15 PHE 0.016 0.001 PHE F 32 TYR 0.012 0.001 TYR F 22 ARG 0.005 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 844) hydrogen bonds : angle 3.80270 ( 2508) covalent geometry : bond 0.00252 (10276) covalent geometry : angle 0.54633 (13935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4978.05 seconds wall clock time: 87 minutes 30.49 seconds (5250.49 seconds total)