Starting phenix.real_space_refine on Wed Sep 17 17:03:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lub_63393/09_2025/9lub_63393.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lub_63393/09_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_63393/09_2025/9lub_63393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lub_63393/09_2025/9lub_63393.map" model { file = "/net/cci-nas-00/data/ceres_data/9lub_63393/09_2025/9lub_63393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lub_63393/09_2025/9lub_63393.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.035 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.24, per 1000 atoms: 0.22 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: 0.73 Conformation dependent library (CDL) restraints added in 386.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.74 Time building geometry restraints manager: 1.01 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: 1.430 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.110 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.220 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (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 ARG 0.069 0.007 ARG F 41 TYR 0.067 0.012 TYR D 51 PHE 0.048 0.009 PHE C 40 TRP 0.033 0.007 TRP F 18 HIS 0.017 0.006 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00940 (10276) covalent geometry : angle 1.40858 (13935) hydrogen bonds : bond 0.23375 ( 844) hydrogen bonds : angle 8.25889 ( 2508) *********************** 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 : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 VAL cc_start: 0.8611 (m) cc_final: 0.8249 (p) REVERT: A 169 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (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: 0.8879 (t0) REVERT: D 201 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9019 (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: 0.8166 (mmp) REVERT: E 89 ARG cc_start: 0.7931 (mmm160) cc_final: 0.6922 (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: 0.8422 (ttm) REVERT: E 233 ASN cc_start: 0.7815 (p0) cc_final: 0.7599 (p0) REVERT: G 39 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.5444 (ptt) outliers start: 116 outliers final: 44 residues processed: 349 average time/residue: 0.0903 time to fit residues: 44.5794 Evaluate side-chains 249 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 198 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 91 GLU 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 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 0.0020 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.141340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.108488 restraints weight = 14063.262| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.38 r_work: 0.3236 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10276 Z= 0.161 Angle : 0.594 8.849 13935 Z= 0.314 Chirality : 0.041 0.144 1682 Planarity : 0.005 0.046 1759 Dihedral : 10.084 103.041 1498 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 5.84 % Allowed : 13.16 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.49 (0.22), residues: 1312 helix: 1.98 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.14 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 71 TYR 0.012 0.002 TYR E 191 PHE 0.019 0.002 PHE F 58 TRP 0.006 0.001 TRP G 18 HIS 0.005 0.001 HIS D 54 Details of bonding type rmsd covalent geometry : bond 0.00304 (10276) covalent geometry : angle 0.59409 (13935) hydrogen bonds : bond 0.05896 ( 844) hydrogen bonds : angle 4.65032 ( 2508) *********************** 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: 63 poor density : 235 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 182 ILE cc_start: 0.8692 (tt) cc_final: 0.8458 (tt) REVERT: B 26 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6770 (mm-40) REVERT: B 31 PHE cc_start: 0.6198 (t80) cc_final: 0.5974 (m-80) REVERT: B 76 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7400 (tp30) REVERT: B 80 ASP cc_start: 0.8289 (m-30) cc_final: 0.7844 (m-30) REVERT: C 177 GLN cc_start: 0.7380 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: D 64 LYS cc_start: 0.7797 (mttt) cc_final: 0.7317 (mmtt) REVERT: D 90 ARG cc_start: 0.6726 (mtm110) cc_final: 0.6291 (ttp-170) REVERT: D 117 ASP cc_start: 0.8234 (m-30) cc_final: 0.8009 (m-30) REVERT: D 156 MET cc_start: 0.8935 (mmp) cc_final: 0.8727 (mmp) REVERT: E 64 LYS cc_start: 0.8423 (tptt) cc_final: 0.7674 (mptt) REVERT: E 89 ARG cc_start: 0.8101 (mmm160) cc_final: 0.7332 (ttp-170) REVERT: E 165 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8688 (tt) REVERT: F 41 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6065 (ttp-110) outliers start: 63 outliers final: 26 residues processed: 280 average time/residue: 0.0932 time to fit residues: 36.8298 Evaluate side-chains 226 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 94 LEU 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 40 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 197 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.147282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116597 restraints weight = 13373.331| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.06 r_work: 0.3321 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3657 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= 0.144 Angle : 0.549 9.702 13935 Z= 0.284 Chirality : 0.039 0.135 1682 Planarity : 0.004 0.037 1759 Dihedral : 5.837 74.655 1432 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.34 % Allowed : 17.33 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.23), residues: 1312 helix: 2.37 (0.15), residues: 1109 sheet: None (None), residues: 0 loop : -0.32 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 109 TYR 0.009 0.001 TYR G 22 PHE 0.025 0.001 PHE G 32 TRP 0.004 0.001 TRP E 77 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00303 (10276) covalent geometry : angle 0.54892 (13935) hydrogen bonds : bond 0.05325 ( 844) hydrogen bonds : angle 4.32365 ( 2508) *********************** 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 258 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 0.381 Fit side-chains REVERT: B 31 PHE cc_start: 0.6558 (t80) cc_final: 0.6141 (m-80) REVERT: B 73 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 76 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7598 (mm-30) REVERT: B 80 ASP cc_start: 0.8406 (m-30) cc_final: 0.8126 (m-30) REVERT: B 113 GLN cc_start: 0.7829 (tp-100) cc_final: 0.7317 (mm-40) REVERT: C 230 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7826 (m-40) REVERT: D 64 LYS cc_start: 0.8181 (mttt) cc_final: 0.7663 (mmtt) REVERT: D 90 ARG cc_start: 0.6721 (mtm110) cc_final: 0.6268 (ttp-170) REVERT: D 131 ASP cc_start: 0.8871 (t0) cc_final: 0.8655 (t0) REVERT: E 64 LYS cc_start: 0.8735 (tptt) cc_final: 0.8090 (mptt) REVERT: E 89 ARG cc_start: 0.8056 (mmm160) cc_final: 0.7440 (ttp-170) REVERT: F 30 LEU cc_start: 0.8537 (tp) cc_final: 0.8331 (tp) REVERT: F 41 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.5711 (ttp-110) REVERT: G 43 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.5876 (m-30) outliers start: 36 outliers final: 21 residues processed: 248 average time/residue: 0.1018 time to fit residues: 34.7530 Evaluate side-chains 231 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 206 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 10 ILE 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 63 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 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 195 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 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 26 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3872 r_free = 0.3872 target = 0.151732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119795 restraints weight = 13418.269| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.12 r_work: 0.3337 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10276 Z= 0.134 Angle : 0.524 5.752 13935 Z= 0.272 Chirality : 0.038 0.180 1682 Planarity : 0.004 0.038 1759 Dihedral : 4.813 59.326 1413 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.78 % Allowed : 17.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.23 (0.23), residues: 1312 helix: 2.55 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.34 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 89 TYR 0.019 0.001 TYR F 22 PHE 0.015 0.001 PHE G 32 TRP 0.005 0.001 TRP A 77 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00279 (10276) covalent geometry : angle 0.52399 (13935) hydrogen bonds : bond 0.04853 ( 844) hydrogen bonds : angle 4.13777 ( 2508) *********************** 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 250 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 0.454 Fit side-chains REVERT: A 84 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8320 (mtm) REVERT: A 113 GLN cc_start: 0.8146 (tp40) cc_final: 0.7754 (mm-40) REVERT: B 31 PHE cc_start: 0.6519 (t80) cc_final: 0.6109 (m-80) REVERT: B 73 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: B 76 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7572 (mm-30) REVERT: B 80 ASP cc_start: 0.8419 (m-30) cc_final: 0.8153 (m-30) REVERT: B 113 GLN cc_start: 0.7917 (tp-100) cc_final: 0.7498 (mm-40) REVERT: D 64 LYS cc_start: 0.8139 (mttt) cc_final: 0.7597 (mmtt) REVERT: D 131 ASP cc_start: 0.8829 (t0) cc_final: 0.8597 (t0) REVERT: E 64 LYS cc_start: 0.8655 (tptt) cc_final: 0.8005 (mptt) REVERT: E 89 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7385 (ttp-170) REVERT: F 30 LEU cc_start: 0.8475 (tp) cc_final: 0.8252 (tp) REVERT: F 41 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.5758 (ttp-110) REVERT: G 43 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6083 (m-30) outliers start: 30 outliers final: 18 residues processed: 240 average time/residue: 0.1034 time to fit residues: 34.5713 Evaluate side-chains 229 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 87 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 171 HIS A 230 ASN B 121 GLN C 197 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.148590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.117732 restraints weight = 13380.501| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.09 r_work: 0.3325 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10276 Z= 0.136 Angle : 0.523 6.531 13935 Z= 0.269 Chirality : 0.038 0.172 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.531 59.091 1409 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.61 % Allowed : 17.89 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.25 (0.23), residues: 1312 helix: 2.57 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.42 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 109 TYR 0.008 0.001 TYR G 22 PHE 0.014 0.001 PHE G 32 TRP 0.011 0.001 TRP D 77 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00294 (10276) covalent geometry : angle 0.52261 (13935) hydrogen bonds : bond 0.04804 ( 844) hydrogen bonds : angle 4.07977 ( 2508) *********************** 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 248 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7623 (ttm-80) REVERT: A 113 GLN cc_start: 0.8156 (tp40) cc_final: 0.7491 (mm-40) REVERT: A 117 ASP cc_start: 0.7652 (m-30) cc_final: 0.7416 (t0) REVERT: A 163 MET cc_start: 0.8607 (mtp) cc_final: 0.8405 (mtp) REVERT: B 31 PHE cc_start: 0.6597 (t80) cc_final: 0.6137 (m-80) REVERT: B 73 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: B 76 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7562 (mm-30) REVERT: B 80 ASP cc_start: 0.8476 (m-30) cc_final: 0.8208 (m-30) REVERT: B 90 ARG cc_start: 0.6730 (ttp80) cc_final: 0.6418 (ttp80) REVERT: B 113 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7537 (mm-40) REVERT: B 131 ASP cc_start: 0.9004 (t0) cc_final: 0.8717 (t0) REVERT: D 64 LYS cc_start: 0.8145 (mttt) cc_final: 0.7589 (mmtt) REVERT: D 131 ASP cc_start: 0.8831 (t0) cc_final: 0.8592 (t0) REVERT: D 156 MET cc_start: 0.9215 (mmp) cc_final: 0.8994 (mmp) REVERT: D 168 VAL cc_start: 0.8957 (p) cc_final: 0.8722 (p) REVERT: E 64 LYS cc_start: 0.8698 (tptt) cc_final: 0.8099 (mptt) REVERT: E 71 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7545 (mmm160) REVERT: E 89 ARG cc_start: 0.8021 (mmm160) cc_final: 0.7409 (ttp-170) REVERT: F 30 LEU cc_start: 0.8527 (tp) cc_final: 0.8323 (tp) REVERT: G 36 MET cc_start: 0.7894 (mmt) cc_final: 0.7529 (mmm) REVERT: G 43 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6763 (m-30) outliers start: 39 outliers final: 27 residues processed: 237 average time/residue: 0.0998 time to fit residues: 32.9048 Evaluate side-chains 235 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 206 time to evaluate : 0.247 ------------------------------------------------------------------------------- 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 245 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 73 GLU 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 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 E residue 30 LEU Chi-restraints excluded: chain E residue 98 GLN Chi-restraints excluded: chain E residue 124 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.146506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115594 restraints weight = 13627.536| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.12 r_work: 0.3296 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10276 Z= 0.153 Angle : 0.542 6.701 13935 Z= 0.280 Chirality : 0.039 0.178 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.319 58.884 1407 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.80 % Allowed : 17.89 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.23), residues: 1312 helix: 2.50 (0.15), residues: 1112 sheet: None (None), residues: 0 loop : -0.47 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.021 0.001 TYR F 22 PHE 0.015 0.001 PHE F 58 TRP 0.006 0.001 TRP D 77 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00350 (10276) covalent geometry : angle 0.54178 (13935) hydrogen bonds : bond 0.05086 ( 844) hydrogen bonds : angle 4.12171 ( 2508) *********************** 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 247 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 206 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8136 (tp40) cc_final: 0.7438 (mm-40) REVERT: A 235 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7256 (mm) REVERT: B 31 PHE cc_start: 0.6540 (t80) cc_final: 0.5964 (m-80) REVERT: B 73 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: B 76 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7531 (mm-30) REVERT: B 80 ASP cc_start: 0.8455 (m-30) cc_final: 0.8129 (m-30) REVERT: B 113 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7587 (mm-40) REVERT: B 131 ASP cc_start: 0.9064 (t0) cc_final: 0.8782 (t0) REVERT: C 117 ASP cc_start: 0.7731 (m-30) cc_final: 0.7494 (m-30) REVERT: D 64 LYS cc_start: 0.8153 (mttt) cc_final: 0.7534 (mmtt) REVERT: D 131 ASP cc_start: 0.8887 (t0) cc_final: 0.8637 (t0) REVERT: D 156 MET cc_start: 0.9291 (mmp) cc_final: 0.8991 (mmp) REVERT: D 168 VAL cc_start: 0.8928 (p) cc_final: 0.8705 (p) REVERT: D 171 HIS cc_start: 0.6169 (OUTLIER) cc_final: 0.5692 (m-70) REVERT: E 64 LYS cc_start: 0.8602 (tptt) cc_final: 0.7990 (mptt) REVERT: E 71 ARG cc_start: 0.7946 (mmm-85) cc_final: 0.7706 (mmm160) REVERT: E 86 MET cc_start: 0.8214 (mmp) cc_final: 0.7976 (tpp) REVERT: E 89 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7394 (ttp-170) REVERT: F 30 LEU cc_start: 0.8489 (tp) cc_final: 0.8274 (tp) REVERT: G 36 MET cc_start: 0.7952 (mmt) cc_final: 0.7544 (mmm) REVERT: G 43 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6744 (m-30) outliers start: 41 outliers final: 30 residues processed: 231 average time/residue: 0.1027 time to fit residues: 33.0416 Evaluate side-chains 233 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 63 ILE Chi-restraints excluded: chain B residue 73 GLU 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 C residue 63 ILE Chi-restraints excluded: chain C residue 98 GLN 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 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 171 HIS Chi-restraints excluded: chain D residue 184 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN E 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.119011 restraints weight = 14422.867| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.41 r_work: 0.3465 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10276 Z= 0.163 Angle : 0.555 8.064 13935 Z= 0.287 Chirality : 0.039 0.176 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.334 58.470 1407 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.71 % Allowed : 17.70 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.23), residues: 1312 helix: 2.42 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.50 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.009 0.001 TYR G 22 PHE 0.015 0.001 PHE F 58 TRP 0.006 0.001 TRP A 22 HIS 0.005 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00380 (10276) covalent geometry : angle 0.55546 (13935) hydrogen bonds : bond 0.05249 ( 844) hydrogen bonds : angle 4.15288 ( 2508) *********************** 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 248 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 113 GLN cc_start: 0.8048 (tp40) cc_final: 0.7409 (mm-40) REVERT: A 235 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7186 (mm) REVERT: B 31 PHE cc_start: 0.6342 (t80) cc_final: 0.5926 (m-80) REVERT: B 76 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7419 (mm-30) REVERT: B 80 ASP cc_start: 0.8322 (m-30) cc_final: 0.7981 (m-30) REVERT: B 113 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7582 (mm-40) REVERT: C 230 ASN cc_start: 0.8300 (OUTLIER) cc_final: 0.7959 (m110) REVERT: D 64 LYS cc_start: 0.8011 (mttt) cc_final: 0.7452 (mmtt) REVERT: D 89 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7688 (ttp-110) REVERT: D 156 MET cc_start: 0.9166 (mmp) cc_final: 0.8837 (mmp) REVERT: D 168 VAL cc_start: 0.8918 (p) cc_final: 0.8684 (p) REVERT: D 171 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5744 (m-70) REVERT: E 64 LYS cc_start: 0.8470 (tptt) cc_final: 0.7887 (mptt) REVERT: E 71 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7626 (mmm160) REVERT: E 89 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7324 (ttp-170) REVERT: G 36 MET cc_start: 0.7908 (mmt) cc_final: 0.7523 (mmm) REVERT: G 43 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6808 (m-30) outliers start: 40 outliers final: 31 residues processed: 234 average time/residue: 0.0998 time to fit residues: 32.3988 Evaluate side-chains 239 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 226 LEU 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 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 80 ASP 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 98 GLN Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 109 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 49 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.156906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.123319 restraints weight = 14195.985| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.40 r_work: 0.3489 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4598 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= 0.125 Angle : 0.526 9.598 13935 Z= 0.267 Chirality : 0.037 0.164 1682 Planarity : 0.004 0.038 1759 Dihedral : 4.236 58.576 1407 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.15 % Allowed : 19.28 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.31 (0.23), residues: 1312 helix: 2.63 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.53 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.019 0.001 TYR F 22 PHE 0.024 0.001 PHE F 32 TRP 0.012 0.001 TRP D 77 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00255 (10276) covalent geometry : angle 0.52636 (13935) hydrogen bonds : bond 0.04502 ( 844) hydrogen bonds : angle 3.95028 ( 2508) *********************** 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 250 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 0.283 Fit side-chains REVERT: A 113 GLN cc_start: 0.7956 (tp40) cc_final: 0.7341 (mm-40) REVERT: A 235 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7143 (mm) REVERT: B 31 PHE cc_start: 0.6298 (t80) cc_final: 0.5824 (m-80) REVERT: B 73 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7401 (mp0) REVERT: B 76 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7356 (mm-30) REVERT: B 80 ASP cc_start: 0.8395 (m-30) cc_final: 0.8096 (m-30) REVERT: B 113 GLN cc_start: 0.7944 (tp-100) cc_final: 0.7538 (mm-40) REVERT: B 230 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.7103 (m-40) REVERT: C 230 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7807 (m110) REVERT: D 64 LYS cc_start: 0.7990 (mttt) cc_final: 0.7383 (mmtt) REVERT: D 89 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7645 (ttp-110) REVERT: D 156 MET cc_start: 0.9160 (mmp) cc_final: 0.8826 (mmp) REVERT: E 53 MET cc_start: 0.8029 (tpt) cc_final: 0.7829 (tpp) REVERT: E 64 LYS cc_start: 0.8377 (tptt) cc_final: 0.7798 (mptt) REVERT: E 71 ARG cc_start: 0.8016 (mmm-85) cc_final: 0.7778 (mmm160) REVERT: E 89 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7334 (ttp-170) REVERT: F 30 LEU cc_start: 0.8328 (tp) cc_final: 0.8057 (tp) REVERT: F 41 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.5809 (ttp-110) REVERT: G 43 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6130 (m-30) outliers start: 34 outliers final: 24 residues processed: 237 average time/residue: 0.1034 time to fit residues: 33.7377 Evaluate side-chains 238 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 184 VAL 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 173 THR 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 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 184 VAL Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 SER 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 73 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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** E 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126064 restraints weight = 14506.198| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.31 r_work: 0.3481 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10276 Z= 0.133 Angle : 0.541 10.170 13935 Z= 0.274 Chirality : 0.038 0.224 1682 Planarity : 0.004 0.039 1759 Dihedral : 4.213 58.351 1407 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.78 % Allowed : 20.39 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.28 (0.23), residues: 1312 helix: 2.61 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.58 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.007 0.001 TYR G 22 PHE 0.013 0.001 PHE F 58 TRP 0.012 0.001 TRP D 77 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00290 (10276) covalent geometry : angle 0.54087 (13935) hydrogen bonds : bond 0.04655 ( 844) hydrogen bonds : angle 3.95665 ( 2508) *********************** 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 235 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.379 Fit side-chains REVERT: A 113 GLN cc_start: 0.8004 (tp40) cc_final: 0.7479 (mt0) REVERT: A 128 MET cc_start: 0.8504 (mmm) cc_final: 0.7837 (mtt) REVERT: A 235 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7121 (mm) REVERT: B 31 PHE cc_start: 0.6315 (t80) cc_final: 0.5902 (m-80) REVERT: B 76 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7385 (mm-30) REVERT: B 80 ASP cc_start: 0.8389 (m-30) cc_final: 0.8063 (m-30) REVERT: B 113 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7543 (mm-40) REVERT: B 168 VAL cc_start: 0.7071 (p) cc_final: 0.6862 (t) REVERT: C 230 ASN cc_start: 0.8195 (OUTLIER) cc_final: 0.7892 (m110) REVERT: D 64 LYS cc_start: 0.8037 (mttt) cc_final: 0.7453 (mmtt) REVERT: D 89 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7670 (ttp-110) REVERT: D 97 GLU cc_start: 0.7218 (tp30) cc_final: 0.6610 (tt0) REVERT: D 156 MET cc_start: 0.9146 (mmp) cc_final: 0.8819 (mmp) REVERT: E 53 MET cc_start: 0.8090 (tpt) cc_final: 0.7887 (tpp) REVERT: E 64 LYS cc_start: 0.8445 (tptt) cc_final: 0.7844 (mptt) REVERT: E 71 ARG cc_start: 0.7992 (mmm-85) cc_final: 0.7754 (mmm160) REVERT: E 86 MET cc_start: 0.8700 (tpp) cc_final: 0.8415 (mmp) REVERT: E 89 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7347 (ttp-170) REVERT: F 30 LEU cc_start: 0.8386 (tp) cc_final: 0.8185 (tp) REVERT: F 41 ARG cc_start: 0.7344 (OUTLIER) cc_final: 0.5885 (mtm180) REVERT: G 36 MET cc_start: 0.7772 (mmt) cc_final: 0.7371 (mmm) REVERT: G 39 MET cc_start: 0.4993 (tmm) cc_final: 0.4190 (ptt) REVERT: G 43 ASP cc_start: 0.7241 (OUTLIER) cc_final: 0.6437 (m-30) outliers start: 30 outliers final: 22 residues processed: 225 average time/residue: 0.1095 time to fit residues: 34.1040 Evaluate side-chains 228 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 C residue 63 ILE Chi-restraints excluded: chain C residue 119 THR 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 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 30 LEU Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 176 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 54 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 108 optimal weight: 0.0370 chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129499 restraints weight = 14184.300| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.30 r_work: 0.3562 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.4876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10276 Z= 0.120 Angle : 0.525 10.035 13935 Z= 0.265 Chirality : 0.037 0.217 1682 Planarity : 0.004 0.038 1759 Dihedral : 4.132 58.159 1407 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.41 % Allowed : 20.95 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.43 (0.23), residues: 1312 helix: 2.73 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -0.60 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 89 TYR 0.022 0.001 TYR F 22 PHE 0.011 0.001 PHE F 58 TRP 0.010 0.001 TRP D 77 HIS 0.002 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00244 (10276) covalent geometry : angle 0.52460 (13935) hydrogen bonds : bond 0.04173 ( 844) hydrogen bonds : angle 3.83065 ( 2508) ********************** 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 244 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 0.350 Fit side-chains REVERT: A 113 GLN cc_start: 0.8145 (tp40) cc_final: 0.7584 (mt0) REVERT: A 128 MET cc_start: 0.8405 (mmm) cc_final: 0.8131 (mtt) REVERT: A 235 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.7144 (mm) REVERT: B 31 PHE cc_start: 0.6485 (t80) cc_final: 0.5973 (m-80) REVERT: B 76 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7467 (mm-30) REVERT: B 80 ASP cc_start: 0.8478 (m-30) cc_final: 0.8180 (m-30) REVERT: B 113 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7572 (mm-40) REVERT: C 147 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: C 230 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7836 (m110) REVERT: D 64 LYS cc_start: 0.8111 (mttt) cc_final: 0.7525 (mmtt) REVERT: D 86 MET cc_start: 0.8440 (mtm) cc_final: 0.8153 (tpt) REVERT: D 97 GLU cc_start: 0.7167 (tp30) cc_final: 0.6679 (tt0) REVERT: D 156 MET cc_start: 0.9202 (mmp) cc_final: 0.8878 (mmp) REVERT: D 171 HIS cc_start: 0.6148 (OUTLIER) cc_final: 0.5554 (m90) REVERT: E 64 LYS cc_start: 0.8567 (tptt) cc_final: 0.7967 (mptt) REVERT: E 71 ARG cc_start: 0.7924 (mmm-85) cc_final: 0.7716 (mmm160) REVERT: E 89 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7417 (ttp-170) REVERT: F 41 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.5891 (mtm180) REVERT: F 46 LYS cc_start: 0.6705 (mppt) cc_final: 0.5885 (tptp) REVERT: G 39 MET cc_start: 0.4972 (tmm) cc_final: 0.4403 (ptt) REVERT: G 43 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6397 (m-30) outliers start: 26 outliers final: 17 residues processed: 238 average time/residue: 0.1072 time to fit residues: 35.4154 Evaluate side-chains 227 residues out of total 1079 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 C residue 63 ILE Chi-restraints excluded: chain C residue 147 GLU 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 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 176 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 47 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 105 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 GLN A 229 GLN E 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.158870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.124585 restraints weight = 14224.887| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.45 r_work: 0.3530 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10276 Z= 0.125 Angle : 0.549 11.189 13935 Z= 0.273 Chirality : 0.038 0.255 1682 Planarity : 0.004 0.044 1759 Dihedral : 4.099 58.068 1407 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.59 % Allowed : 21.04 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.42 (0.23), residues: 1312 helix: 2.73 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -0.63 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 89 TYR 0.015 0.001 TYR F 22 PHE 0.021 0.001 PHE F 32 TRP 0.011 0.001 TRP D 77 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00266 (10276) covalent geometry : angle 0.54891 (13935) hydrogen bonds : bond 0.04307 ( 844) hydrogen bonds : angle 3.83840 ( 2508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2301.06 seconds wall clock time: 40 minutes 7.94 seconds (2407.94 seconds total)