Starting phenix.real_space_refine on Wed Mar 4 01:46:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysf_10895/03_2026/6ysf_10895.cif" } resolution = 3.4 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= 0.000 sd= 0.003 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 95 5.16 5 C 6543 2.51 5 N 1674 2.21 5 O 1908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10220 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 239 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 267 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "E" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "C" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1934 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 8, 'TRANS': 243} Time building chain proxies: 2.35, per 1000 atoms: 0.23 Number of scatterers: 10220 At special positions: 0 Unit cell: (94.53, 114.258, 103.572, 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 95 16.00 O 1908 8.00 N 1674 7.00 C 6543 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: 0.75 Conformation dependent library (CDL) restraints added in 474.3 milliseconds 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2408 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 37 Processing helix chain 'B' and resid 17 through 43 removed outlier: 3.884A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N THR B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 23 " --> pdb=" O TRP B 19 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 32 " --> pdb=" O THR B 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 25 removed outlier: 4.406A pdb=" N VAL E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL E 19 " --> pdb=" O CYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.604A pdb=" N VAL E 32 " --> pdb=" O ASN E 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 34 " --> pdb=" O LYS E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.682A pdb=" N VAL E 39 " --> pdb=" O ASP E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.692A pdb=" N GLN E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.835A pdb=" N MET E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 173 removed outlier: 4.135A pdb=" N GLU E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Proline residue: E 157 - end of helix removed outlier: 3.679A pdb=" N GLN E 170 " --> pdb=" O ILE E 166 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET E 171 " --> pdb=" O GLY E 167 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU E 172 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA E 173 " --> pdb=" O ILE E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 202 removed outlier: 3.721A pdb=" N MET E 185 " --> pdb=" O ILE E 181 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE E 190 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N THR E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N THR E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 232 Processing helix chain 'E' and resid 239 through 246 removed outlier: 3.591A pdb=" N SER E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 removed outlier: 3.617A pdb=" N LYS E 258 " --> pdb=" O GLN E 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.725A pdb=" N VAL C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU C 14 " --> pdb=" O ILE C 10 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL C 19 " --> pdb=" O CYS C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 62 through 71 removed outlier: 4.908A pdb=" N GLN C 68 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N PHE C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.946A pdb=" N GLN C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 removed outlier: 3.762A pdb=" N GLY C 114 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C 119 " --> pdb=" O LEU C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 172 removed outlier: 3.519A pdb=" N ILE C 127 " --> pdb=" O GLU C 123 " (cutoff:3.500A) Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 179 through 234 removed outlier: 4.438A pdb=" N SER C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N THR C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N ASN C 204 " --> pdb=" O ASN C 200 " (cutoff:3.500A) Proline residue: C 205 - end of helix removed outlier: 4.536A pdb=" N GLY C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.509A pdb=" N GLN C 254 " --> pdb=" O PRO C 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 24 removed outlier: 3.523A pdb=" N CYS D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 removed outlier: 4.134A pdb=" N VAL D 32 " --> pdb=" O ASN D 29 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TRP D 34 " --> pdb=" O LYS D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 54 Processing helix chain 'D' and resid 58 through 64 removed outlier: 3.785A pdb=" N LEU D 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE D 64 " --> pdb=" O ARG D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 70 removed outlier: 4.014A pdb=" N PHE D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.608A pdb=" N LYS D 90 " --> pdb=" O ASP D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.695A pdb=" N ASN D 104 " --> pdb=" O ASP D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 123 through 172 removed outlier: 3.921A pdb=" N ILE D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 179 through 203 removed outlier: 3.798A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 233 removed outlier: 4.032A pdb=" N MET D 211 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 212 " --> pdb=" O ALA D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 245 removed outlier: 3.875A pdb=" N GLU D 242 " --> pdb=" O ARG D 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 243 " --> pdb=" O ILE D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 249 through 257 removed outlier: 4.375A pdb=" N GLN D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 22 removed outlier: 3.548A pdb=" N ILE F 10 " --> pdb=" O ILE F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 26 removed outlier: 4.208A pdb=" N GLY F 26 " --> pdb=" O MET F 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 23 through 26' Processing helix chain 'F' and resid 30 through 34 removed outlier: 3.617A pdb=" N PHE F 33 " --> pdb=" O LEU F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 54 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 61 through 66 Processing helix chain 'F' and resid 66 through 72 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.194A pdb=" N LEU F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 120 removed outlier: 3.651A pdb=" N LYS F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP F 120 " --> pdb=" O ARG F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 174 removed outlier: 3.525A pdb=" N GLU F 137 " --> pdb=" O LEU F 133 " (cutoff:3.500A) Proline residue: F 157 - end of helix removed outlier: 3.910A pdb=" N ASN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 202 removed outlier: 3.524A pdb=" N ALA F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN F 200 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 234 removed outlier: 3.535A pdb=" N MET F 206 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET F 211 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE F 212 " --> pdb=" O ALA F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 245 removed outlier: 3.626A pdb=" N GLU F 241 " --> pdb=" O PRO F 237 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LYS F 243 " --> pdb=" O ILE F 239 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU F 244 " --> pdb=" O MET F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 255 removed outlier: 3.905A pdb=" N GLN F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 3.795A pdb=" N LEU G 20 " --> pdb=" O PHE G 16 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 22 " --> pdb=" O LEU G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.077A pdb=" N VAL G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 69 removed outlier: 3.539A pdb=" N GLN G 68 " --> pdb=" O ILE G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 90 removed outlier: 4.255A pdb=" N ILE G 81 " --> pdb=" O ASN G 77 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL G 85 " --> pdb=" O ILE G 81 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 116 Processing helix chain 'G' and resid 125 through 171 Proline residue: G 157 - end of helix removed outlier: 3.783A pdb=" N MET G 171 " --> pdb=" O GLY G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 234 removed outlier: 4.576A pdb=" N THR G 191 " --> pdb=" O LYS G 187 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ASN G 204 " --> pdb=" O ASN G 200 " (cutoff:3.500A) Proline residue: G 205 - end of helix removed outlier: 3.670A pdb=" N SER G 233 " --> pdb=" O LEU G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 249 through 259 removed outlier: 4.109A pdb=" N LYS G 258 " --> pdb=" O GLN G 254 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N VAL G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) 701 hydrogen bonds defined for protein. 2085 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: 1.63 Time building geometry restraints manager: 1.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3280 1.34 - 1.46: 2155 1.46 - 1.58: 4767 1.58 - 1.70: 0 1.70 - 1.81: 185 Bond restraints: 10387 Sorted by residual: bond pdb=" N ILE F 135 " pdb=" CA ILE F 135 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.21e-02 6.83e+03 7.61e+00 bond pdb=" N LYS F 113 " pdb=" CA LYS F 113 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.19e-02 7.06e+03 6.41e+00 bond pdb=" N ARG C 238 " pdb=" CA ARG C 238 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" N LEU F 133 " pdb=" CA LEU F 133 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.33e-02 5.65e+03 5.33e+00 bond pdb=" N LYS C 113 " pdb=" CA LYS C 113 " ideal model delta sigma weight residual 1.459 1.487 -0.029 1.25e-02 6.40e+03 5.28e+00 ... (remaining 10382 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 13495 1.72 - 3.44: 417 3.44 - 5.16: 57 5.16 - 6.88: 26 6.88 - 8.60: 7 Bond angle restraints: 14002 Sorted by residual: angle pdb=" N ILE F 78 " pdb=" CA ILE F 78 " pdb=" C ILE F 78 " ideal model delta sigma weight residual 113.71 108.08 5.63 9.50e-01 1.11e+00 3.51e+01 angle pdb=" N ARG F 116 " pdb=" CA ARG F 116 " pdb=" C ARG F 116 " ideal model delta sigma weight residual 111.82 106.55 5.27 1.16e+00 7.43e-01 2.06e+01 angle pdb=" C THR F 107 " pdb=" N ASP F 108 " pdb=" CA ASP F 108 " ideal model delta sigma weight residual 120.82 127.40 -6.58 1.47e+00 4.63e-01 2.00e+01 angle pdb=" C ARG E 92 " pdb=" N ARG E 93 " pdb=" CA ARG E 93 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N ARG C 253 " pdb=" CA ARG C 253 " pdb=" C ARG C 253 " ideal model delta sigma weight residual 111.82 107.48 4.34 1.16e+00 7.43e-01 1.40e+01 ... (remaining 13997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5511 17.91 - 35.81: 616 35.81 - 53.72: 106 53.72 - 71.62: 19 71.62 - 89.53: 9 Dihedral angle restraints: 6261 sinusoidal: 2501 harmonic: 3760 Sorted by residual: dihedral pdb=" CA ASP F 108 " pdb=" C ASP F 108 " pdb=" N ASP F 109 " pdb=" CA ASP F 109 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA ASP E 108 " pdb=" C ASP E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASN G 236 " pdb=" C ASN G 236 " pdb=" N PRO G 237 " pdb=" CA PRO G 237 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1069 0.040 - 0.079: 435 0.079 - 0.119: 99 0.119 - 0.158: 10 0.158 - 0.198: 5 Chirality restraints: 1618 Sorted by residual: chirality pdb=" CA ILE F 135 " pdb=" N ILE F 135 " pdb=" C ILE F 135 " pdb=" CB ILE F 135 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.76e-01 chirality pdb=" CA LEU F 133 " pdb=" N LEU F 133 " pdb=" C LEU F 133 " pdb=" CB LEU F 133 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA ARG F 116 " pdb=" N ARG F 116 " pdb=" C ARG F 116 " pdb=" CB ARG F 116 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1615 not shown) Planarity restraints: 1764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 236 " -0.035 5.00e-02 4.00e+02 5.26e-02 4.42e+00 pdb=" N PRO G 237 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 237 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU F 115 " -0.009 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C LEU F 115 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU F 115 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG F 116 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 41 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.12e+00 pdb=" C ILE D 41 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE D 41 " -0.011 2.00e-02 2.50e+03 pdb=" N THR D 42 " -0.010 2.00e-02 2.50e+03 ... (remaining 1761 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 56 2.48 - 3.08: 7683 3.08 - 3.69: 15875 3.69 - 4.29: 22858 4.29 - 4.90: 37509 Nonbonded interactions: 83981 Sorted by model distance: nonbonded pdb=" NH2 ARG C 238 " pdb=" OD2 ASP D 120 " model vdw 1.874 3.120 nonbonded pdb=" OE2 GLU C 242 " pdb=" NZ LYS D 113 " model vdw 1.893 3.120 nonbonded pdb=" NZ LYS D 113 " pdb=" OE2 GLU D 134 " model vdw 2.012 3.120 nonbonded pdb=" CE LYS D 113 " pdb=" OE2 GLU D 134 " model vdw 2.041 3.440 nonbonded pdb=" O ALA E 49 " pdb=" OG1 THR E 53 " model vdw 2.122 3.040 ... (remaining 83976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 42) } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = (chain 'F' and resid 8 through 259) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.150 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 10.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 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 : 0.004 0.053 10387 Z= 0.208 Angle : 0.765 8.602 14002 Z= 0.452 Chirality : 0.043 0.198 1618 Planarity : 0.005 0.053 1764 Dihedral : 15.307 89.525 3853 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Rotamer: Outliers : 0.90 % Allowed : 6.21 % Favored : 92.90 % 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 are not related in a simple way. whole: -3.39 (0.20), residues: 1313 helix: -1.53 (0.15), residues: 946 sheet: None (None), residues: 0 loop : -3.91 (0.28), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 116 TYR 0.011 0.002 TYR G 155 PHE 0.011 0.001 PHE D 212 TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00424 (10387) covalent geometry : angle 0.76512 (14002) hydrogen bonds : bond 0.15394 ( 701) hydrogen bonds : angle 6.50998 ( 2085) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 365 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: E 79 ASP cc_start: 0.5379 (t0) cc_final: 0.5156 (t0) REVERT: E 124 PRO cc_start: 0.7500 (Cg_exo) cc_final: 0.7184 (Cg_endo) REVERT: E 131 MET cc_start: 0.7107 (mmt) cc_final: 0.6810 (mmt) REVERT: E 139 GLU cc_start: 0.6281 (mt-10) cc_final: 0.6002 (mt-10) REVERT: E 236 ASN cc_start: 0.7773 (p0) cc_final: 0.7527 (p0) REVERT: E 240 MET cc_start: 0.7599 (tmm) cc_final: 0.6962 (tmm) REVERT: C 113 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7229 (ttpt) REVERT: C 185 MET cc_start: 0.7196 (mtp) cc_final: 0.6957 (mtp) REVERT: C 242 GLU cc_start: 0.6484 (tp30) cc_final: 0.6235 (tp30) REVERT: C 254 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7240 (pt0) REVERT: D 71 LYS cc_start: 0.6348 (pttt) cc_final: 0.6034 (pttt) REVERT: D 82 GLN cc_start: 0.7808 (mt0) cc_final: 0.7576 (tt0) REVERT: D 112 LYS cc_start: 0.7616 (mtpt) cc_final: 0.7352 (mtmt) REVERT: F 112 LYS cc_start: 0.7855 (mttt) cc_final: 0.7157 (tmtt) REVERT: G 57 ASP cc_start: 0.7552 (t70) cc_final: 0.7341 (t0) REVERT: G 71 LYS cc_start: 0.7383 (mttm) cc_final: 0.7086 (mtmt) REVERT: G 75 MET cc_start: 0.4236 (mmm) cc_final: 0.3700 (mmt) REVERT: G 111 MET cc_start: 0.6719 (mpp) cc_final: 0.6356 (mpp) REVERT: G 131 MET cc_start: 0.5546 (mmp) cc_final: 0.5137 (mtp) outliers start: 10 outliers final: 3 residues processed: 371 average time/residue: 0.1081 time to fit residues: 54.5679 Evaluate side-chains 289 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 284 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LYS Chi-restraints excluded: chain C residue 254 GLN Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 ASN E 232 GLN C 77 ASN C 204 ASN D 170 GLN G 83 ASN G 104 ASN G 204 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.167999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134579 restraints weight = 14597.486| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.81 r_work: 0.3563 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10387 Z= 0.138 Angle : 0.659 13.103 14002 Z= 0.337 Chirality : 0.042 0.183 1618 Planarity : 0.005 0.049 1764 Dihedral : 5.833 64.078 1425 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.35 % Allowed : 17.27 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1313 helix: -0.10 (0.16), residues: 988 sheet: None (None), residues: 0 loop : -3.75 (0.29), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 89 TYR 0.021 0.002 TYR E 110 PHE 0.014 0.001 PHE B 33 TRP 0.017 0.001 TRP D 21 HIS 0.002 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00298 (10387) covalent geometry : angle 0.65903 (14002) hydrogen bonds : bond 0.04044 ( 701) hydrogen bonds : angle 4.68656 ( 2085) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 348 time to evaluate : 0.391 Fit side-chains REVERT: A 17 ASP cc_start: 0.7298 (t0) cc_final: 0.6835 (p0) REVERT: E 124 PRO cc_start: 0.7651 (Cg_exo) cc_final: 0.7252 (Cg_endo) REVERT: E 240 MET cc_start: 0.7820 (tmm) cc_final: 0.7350 (tmm) REVERT: C 250 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.7964 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7041 (mt-10) REVERT: D 82 GLN cc_start: 0.8026 (mt0) cc_final: 0.7808 (tt0) REVERT: D 113 LYS cc_start: 0.8029 (tmtp) cc_final: 0.7554 (ttpp) REVERT: F 75 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6430 (ptm) REVERT: F 112 LYS cc_start: 0.7877 (tttt) cc_final: 0.7094 (tmtt) REVERT: F 131 MET cc_start: 0.7800 (mmt) cc_final: 0.7284 (mmm) REVERT: F 222 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8167 (mm-30) REVERT: F 238 ARG cc_start: 0.7876 (tpm170) cc_final: 0.7646 (tmt170) REVERT: G 57 ASP cc_start: 0.8194 (t70) cc_final: 0.7950 (t0) REVERT: G 71 LYS cc_start: 0.7237 (mttm) cc_final: 0.6950 (mtmt) REVERT: G 75 MET cc_start: 0.4680 (mmm) cc_final: 0.3901 (mmt) REVERT: G 111 MET cc_start: 0.6965 (mpp) cc_final: 0.6496 (mpp) REVERT: G 131 MET cc_start: 0.6306 (mmp) cc_final: 0.5166 (mtt) REVERT: G 221 ARG cc_start: 0.8027 (mtt-85) cc_final: 0.7786 (mtt-85) outliers start: 15 outliers final: 6 residues processed: 355 average time/residue: 0.0964 time to fit residues: 48.1244 Evaluate side-chains 303 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 296 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 16 optimal weight: 1.9990 chunk 107 optimal weight: 0.0050 chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 30.0000 chunk 4 optimal weight: 0.7980 chunk 106 optimal weight: 0.0770 chunk 75 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN C 82 GLN D 170 GLN F 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.168147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135245 restraints weight = 14742.497| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.79 r_work: 0.3574 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10387 Z= 0.137 Angle : 0.638 13.999 14002 Z= 0.327 Chirality : 0.042 0.199 1618 Planarity : 0.005 0.049 1764 Dihedral : 4.915 32.461 1412 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.79 % Allowed : 19.60 % Favored : 77.61 % 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 are not related in a simple way. whole: -0.83 (0.23), residues: 1313 helix: 0.41 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -3.59 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 89 TYR 0.019 0.002 TYR G 155 PHE 0.015 0.001 PHE F 203 TRP 0.017 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00308 (10387) covalent geometry : angle 0.63831 (14002) hydrogen bonds : bond 0.03876 ( 701) hydrogen bonds : angle 4.54840 ( 2085) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 323 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7124 (OUTLIER) cc_final: 0.6874 (tp) REVERT: E 124 PRO cc_start: 0.7595 (Cg_exo) cc_final: 0.7253 (Cg_endo) REVERT: E 161 MET cc_start: 0.7882 (OUTLIER) cc_final: 0.7373 (mpp) REVERT: E 240 MET cc_start: 0.8023 (tmm) cc_final: 0.7563 (tmm) REVERT: C 241 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7382 (tt0) REVERT: C 250 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8018 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6715 (pp) REVERT: D 82 GLN cc_start: 0.7977 (mt0) cc_final: 0.7670 (tt0) REVERT: D 113 LYS cc_start: 0.7818 (tmtp) cc_final: 0.6987 (tttp) REVERT: D 238 ARG cc_start: 0.7866 (mmp-170) cc_final: 0.7564 (mmm160) REVERT: F 112 LYS cc_start: 0.7625 (mttt) cc_final: 0.6809 (tmtt) REVERT: F 238 ARG cc_start: 0.7827 (tpm170) cc_final: 0.7615 (tmt170) REVERT: G 33 PHE cc_start: 0.8300 (m-80) cc_final: 0.7877 (m-10) REVERT: G 71 LYS cc_start: 0.7191 (mttm) cc_final: 0.6883 (mtmt) REVERT: G 75 MET cc_start: 0.4536 (mmm) cc_final: 0.3807 (mmt) REVERT: G 111 MET cc_start: 0.6997 (mpp) cc_final: 0.6493 (mpp) REVERT: G 131 MET cc_start: 0.6097 (mmp) cc_final: 0.5052 (mtt) REVERT: G 132 GLU cc_start: 0.7497 (mm-30) cc_final: 0.7225 (mm-30) outliers start: 31 outliers final: 12 residues processed: 336 average time/residue: 0.0908 time to fit residues: 43.8067 Evaluate side-chains 298 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 283 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 0.0970 chunk 51 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 110 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN F 170 GLN F 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.169189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135512 restraints weight = 14759.051| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.82 r_work: 0.3580 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10387 Z= 0.131 Angle : 0.626 14.300 14002 Z= 0.319 Chirality : 0.041 0.196 1618 Planarity : 0.005 0.049 1764 Dihedral : 4.843 35.277 1412 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.15 % Allowed : 20.68 % Favored : 76.17 % 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 are not related in a simple way. whole: -0.58 (0.23), residues: 1313 helix: 0.57 (0.17), residues: 994 sheet: None (None), residues: 0 loop : -3.45 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 89 TYR 0.017 0.002 TYR G 110 PHE 0.015 0.001 PHE E 33 TRP 0.017 0.001 TRP D 21 HIS 0.001 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00289 (10387) covalent geometry : angle 0.62604 (14002) hydrogen bonds : bond 0.03771 ( 701) hydrogen bonds : angle 4.45219 ( 2085) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 312 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6842 (tp) REVERT: E 124 PRO cc_start: 0.7686 (Cg_exo) cc_final: 0.6854 (Cg_endo) REVERT: E 161 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7393 (mpp) REVERT: E 240 MET cc_start: 0.8052 (tmm) cc_final: 0.7630 (tmm) REVERT: C 56 MET cc_start: 0.6551 (mmm) cc_final: 0.6018 (mmt) REVERT: C 136 ASP cc_start: 0.7825 (m-30) cc_final: 0.7566 (m-30) REVERT: C 241 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7308 (tt0) REVERT: C 250 PRO cc_start: 0.8285 (Cg_exo) cc_final: 0.8029 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.6809 (pp) REVERT: D 101 ASP cc_start: 0.7689 (p0) cc_final: 0.7352 (t0) REVERT: D 238 ARG cc_start: 0.7827 (mmp-170) cc_final: 0.7534 (mmm160) REVERT: D 252 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: F 75 MET cc_start: 0.6048 (ptm) cc_final: 0.5401 (mmp) REVERT: F 112 LYS cc_start: 0.7721 (tttt) cc_final: 0.6861 (tmtt) REVERT: F 131 MET cc_start: 0.8001 (mmm) cc_final: 0.7458 (mmm) REVERT: F 238 ARG cc_start: 0.7835 (tpm170) cc_final: 0.7611 (tmt170) REVERT: G 50 MET cc_start: 0.8687 (mmm) cc_final: 0.8474 (mmm) REVERT: G 71 LYS cc_start: 0.7222 (mttm) cc_final: 0.6893 (mtmt) REVERT: G 111 MET cc_start: 0.6965 (mpp) cc_final: 0.6439 (mpp) REVERT: G 131 MET cc_start: 0.6084 (mmp) cc_final: 0.5040 (mtt) REVERT: G 222 GLU cc_start: 0.7891 (tp30) cc_final: 0.7169 (tp30) outliers start: 35 outliers final: 21 residues processed: 329 average time/residue: 0.0916 time to fit residues: 43.1715 Evaluate side-chains 311 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 286 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 12 PHE Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 68 GLN D 170 GLN F 170 GLN F 200 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.163989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131629 restraints weight = 14833.172| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.07 r_work: 0.3502 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10387 Z= 0.191 Angle : 0.682 14.193 14002 Z= 0.346 Chirality : 0.044 0.172 1618 Planarity : 0.005 0.055 1764 Dihedral : 5.100 39.731 1412 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.51 % Allowed : 22.21 % Favored : 74.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.23), residues: 1313 helix: 0.46 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -3.43 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 89 TYR 0.017 0.002 TYR G 110 PHE 0.017 0.002 PHE E 33 TRP 0.017 0.001 TRP D 21 HIS 0.003 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00454 (10387) covalent geometry : angle 0.68168 (14002) hydrogen bonds : bond 0.04081 ( 701) hydrogen bonds : angle 4.73502 ( 2085) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 298 time to evaluate : 0.337 Fit side-chains REVERT: E 78 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6917 (tp) REVERT: E 94 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6092 (pp20) REVERT: E 123 GLU cc_start: 0.7995 (tp30) cc_final: 0.7597 (pt0) REVERT: E 124 PRO cc_start: 0.7528 (Cg_exo) cc_final: 0.7325 (Cg_endo) REVERT: E 161 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7753 (mpp) REVERT: E 240 MET cc_start: 0.8121 (tmm) cc_final: 0.7568 (tmm) REVERT: C 123 GLU cc_start: 0.7151 (pt0) cc_final: 0.6730 (tt0) REVERT: C 136 ASP cc_start: 0.8017 (m-30) cc_final: 0.7759 (m-30) REVERT: C 250 PRO cc_start: 0.8454 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6696 (pp) REVERT: D 112 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7627 (mtmm) REVERT: D 132 GLU cc_start: 0.7231 (tp30) cc_final: 0.6886 (tp30) REVERT: D 252 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8443 (tp30) REVERT: F 112 LYS cc_start: 0.7914 (tttt) cc_final: 0.7051 (tmtt) REVERT: F 131 MET cc_start: 0.8227 (mmm) cc_final: 0.7713 (mmm) REVERT: F 238 ARG cc_start: 0.7920 (tpm170) cc_final: 0.7650 (tmt170) REVERT: G 111 MET cc_start: 0.6749 (mpp) cc_final: 0.6230 (mpp) REVERT: G 131 MET cc_start: 0.6237 (mmp) cc_final: 0.5070 (mtp) outliers start: 39 outliers final: 26 residues processed: 319 average time/residue: 0.0868 time to fit residues: 40.0565 Evaluate side-chains 310 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 279 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 113 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 93 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 68 GLN C 170 GLN F 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.168924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.135567 restraints weight = 14831.379| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.82 r_work: 0.3575 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10387 Z= 0.132 Angle : 0.645 14.280 14002 Z= 0.328 Chirality : 0.042 0.233 1618 Planarity : 0.005 0.052 1764 Dihedral : 4.874 47.131 1412 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 3.60 % Allowed : 23.02 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1313 helix: 0.66 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -3.25 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 89 TYR 0.017 0.002 TYR G 155 PHE 0.018 0.001 PHE E 33 TRP 0.018 0.001 TRP D 21 HIS 0.001 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00295 (10387) covalent geometry : angle 0.64460 (14002) hydrogen bonds : bond 0.03835 ( 701) hydrogen bonds : angle 4.47125 ( 2085) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 307 time to evaluate : 0.363 Fit side-chains REVERT: E 78 ILE cc_start: 0.7042 (OUTLIER) cc_final: 0.6824 (tp) REVERT: E 94 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.6092 (pp20) REVERT: E 124 PRO cc_start: 0.7558 (Cg_exo) cc_final: 0.7283 (Cg_endo) REVERT: E 161 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7310 (mpp) REVERT: E 240 MET cc_start: 0.7969 (tmm) cc_final: 0.7589 (tmm) REVERT: C 56 MET cc_start: 0.6395 (mmm) cc_final: 0.6045 (mmt) REVERT: C 136 ASP cc_start: 0.7967 (m-30) cc_final: 0.7733 (m-30) REVERT: C 250 PRO cc_start: 0.8303 (Cg_exo) cc_final: 0.8068 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6793 (pp) REVERT: D 112 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7700 (mttt) REVERT: D 132 GLU cc_start: 0.7221 (tp30) cc_final: 0.6899 (tp30) REVERT: F 50 MET cc_start: 0.8070 (mmm) cc_final: 0.7776 (mmm) REVERT: F 75 MET cc_start: 0.6030 (ptm) cc_final: 0.5514 (mmt) REVERT: F 112 LYS cc_start: 0.7761 (tttt) cc_final: 0.6934 (tmtt) REVERT: F 131 MET cc_start: 0.8023 (mmm) cc_final: 0.7609 (mmm) REVERT: F 238 ARG cc_start: 0.7804 (tpm170) cc_final: 0.7584 (tmt170) REVERT: F 256 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.4787 (p90) REVERT: G 111 MET cc_start: 0.6834 (mpp) cc_final: 0.6348 (mpp) REVERT: G 131 MET cc_start: 0.6043 (mmp) cc_final: 0.5078 (mtt) REVERT: G 222 GLU cc_start: 0.7889 (tp30) cc_final: 0.7196 (tp30) outliers start: 40 outliers final: 27 residues processed: 328 average time/residue: 0.0893 time to fit residues: 42.3445 Evaluate side-chains 314 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 282 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 49 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 77 optimal weight: 0.0470 chunk 71 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 chunk 69 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN E 232 GLN C 68 GLN D 170 GLN F 170 GLN F 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.170990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.137833 restraints weight = 14745.046| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 1.81 r_work: 0.3610 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10387 Z= 0.131 Angle : 0.651 13.874 14002 Z= 0.331 Chirality : 0.042 0.191 1618 Planarity : 0.005 0.046 1764 Dihedral : 4.768 47.413 1412 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.60 % Allowed : 23.29 % Favored : 73.11 % 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 are not related in a simple way. whole: -0.14 (0.24), residues: 1313 helix: 0.84 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -3.11 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 89 TYR 0.020 0.002 TYR G 110 PHE 0.016 0.001 PHE E 33 TRP 0.018 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00287 (10387) covalent geometry : angle 0.65129 (14002) hydrogen bonds : bond 0.03823 ( 701) hydrogen bonds : angle 4.37773 ( 2085) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 0.440 Fit side-chains REVERT: E 73 ASN cc_start: 0.7807 (m-40) cc_final: 0.7568 (m110) REVERT: E 94 GLU cc_start: 0.6440 (OUTLIER) cc_final: 0.6050 (pp20) REVERT: E 124 PRO cc_start: 0.7481 (Cg_exo) cc_final: 0.7249 (Cg_endo) REVERT: E 172 LEU cc_start: 0.8846 (pp) cc_final: 0.8326 (mt) REVERT: E 240 MET cc_start: 0.7940 (tmm) cc_final: 0.7572 (tmm) REVERT: C 56 MET cc_start: 0.6396 (mmm) cc_final: 0.6173 (mmt) REVERT: C 136 ASP cc_start: 0.8005 (m-30) cc_final: 0.7784 (m-30) REVERT: C 250 PRO cc_start: 0.8310 (Cg_exo) cc_final: 0.8083 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6866 (pp) REVERT: D 112 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7544 (mttm) REVERT: D 132 GLU cc_start: 0.7132 (tp30) cc_final: 0.6895 (tp30) REVERT: F 23 MET cc_start: 0.7243 (mpp) cc_final: 0.6713 (mpp) REVERT: F 47 MET cc_start: 0.7855 (tpt) cc_final: 0.7582 (tpt) REVERT: F 50 MET cc_start: 0.7918 (mmm) cc_final: 0.7673 (mmm) REVERT: F 112 LYS cc_start: 0.7833 (tttt) cc_final: 0.6907 (tmtt) REVERT: F 131 MET cc_start: 0.7973 (mmm) cc_final: 0.7554 (mmm) REVERT: F 256 TYR cc_start: 0.6212 (OUTLIER) cc_final: 0.4758 (p90) REVERT: G 50 MET cc_start: 0.8558 (mmm) cc_final: 0.7999 (mmm) REVERT: G 111 MET cc_start: 0.6849 (mpp) cc_final: 0.6349 (mpp) REVERT: G 131 MET cc_start: 0.6030 (mmp) cc_final: 0.5214 (mtt) REVERT: G 222 GLU cc_start: 0.7853 (tp30) cc_final: 0.7126 (tp30) REVERT: G 240 MET cc_start: 0.8747 (tpp) cc_final: 0.8538 (tpp) outliers start: 40 outliers final: 26 residues processed: 341 average time/residue: 0.0893 time to fit residues: 43.9934 Evaluate side-chains 315 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN F 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.170287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137017 restraints weight = 14718.001| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 1.82 r_work: 0.3599 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 10387 Z= 0.144 Angle : 0.692 13.976 14002 Z= 0.349 Chirality : 0.043 0.206 1618 Planarity : 0.005 0.044 1764 Dihedral : 4.770 47.151 1412 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.33 % Allowed : 24.37 % Favored : 72.30 % 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 are not related in a simple way. whole: -0.13 (0.24), residues: 1313 helix: 0.86 (0.17), residues: 995 sheet: None (None), residues: 0 loop : -3.14 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 89 TYR 0.018 0.002 TYR G 110 PHE 0.021 0.001 PHE D 16 TRP 0.020 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00325 (10387) covalent geometry : angle 0.69221 (14002) hydrogen bonds : bond 0.03945 ( 701) hydrogen bonds : angle 4.43684 ( 2085) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.416 Fit side-chains REVERT: A 40 PHE cc_start: 0.5137 (p90) cc_final: 0.4271 (t80) REVERT: E 73 ASN cc_start: 0.7814 (m-40) cc_final: 0.7576 (m110) REVERT: E 94 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.6049 (pp20) REVERT: E 112 LYS cc_start: 0.7199 (tptm) cc_final: 0.6313 (tttm) REVERT: E 124 PRO cc_start: 0.7574 (Cg_exo) cc_final: 0.7362 (Cg_endo) REVERT: E 172 LEU cc_start: 0.8872 (pp) cc_final: 0.8393 (mt) REVERT: E 187 LYS cc_start: 0.8897 (tmtt) cc_final: 0.8637 (tppt) REVERT: E 240 MET cc_start: 0.7903 (tmm) cc_final: 0.7579 (tmm) REVERT: C 56 MET cc_start: 0.6416 (mmm) cc_final: 0.6202 (mmt) REVERT: C 136 ASP cc_start: 0.7985 (m-30) cc_final: 0.7723 (m-30) REVERT: C 250 PRO cc_start: 0.8343 (Cg_exo) cc_final: 0.8124 (Cg_endo) REVERT: C 254 GLN cc_start: 0.7457 (pp30) cc_final: 0.7180 (pp30) REVERT: D 62 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6854 (pp) REVERT: D 132 GLU cc_start: 0.7134 (tp30) cc_final: 0.6919 (tp30) REVERT: D 170 GLN cc_start: 0.8603 (tt0) cc_final: 0.8268 (tt0) REVERT: D 253 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7557 (mtt90) REVERT: F 23 MET cc_start: 0.7335 (mpp) cc_final: 0.6807 (mpp) REVERT: F 47 MET cc_start: 0.7988 (tpt) cc_final: 0.7735 (tpt) REVERT: F 50 MET cc_start: 0.7914 (mmm) cc_final: 0.7699 (mmm) REVERT: F 112 LYS cc_start: 0.7855 (tttt) cc_final: 0.6947 (tmtt) REVERT: F 131 MET cc_start: 0.7978 (mmm) cc_final: 0.7558 (mmm) REVERT: F 256 TYR cc_start: 0.6135 (OUTLIER) cc_final: 0.4903 (p90) REVERT: G 111 MET cc_start: 0.6887 (mpp) cc_final: 0.6383 (mpp) REVERT: G 131 MET cc_start: 0.5975 (mmp) cc_final: 0.5047 (mtt) REVERT: G 240 MET cc_start: 0.8749 (tpp) cc_final: 0.8538 (tpp) outliers start: 37 outliers final: 27 residues processed: 324 average time/residue: 0.0873 time to fit residues: 41.0797 Evaluate side-chains 312 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 282 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 107 optimal weight: 0.0470 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.0370 chunk 102 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 114 optimal weight: 0.3980 chunk 45 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN F 200 ASN F 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.173038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140173 restraints weight = 14750.974| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.84 r_work: 0.3646 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10387 Z= 0.138 Angle : 0.729 21.234 14002 Z= 0.357 Chirality : 0.044 0.223 1618 Planarity : 0.005 0.045 1764 Dihedral : 4.707 47.868 1412 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.15 % Allowed : 25.00 % Favored : 71.85 % 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 are not related in a simple way. whole: -0.03 (0.24), residues: 1313 helix: 0.97 (0.17), residues: 983 sheet: None (None), residues: 0 loop : -3.10 (0.32), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 89 TYR 0.020 0.002 TYR G 110 PHE 0.019 0.001 PHE E 33 TRP 0.024 0.001 TRP D 21 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00299 (10387) covalent geometry : angle 0.72939 (14002) hydrogen bonds : bond 0.03882 ( 701) hydrogen bonds : angle 4.41308 ( 2085) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 314 time to evaluate : 0.270 Fit side-chains REVERT: E 94 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6028 (pp20) REVERT: E 112 LYS cc_start: 0.7120 (tptm) cc_final: 0.6171 (tttm) REVERT: E 124 PRO cc_start: 0.7597 (Cg_exo) cc_final: 0.7390 (Cg_endo) REVERT: E 172 LEU cc_start: 0.8838 (pp) cc_final: 0.8463 (mt) REVERT: E 187 LYS cc_start: 0.8894 (tmtt) cc_final: 0.8693 (tppt) REVERT: C 13 VAL cc_start: 0.8487 (p) cc_final: 0.8251 (m) REVERT: C 50 MET cc_start: 0.8357 (mmm) cc_final: 0.7551 (mmm) REVERT: C 56 MET cc_start: 0.6262 (mmm) cc_final: 0.6028 (mmt) REVERT: C 136 ASP cc_start: 0.8063 (m-30) cc_final: 0.7620 (m-30) REVERT: C 250 PRO cc_start: 0.8324 (Cg_exo) cc_final: 0.8074 (Cg_endo) REVERT: C 254 GLN cc_start: 0.7487 (pp30) cc_final: 0.7200 (pp30) REVERT: D 62 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6713 (pp) REVERT: D 149 LEU cc_start: 0.8903 (mt) cc_final: 0.8600 (mt) REVERT: F 23 MET cc_start: 0.7303 (mpp) cc_final: 0.6837 (mpp) REVERT: F 50 MET cc_start: 0.7945 (mmm) cc_final: 0.7702 (mmm) REVERT: F 112 LYS cc_start: 0.7824 (tttt) cc_final: 0.6948 (tmtt) REVERT: F 131 MET cc_start: 0.8006 (mmm) cc_final: 0.7556 (mmm) REVERT: F 256 TYR cc_start: 0.6030 (OUTLIER) cc_final: 0.4901 (p90) REVERT: G 111 MET cc_start: 0.6846 (mpp) cc_final: 0.6337 (mpp) REVERT: G 131 MET cc_start: 0.5953 (mmp) cc_final: 0.4832 (mtt) REVERT: G 211 MET cc_start: 0.7602 (mmt) cc_final: 0.7385 (mmm) outliers start: 35 outliers final: 28 residues processed: 334 average time/residue: 0.0809 time to fit residues: 40.0244 Evaluate side-chains 325 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 294 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 57 ASP Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 99 optimal weight: 0.0470 chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 68 GLN F 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.171553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.140054 restraints weight = 14712.167| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.75 r_work: 0.3623 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10387 Z= 0.151 Angle : 0.769 14.580 14002 Z= 0.383 Chirality : 0.046 0.407 1618 Planarity : 0.005 0.044 1764 Dihedral : 4.742 47.840 1412 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.24 % Allowed : 26.17 % Favored : 70.59 % 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 are not related in a simple way. whole: -0.09 (0.24), residues: 1313 helix: 0.92 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -3.02 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 89 TYR 0.029 0.002 TYR D 194 PHE 0.035 0.001 PHE A 34 TRP 0.024 0.001 TRP D 21 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00344 (10387) covalent geometry : angle 0.76938 (14002) hydrogen bonds : bond 0.04037 ( 701) hydrogen bonds : angle 4.52187 ( 2085) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2626 Ramachandran restraints generated. 1313 Oldfield, 0 Emsley, 1313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 294 time to evaluate : 0.421 Fit side-chains REVERT: E 94 GLU cc_start: 0.6391 (OUTLIER) cc_final: 0.6028 (pp20) REVERT: E 112 LYS cc_start: 0.7187 (tptm) cc_final: 0.6229 (tttm) REVERT: E 124 PRO cc_start: 0.7573 (Cg_exo) cc_final: 0.7344 (Cg_endo) REVERT: E 172 LEU cc_start: 0.8836 (pp) cc_final: 0.8453 (mt) REVERT: E 231 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8243 (mp) REVERT: C 250 PRO cc_start: 0.8349 (Cg_exo) cc_final: 0.8112 (Cg_endo) REVERT: C 254 GLN cc_start: 0.7497 (pp30) cc_final: 0.7204 (pp30) REVERT: D 62 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6746 (pp) REVERT: D 113 LYS cc_start: 0.7451 (ttpp) cc_final: 0.7016 (tttm) REVERT: F 23 MET cc_start: 0.7415 (mpp) cc_final: 0.6932 (mpp) REVERT: F 50 MET cc_start: 0.7974 (mmm) cc_final: 0.7739 (mmm) REVERT: F 75 MET cc_start: 0.6289 (ptm) cc_final: 0.5369 (mmp) REVERT: F 112 LYS cc_start: 0.8190 (tttt) cc_final: 0.7187 (tmtt) REVERT: F 131 MET cc_start: 0.8043 (mmm) cc_final: 0.7601 (mmm) REVERT: F 256 TYR cc_start: 0.6002 (OUTLIER) cc_final: 0.4887 (p90) REVERT: G 111 MET cc_start: 0.6867 (mpp) cc_final: 0.6332 (mpp) REVERT: G 131 MET cc_start: 0.5918 (mmp) cc_final: 0.4756 (mtt) outliers start: 36 outliers final: 28 residues processed: 314 average time/residue: 0.0840 time to fit residues: 38.7911 Evaluate side-chains 316 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 284 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 232 GLN Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 198 MET Chi-restraints excluded: chain F residue 200 ASN Chi-restraints excluded: chain F residue 256 TYR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 106 optimal weight: 0.0980 chunk 116 optimal weight: 0.9990 chunk 71 optimal weight: 0.0570 chunk 3 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 123 optimal weight: 0.8980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 68 GLN F 200 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.174111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.142183 restraints weight = 14793.549| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.79 r_work: 0.3670 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10387 Z= 0.148 Angle : 0.766 14.140 14002 Z= 0.383 Chirality : 0.046 0.399 1618 Planarity : 0.005 0.045 1764 Dihedral : 4.735 47.843 1412 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.33 % Allowed : 25.99 % Favored : 70.68 % 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 are not related in a simple way. whole: -0.05 (0.24), residues: 1313 helix: 0.94 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -3.00 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 221 TYR 0.022 0.002 TYR G 110 PHE 0.011 0.001 PHE D 212 TRP 0.024 0.001 TRP D 21 HIS 0.003 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00325 (10387) covalent geometry : angle 0.76635 (14002) hydrogen bonds : bond 0.04081 ( 701) hydrogen bonds : angle 4.51121 ( 2085) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2769.96 seconds wall clock time: 47 minutes 59.63 seconds (2879.63 seconds total)