Starting phenix.real_space_refine on Mon Jul 28 02:58:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysf_10895/07_2025/6ysf_10895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysf_10895/07_2025/6ysf_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_10895/07_2025/6ysf_10895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysf_10895/07_2025/6ysf_10895.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysf_10895/07_2025/6ysf_10895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysf_10895/07_2025/6ysf_10895.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.50, per 1000 atoms: 0.64 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.94 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: 2.81 Time building geometry restraints manager: 3.09 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.610 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- 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 : 13.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.20), 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 TRP 0.007 0.001 TRP B 19 HIS 0.002 0.001 HIS F 142 PHE 0.011 0.001 PHE D 212 TYR 0.011 0.002 TYR G 155 ARG 0.005 0.000 ARG C 116 Details of bonding type rmsd hydrogen bonds : bond 0.15394 ( 701) hydrogen bonds : angle 6.50998 ( 2085) covalent geometry : bond 0.00424 (10387) covalent geometry : angle 0.76512 (14002) *********************** 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 : 1.088 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: 0.7195 (mtp) cc_final: 0.6957 (mtp) REVERT: C 242 GLU cc_start: 0.6484 (tp30) cc_final: 0.6236 (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: 0.7615 (mtpt) cc_final: 0.7351 (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: 0.2621 time to fit residues: 130.5525 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 : 1.132 ------------------------------------------------------------------------------- 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 109 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 F 105 ASN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4064 r_free = 0.4064 target = 0.163932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.130143 restraints weight = 14725.206| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.82 r_work: 0.3495 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10387 Z= 0.168 Angle : 0.685 13.003 14002 Z= 0.350 Chirality : 0.043 0.186 1618 Planarity : 0.005 0.050 1764 Dihedral : 5.964 64.844 1425 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.71 % Allowed : 17.45 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.23), residues: 1313 helix: -0.23 (0.16), residues: 989 sheet: None (None), residues: 0 loop : -3.82 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.014 0.002 PHE B 33 TYR 0.021 0.002 TYR E 110 ARG 0.005 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 701) hydrogen bonds : angle 4.89066 ( 2085) covalent geometry : bond 0.00386 (10387) covalent geometry : angle 0.68459 (14002) *********************** 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 339 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 320 time to evaluate : 1.275 Fit side-chains REVERT: A 17 ASP cc_start: 0.7398 (t0) cc_final: 0.6842 (p0) REVERT: B 37 LEU cc_start: 0.8676 (mp) cc_final: 0.8448 (mp) REVERT: E 124 PRO cc_start: 0.7664 (Cg_exo) cc_final: 0.7241 (Cg_endo) REVERT: E 131 MET cc_start: 0.7741 (mmt) cc_final: 0.7265 (mmt) REVERT: E 240 MET cc_start: 0.7888 (tmm) cc_final: 0.7397 (tmm) REVERT: C 56 MET cc_start: 0.6287 (mmm) cc_final: 0.6084 (mmt) REVERT: C 250 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8067 (Cg_endo) REVERT: D 16 PHE cc_start: 0.8211 (m-80) cc_final: 0.7978 (m-80) REVERT: D 62 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6783 (pp) REVERT: D 82 GLN cc_start: 0.8092 (mt0) cc_final: 0.7880 (tt0) REVERT: D 113 LYS cc_start: 0.7978 (tmtp) cc_final: 0.7709 (ttpp) REVERT: F 50 MET cc_start: 0.8379 (mmm) cc_final: 0.8122 (mmm) REVERT: F 75 MET cc_start: 0.6944 (OUTLIER) cc_final: 0.6481 (ptm) REVERT: F 112 LYS cc_start: 0.7922 (tttt) cc_final: 0.7178 (tmtt) REVERT: F 131 MET cc_start: 0.7918 (mmt) cc_final: 0.7256 (mmm) REVERT: F 222 GLU cc_start: 0.8457 (mm-30) cc_final: 0.8181 (mm-30) REVERT: F 238 ARG cc_start: 0.7880 (tpm170) cc_final: 0.7666 (tmt170) REVERT: G 50 MET cc_start: 0.8914 (mmm) cc_final: 0.8398 (mmm) REVERT: G 57 ASP cc_start: 0.8372 (t70) cc_final: 0.8149 (t0) REVERT: G 71 LYS cc_start: 0.7344 (mttm) cc_final: 0.7023 (mtmt) REVERT: G 75 MET cc_start: 0.4690 (mmm) cc_final: 0.3769 (mmt) REVERT: G 111 MET cc_start: 0.6968 (mpp) cc_final: 0.6417 (mpp) REVERT: G 131 MET cc_start: 0.6506 (mmp) cc_final: 0.5272 (mtp) outliers start: 19 outliers final: 10 residues processed: 329 average time/residue: 0.2231 time to fit residues: 102.0384 Evaluate side-chains 297 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 285 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 62 LEU 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 39 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 60 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 82 GLN D 170 GLN G 83 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.167481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134319 restraints weight = 14786.599| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.81 r_work: 0.3566 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2619 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= 0.138 Angle : 0.634 14.166 14002 Z= 0.325 Chirality : 0.041 0.206 1618 Planarity : 0.005 0.050 1764 Dihedral : 4.951 32.545 1412 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.70 % Allowed : 19.06 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.23), residues: 1313 helix: 0.37 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -3.57 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.002 0.001 HIS F 142 PHE 0.013 0.001 PHE D 203 TYR 0.016 0.002 TYR G 155 ARG 0.005 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.03837 ( 701) hydrogen bonds : angle 4.59750 ( 2085) covalent geometry : bond 0.00304 (10387) covalent geometry : angle 0.63424 (14002) *********************** 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 352 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 322 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 PRO cc_start: 0.7625 (Cg_exo) cc_final: 0.7112 (Cg_endo) REVERT: E 161 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7319 (mpp) REVERT: E 240 MET cc_start: 0.8077 (tmm) cc_final: 0.7579 (tmm) REVERT: C 47 MET cc_start: 0.8126 (mmm) cc_final: 0.7843 (mmm) REVERT: C 242 GLU cc_start: 0.7748 (tp30) cc_final: 0.7333 (tp30) REVERT: C 250 PRO cc_start: 0.8366 (Cg_exo) cc_final: 0.8080 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7395 (mm-30) cc_final: 0.6999 (mt-10) REVERT: D 62 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.6784 (pp) REVERT: D 82 GLN cc_start: 0.8095 (mt0) cc_final: 0.7757 (tt0) REVERT: D 113 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7254 (tmtp) REVERT: D 238 ARG cc_start: 0.7851 (mmp-170) cc_final: 0.7544 (mmm160) REVERT: F 23 MET cc_start: 0.7344 (mpp) cc_final: 0.6665 (mpp) REVERT: F 75 MET cc_start: 0.6833 (ptt) cc_final: 0.6441 (ptm) REVERT: F 112 LYS cc_start: 0.7771 (tttt) cc_final: 0.6927 (tmtt) REVERT: F 131 MET cc_start: 0.7840 (mmt) cc_final: 0.7261 (mmm) REVERT: F 222 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8249 (mm-30) REVERT: F 238 ARG cc_start: 0.7929 (tpm170) cc_final: 0.7637 (tmt170) REVERT: G 50 MET cc_start: 0.8845 (mmm) cc_final: 0.8293 (mmm) REVERT: G 57 ASP cc_start: 0.8199 (t70) cc_final: 0.7992 (t0) REVERT: G 75 MET cc_start: 0.4648 (mmm) cc_final: 0.3835 (mmt) REVERT: G 111 MET cc_start: 0.6900 (mpp) cc_final: 0.6418 (mpp) REVERT: G 131 MET cc_start: 0.6207 (mmp) cc_final: 0.5113 (mtp) REVERT: G 222 GLU cc_start: 0.7872 (tp30) cc_final: 0.7257 (tp30) outliers start: 30 outliers final: 14 residues processed: 338 average time/residue: 0.2141 time to fit residues: 101.7883 Evaluate side-chains 292 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 275 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 13 VAL 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 127 ILE Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 62 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.2980 chunk 65 optimal weight: 0.0570 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 GLN F 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.134859 restraints weight = 14615.995| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.79 r_work: 0.3582 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2945 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= 0.133 Angle : 0.634 14.355 14002 Z= 0.323 Chirality : 0.041 0.197 1618 Planarity : 0.005 0.048 1764 Dihedral : 4.868 35.218 1412 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 2.97 % Allowed : 21.67 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.24), residues: 1313 helix: 0.60 (0.17), residues: 994 sheet: None (None), residues: 0 loop : -3.48 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.001 0.001 HIS G 142 PHE 0.014 0.001 PHE G 212 TYR 0.026 0.002 TYR C 110 ARG 0.005 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 701) hydrogen bonds : angle 4.50165 ( 2085) covalent geometry : bond 0.00295 (10387) covalent geometry : angle 0.63366 (14002) *********************** 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 338 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7208 (OUTLIER) cc_final: 0.6989 (tp) REVERT: E 240 MET cc_start: 0.8091 (tmm) cc_final: 0.7694 (tmm) REVERT: C 54 TYR cc_start: 0.8038 (m-80) cc_final: 0.7832 (m-80) REVERT: C 136 ASP cc_start: 0.7884 (m-30) cc_final: 0.7622 (m-30) REVERT: C 241 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7176 (tt0) REVERT: C 250 PRO cc_start: 0.8372 (Cg_exo) cc_final: 0.8112 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7044 (mt-10) REVERT: D 82 GLN cc_start: 0.8110 (mt0) cc_final: 0.7876 (tt0) REVERT: D 113 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7067 (tttp) REVERT: D 132 GLU cc_start: 0.7276 (tp30) cc_final: 0.7053 (tp30) REVERT: D 238 ARG cc_start: 0.7822 (mmp-170) cc_final: 0.7518 (mmm160) REVERT: F 23 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6801 (mpp) REVERT: F 75 MET cc_start: 0.6725 (ptt) cc_final: 0.6443 (ptm) REVERT: F 112 LYS cc_start: 0.7776 (tttt) cc_final: 0.6944 (tmtt) REVERT: F 131 MET cc_start: 0.7838 (mmt) cc_final: 0.7327 (mmm) REVERT: F 238 ARG cc_start: 0.7841 (tpm170) cc_final: 0.7599 (tmt170) REVERT: G 33 PHE cc_start: 0.8246 (m-80) cc_final: 0.7911 (m-80) REVERT: G 50 MET cc_start: 0.8712 (mmm) cc_final: 0.8223 (mmm) REVERT: G 71 LYS cc_start: 0.7252 (mttm) cc_final: 0.6936 (mtmt) REVERT: G 111 MET cc_start: 0.6858 (mpp) cc_final: 0.6336 (mpp) REVERT: G 131 MET cc_start: 0.6082 (mmp) cc_final: 0.5061 (mtt) outliers start: 33 outliers final: 23 residues processed: 316 average time/residue: 0.2055 time to fit residues: 91.9856 Evaluate side-chains 303 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 239 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 127 ILE 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 75 MET Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE 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 23 MET Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN F 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.162241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130043 restraints weight = 14745.790| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.10 r_work: 0.3483 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2920 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= 0.209 Angle : 0.694 14.246 14002 Z= 0.352 Chirality : 0.045 0.191 1618 Planarity : 0.005 0.049 1764 Dihedral : 5.161 39.253 1412 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.77 % Allowed : 21.40 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.23), residues: 1313 helix: 0.42 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -3.44 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 21 HIS 0.003 0.001 HIS G 142 PHE 0.013 0.002 PHE B 40 TYR 0.020 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 701) hydrogen bonds : angle 4.80478 ( 2085) covalent geometry : bond 0.00499 (10387) covalent geometry : angle 0.69407 (14002) *********************** 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 340 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 287 time to evaluate : 1.304 Fit side-chains REVERT: A 14 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6874 (mp) REVERT: E 78 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.7052 (tp) REVERT: E 94 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6106 (pp20) REVERT: E 231 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8358 (mp) REVERT: E 240 MET cc_start: 0.8151 (tmm) cc_final: 0.7656 (tmm) REVERT: E 244 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8737 (mm) REVERT: C 56 MET cc_start: 0.6580 (mmm) cc_final: 0.6097 (mmt) REVERT: C 123 GLU cc_start: 0.7199 (pt0) cc_final: 0.6750 (tt0) REVERT: C 136 ASP cc_start: 0.8037 (m-30) cc_final: 0.7792 (m-30) REVERT: C 250 PRO cc_start: 0.8404 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7063 (mt-10) REVERT: D 62 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6718 (pp) REVERT: D 82 GLN cc_start: 0.8262 (mt0) cc_final: 0.7849 (tt0) REVERT: D 112 LYS cc_start: 0.8172 (mtmt) cc_final: 0.7920 (mttm) REVERT: D 132 GLU cc_start: 0.7411 (tp30) cc_final: 0.7133 (tp30) REVERT: D 252 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8392 (tp30) REVERT: F 23 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6824 (mpp) REVERT: F 75 MET cc_start: 0.6795 (ptt) cc_final: 0.6588 (ptm) REVERT: F 112 LYS cc_start: 0.7929 (tttt) cc_final: 0.7164 (tmtt) REVERT: F 238 ARG cc_start: 0.7946 (tpm170) cc_final: 0.7663 (tmt170) REVERT: G 50 MET cc_start: 0.8816 (mmm) cc_final: 0.8478 (mmm) REVERT: G 75 MET cc_start: 0.4185 (mmt) cc_final: 0.3622 (mmt) REVERT: G 111 MET cc_start: 0.6679 (mpp) cc_final: 0.6117 (mpp) REVERT: G 131 MET cc_start: 0.6286 (mmp) cc_final: 0.5105 (mtp) outliers start: 53 outliers final: 34 residues processed: 311 average time/residue: 0.2102 time to fit residues: 93.2304 Evaluate side-chains 307 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 265 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 30 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 64 ILE 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 172 LEU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 82 GLN Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 127 ILE 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 13 VAL Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 198 MET 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 138 MET Chi-restraints excluded: chain G residue 148 MET Chi-restraints excluded: chain G residue 164 THR 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 50 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 23 optimal weight: 0.0770 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 0.0170 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- 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 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.168389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135148 restraints weight = 14720.985| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.81 r_work: 0.3570 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3248 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= 0.132 Angle : 0.642 14.017 14002 Z= 0.327 Chirality : 0.042 0.208 1618 Planarity : 0.005 0.042 1764 Dihedral : 4.884 47.447 1412 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.42 % Allowed : 23.02 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1313 helix: 0.75 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -3.16 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 21 HIS 0.001 0.001 HIS F 142 PHE 0.012 0.001 PHE D 203 TYR 0.020 0.002 TYR G 155 ARG 0.007 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 701) hydrogen bonds : angle 4.48012 ( 2085) covalent geometry : bond 0.00290 (10387) covalent geometry : angle 0.64210 (14002) *********************** 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 338 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 300 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6868 (tp) REVERT: E 94 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6075 (pp20) REVERT: E 124 PRO cc_start: 0.7696 (Cg_exo) cc_final: 0.7332 (Cg_endo) REVERT: E 231 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8356 (mp) REVERT: E 240 MET cc_start: 0.7951 (tmm) cc_final: 0.7609 (tmm) REVERT: C 56 MET cc_start: 0.6546 (mmm) cc_final: 0.6312 (mmt) REVERT: C 136 ASP cc_start: 0.8068 (m-30) cc_final: 0.7826 (m-30) REVERT: C 238 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7695 (ttt-90) REVERT: C 250 PRO cc_start: 0.8340 (Cg_exo) cc_final: 0.8105 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6857 (pp) REVERT: D 82 GLN cc_start: 0.8107 (mt0) cc_final: 0.7771 (tt0) REVERT: D 112 LYS cc_start: 0.8230 (mtmt) cc_final: 0.8024 (mttm) REVERT: D 132 GLU cc_start: 0.7222 (tp30) cc_final: 0.6901 (tp30) REVERT: D 252 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: F 23 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.6662 (mpp) REVERT: F 75 MET cc_start: 0.6786 (ptt) cc_final: 0.6516 (ptm) REVERT: F 112 LYS cc_start: 0.7885 (tttt) cc_final: 0.7099 (tmtt) REVERT: F 131 MET cc_start: 0.7782 (mmm) cc_final: 0.7560 (mmm) REVERT: F 238 ARG cc_start: 0.7879 (tpm170) cc_final: 0.7609 (tmt170) REVERT: G 50 MET cc_start: 0.8661 (mmm) cc_final: 0.8260 (mmm) REVERT: G 111 MET cc_start: 0.6773 (mpp) cc_final: 0.6235 (mpp) REVERT: G 131 MET cc_start: 0.6104 (mmp) cc_final: 0.5062 (mtt) REVERT: G 241 GLU cc_start: 0.7175 (mp0) cc_final: 0.6848 (mp0) outliers start: 38 outliers final: 22 residues processed: 316 average time/residue: 0.2793 time to fit residues: 124.7342 Evaluate side-chains 305 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 15 ARG Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 231 ILE 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 D residue 75 MET Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 198 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 91 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 115 optimal weight: 0.0370 chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 0.4980 chunk 127 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN 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 = 0.4105 r_free = 0.4105 target = 0.167690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.134307 restraints weight = 14884.257| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.82 r_work: 0.3571 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3410 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= 0.138 Angle : 0.655 13.613 14002 Z= 0.332 Chirality : 0.042 0.193 1618 Planarity : 0.005 0.044 1764 Dihedral : 4.841 46.432 1412 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.87 % Allowed : 23.47 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1313 helix: 0.81 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -3.13 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.017 0.001 PHE E 33 TYR 0.018 0.002 TYR G 155 ARG 0.006 0.000 ARG D 221 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 701) hydrogen bonds : angle 4.49007 ( 2085) covalent geometry : bond 0.00313 (10387) covalent geometry : angle 0.65474 (14002) *********************** 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 335 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 292 time to evaluate : 1.339 Fit side-chains revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.6079 (pp20) REVERT: E 231 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8321 (mp) REVERT: E 240 MET cc_start: 0.8030 (tmm) cc_final: 0.7655 (tmm) REVERT: C 136 ASP cc_start: 0.8069 (m-30) cc_final: 0.7807 (m-30) REVERT: C 238 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7708 (ttt-90) REVERT: C 250 PRO cc_start: 0.8425 (Cg_exo) cc_final: 0.8197 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6761 (pp) REVERT: D 82 GLN cc_start: 0.8122 (mt0) cc_final: 0.7796 (tt0) REVERT: D 101 ASP cc_start: 0.7652 (p0) cc_final: 0.7349 (t0) REVERT: D 112 LYS cc_start: 0.8065 (mtmt) cc_final: 0.7857 (mttm) REVERT: D 252 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8295 (tp30) REVERT: F 23 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6709 (mpp) REVERT: F 75 MET cc_start: 0.6676 (ptt) cc_final: 0.6378 (ptm) REVERT: F 112 LYS cc_start: 0.7922 (tttt) cc_final: 0.7109 (tmtt) REVERT: F 238 ARG cc_start: 0.7850 (tpm170) cc_final: 0.7615 (tmt170) REVERT: F 256 TYR cc_start: 0.6131 (OUTLIER) cc_final: 0.4492 (p90) REVERT: G 50 MET cc_start: 0.8649 (mmm) cc_final: 0.8278 (mmm) REVERT: G 111 MET cc_start: 0.6780 (mpp) cc_final: 0.6322 (mpp) REVERT: G 131 MET cc_start: 0.6018 (mmp) cc_final: 0.5161 (mtt) REVERT: G 241 GLU cc_start: 0.7029 (mp0) cc_final: 0.6726 (mp0) outliers start: 43 outliers final: 29 residues processed: 314 average time/residue: 0.2337 time to fit residues: 105.2216 Evaluate side-chains 310 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 275 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 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 94 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 231 ILE 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 D residue 75 MET Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE 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 15 CYS Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 30 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN C 68 GLN D 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 = 0.4101 r_free = 0.4101 target = 0.167311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133739 restraints weight = 14907.754| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.82 r_work: 0.3551 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3494 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= 0.151 Angle : 0.688 13.887 14002 Z= 0.344 Chirality : 0.043 0.199 1618 Planarity : 0.005 0.044 1764 Dihedral : 4.860 45.366 1412 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 3.78 % Allowed : 23.83 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.24), residues: 1313 helix: 0.77 (0.17), residues: 980 sheet: None (None), residues: 0 loop : -3.08 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.018 0.002 PHE E 33 TYR 0.026 0.002 TYR D 110 ARG 0.008 0.000 ARG D 221 Details of bonding type rmsd hydrogen bonds : bond 0.03980 ( 701) hydrogen bonds : angle 4.53818 ( 2085) covalent geometry : bond 0.00349 (10387) covalent geometry : angle 0.68826 (14002) *********************** 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 326 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 284 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: E 73 ASN cc_start: 0.7887 (m-40) cc_final: 0.7661 (m110) REVERT: E 94 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.6002 (pp20) REVERT: E 231 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8360 (mp) REVERT: E 240 MET cc_start: 0.7964 (tmm) cc_final: 0.7690 (tmm) REVERT: C 56 MET cc_start: 0.6285 (mmm) cc_final: 0.5473 (mmt) REVERT: C 60 LYS cc_start: 0.7113 (tttm) cc_final: 0.6385 (mmtt) REVERT: C 136 ASP cc_start: 0.8136 (m-30) cc_final: 0.7898 (m-30) REVERT: C 238 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7760 (ttt-90) REVERT: C 250 PRO cc_start: 0.8417 (Cg_exo) cc_final: 0.8191 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6825 (pp) REVERT: D 82 GLN cc_start: 0.8084 (mt0) cc_final: 0.7787 (tt0) REVERT: D 101 ASP cc_start: 0.7568 (p0) cc_final: 0.7335 (t0) REVERT: D 112 LYS cc_start: 0.7883 (mtmt) cc_final: 0.7646 (mttm) REVERT: D 252 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: F 23 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6673 (mpp) REVERT: F 75 MET cc_start: 0.6638 (ptt) cc_final: 0.6421 (ptm) REVERT: F 112 LYS cc_start: 0.7969 (tttt) cc_final: 0.7234 (tmtt) REVERT: F 256 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.4536 (p90) REVERT: G 50 MET cc_start: 0.8668 (mmm) cc_final: 0.8326 (mmm) REVERT: G 111 MET cc_start: 0.6798 (mpp) cc_final: 0.6332 (mpp) REVERT: G 131 MET cc_start: 0.6078 (mmp) cc_final: 0.5035 (mtt) outliers start: 42 outliers final: 28 residues processed: 308 average time/residue: 0.2023 time to fit residues: 89.5354 Evaluate side-chains 306 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 272 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 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 94 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 231 ILE 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 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 110 TYR Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE 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 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 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 111 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 121 optimal weight: 0.0020 chunk 110 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN 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 = 0.4131 r_free = 0.4131 target = 0.169991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.136675 restraints weight = 14819.702| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.83 r_work: 0.3595 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10387 Z= 0.139 Angle : 0.688 13.660 14002 Z= 0.345 Chirality : 0.042 0.189 1618 Planarity : 0.005 0.041 1764 Dihedral : 4.784 44.999 1412 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.69 % Allowed : 23.92 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.24), residues: 1313 helix: 0.82 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -3.12 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 21 HIS 0.002 0.001 HIS C 142 PHE 0.035 0.002 PHE A 34 TYR 0.027 0.002 TYR G 155 ARG 0.007 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 701) hydrogen bonds : angle 4.48246 ( 2085) covalent geometry : bond 0.00311 (10387) covalent geometry : angle 0.68845 (14002) *********************** 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 341 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 1.438 Fit side-chains REVERT: E 94 GLU cc_start: 0.6442 (OUTLIER) cc_final: 0.6018 (pp20) REVERT: E 187 LYS cc_start: 0.8522 (ptpt) cc_final: 0.8298 (tmtt) REVERT: E 231 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8341 (mp) REVERT: E 240 MET cc_start: 0.7965 (tmm) cc_final: 0.7753 (tmm) REVERT: C 56 MET cc_start: 0.6388 (mmm) cc_final: 0.5806 (mmt) REVERT: C 60 LYS cc_start: 0.6980 (tttm) cc_final: 0.6251 (mmtt) REVERT: C 136 ASP cc_start: 0.8169 (m-30) cc_final: 0.7941 (m-30) REVERT: C 250 PRO cc_start: 0.8385 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.6890 (pp) REVERT: D 82 GLN cc_start: 0.8056 (mt0) cc_final: 0.7709 (tt0) REVERT: D 252 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8025 (tp30) REVERT: F 23 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.6646 (mpp) REVERT: F 75 MET cc_start: 0.6804 (ptt) cc_final: 0.6554 (ptm) REVERT: F 112 LYS cc_start: 0.7896 (tttt) cc_final: 0.7015 (tmtt) REVERT: F 256 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.4547 (p90) REVERT: G 50 MET cc_start: 0.8637 (mmm) cc_final: 0.8220 (mmm) REVERT: G 111 MET cc_start: 0.6810 (mpp) cc_final: 0.6358 (mpp) REVERT: G 131 MET cc_start: 0.5974 (mmp) cc_final: 0.5045 (mtt) REVERT: G 241 GLU cc_start: 0.7109 (mp0) cc_final: 0.6831 (mp0) outliers start: 41 outliers final: 27 residues processed: 322 average time/residue: 0.2082 time to fit residues: 96.6997 Evaluate side-chains 312 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 279 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 231 ILE 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 D residue 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE 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 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 148 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 58 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 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 = 0.4125 r_free = 0.4125 target = 0.169766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.138063 restraints weight = 14929.587| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 1.73 r_work: 0.3587 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10387 Z= 0.153 Angle : 0.745 13.579 14002 Z= 0.371 Chirality : 0.045 0.237 1618 Planarity : 0.005 0.041 1764 Dihedral : 4.847 45.511 1412 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.78 % Allowed : 24.19 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1313 helix: 0.80 (0.17), residues: 975 sheet: None (None), residues: 0 loop : -2.94 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 21 HIS 0.003 0.001 HIS C 142 PHE 0.021 0.002 PHE E 33 TYR 0.036 0.003 TYR F 110 ARG 0.007 0.000 ARG E 89 Details of bonding type rmsd hydrogen bonds : bond 0.04144 ( 701) hydrogen bonds : angle 4.58391 ( 2085) covalent geometry : bond 0.00353 (10387) covalent geometry : angle 0.74462 (14002) ********************** 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 344 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 302 time to evaluate : 1.256 Fit side-chains REVERT: A 15 ARG cc_start: 0.7422 (OUTLIER) cc_final: 0.7054 (ttp-110) REVERT: E 94 GLU cc_start: 0.6435 (OUTLIER) cc_final: 0.6003 (pp20) REVERT: E 187 LYS cc_start: 0.8535 (ptpt) cc_final: 0.8226 (tmtt) REVERT: E 231 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8364 (mp) REVERT: E 240 MET cc_start: 0.7933 (tmm) cc_final: 0.7706 (tmm) REVERT: C 56 MET cc_start: 0.6457 (mmm) cc_final: 0.6118 (mmt) REVERT: C 136 ASP cc_start: 0.8143 (m-30) cc_final: 0.7933 (m-30) REVERT: C 250 PRO cc_start: 0.8388 (Cg_exo) cc_final: 0.8181 (Cg_endo) REVERT: D 62 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.6833 (pp) REVERT: D 82 GLN cc_start: 0.8036 (mt0) cc_final: 0.7494 (tt0) REVERT: D 252 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8028 (tp30) REVERT: F 23 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.6761 (mpp) REVERT: F 75 MET cc_start: 0.6833 (ptt) cc_final: 0.6529 (ptm) REVERT: F 112 LYS cc_start: 0.7859 (tttt) cc_final: 0.7007 (tmtt) REVERT: F 256 TYR cc_start: 0.6203 (OUTLIER) cc_final: 0.4686 (p90) REVERT: G 50 MET cc_start: 0.8651 (mmm) cc_final: 0.8240 (mmm) REVERT: G 111 MET cc_start: 0.6796 (mpp) cc_final: 0.6302 (mpp) REVERT: G 131 MET cc_start: 0.6067 (mmp) cc_final: 0.4971 (mtt) REVERT: G 241 GLU cc_start: 0.7086 (mp0) cc_final: 0.6817 (mp0) outliers start: 42 outliers final: 27 residues processed: 323 average time/residue: 0.2031 time to fit residues: 94.2292 Evaluate side-chains 316 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 282 time to evaluate : 1.217 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 231 ILE 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 13 VAL Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 252 GLU Chi-restraints excluded: chain F residue 23 MET Chi-restraints excluded: chain F residue 40 PHE 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 20 LEU 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 148 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 1 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 20.0000 chunk 27 optimal weight: 0.9990 chunk 113 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN D 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 = 0.4128 r_free = 0.4128 target = 0.169694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137531 restraints weight = 14854.413| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.75 r_work: 0.3583 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 10387 Z= 0.158 Angle : 0.758 13.547 14002 Z= 0.381 Chirality : 0.045 0.255 1618 Planarity : 0.005 0.041 1764 Dihedral : 4.859 45.233 1412 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.24 % Allowed : 25.99 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.24), residues: 1313 helix: 0.77 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -2.91 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 21 HIS 0.004 0.001 HIS C 142 PHE 0.020 0.002 PHE E 33 TYR 0.035 0.002 TYR F 110 ARG 0.009 0.000 ARG D 89 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 701) hydrogen bonds : angle 4.67631 ( 2085) covalent geometry : bond 0.00367 (10387) covalent geometry : angle 0.75821 (14002) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6492.00 seconds wall clock time: 114 minutes 37.71 seconds (6877.71 seconds total)