Starting phenix.real_space_refine on Fri Feb 14 07:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ysf_10895/02_2025/6ysf_10895.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ysf_10895/02_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_10895/02_2025/6ysf_10895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ysf_10895/02_2025/6ysf_10895.map" model { file = "/net/cci-nas-00/data/ceres_data/6ysf_10895/02_2025/6ysf_10895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ysf_10895/02_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-5592/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: 6.44, per 1000 atoms: 0.63 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: 2.97 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: 0.86 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: 3.04 Time building geometry restraints manager: 3.35 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: 0.980 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 25.640 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.620 ------------------------------------------------------------------------------- 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= 0.267 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 *********************** 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 : 1.090 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: 0.2495 time to fit residues: 124.5474 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 : 1.202 ------------------------------------------------------------------------------- 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 = 0.130133 restraints weight = 14725.227| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.82 r_work: 0.3494 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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= 0.239 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 *********************** 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 : 1.181 Fit side-chains REVERT: A 17 ASP cc_start: 0.7405 (t0) cc_final: 0.6840 (p0) REVERT: B 37 LEU cc_start: 0.8675 (mp) cc_final: 0.8448 (mp) REVERT: E 124 PRO cc_start: 0.7666 (Cg_exo) cc_final: 0.7243 (Cg_endo) REVERT: E 131 MET cc_start: 0.7744 (mmt) cc_final: 0.7266 (mmt) REVERT: E 240 MET cc_start: 0.7887 (tmm) cc_final: 0.7398 (tmm) REVERT: C 56 MET cc_start: 0.6291 (mmm) cc_final: 0.6085 (mmt) REVERT: C 250 PRO cc_start: 0.8343 (Cg_exo) cc_final: 0.8069 (Cg_endo) REVERT: D 16 PHE cc_start: 0.8209 (m-80) cc_final: 0.7977 (m-80) REVERT: D 62 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6784 (pp) REVERT: D 82 GLN cc_start: 0.8087 (mt0) cc_final: 0.7881 (tt0) REVERT: D 113 LYS cc_start: 0.7955 (tmtp) cc_final: 0.7693 (ttpp) REVERT: F 50 MET cc_start: 0.8377 (mmm) cc_final: 0.8120 (mmm) REVERT: F 75 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6471 (ptm) REVERT: F 112 LYS cc_start: 0.7923 (tttt) cc_final: 0.7181 (tmtt) REVERT: F 131 MET cc_start: 0.7921 (mmt) cc_final: 0.7263 (mmm) REVERT: F 222 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8169 (mm-30) REVERT: F 238 ARG cc_start: 0.7877 (tpm170) cc_final: 0.7664 (tmt170) REVERT: G 50 MET cc_start: 0.8916 (mmm) cc_final: 0.8400 (mmm) REVERT: G 57 ASP cc_start: 0.8374 (t70) cc_final: 0.8149 (t0) REVERT: G 71 LYS cc_start: 0.7345 (mttm) cc_final: 0.7022 (mtmt) REVERT: G 75 MET cc_start: 0.4686 (mmm) cc_final: 0.3773 (mmt) REVERT: G 111 MET cc_start: 0.6973 (mpp) cc_final: 0.6427 (mpp) REVERT: G 131 MET cc_start: 0.6502 (mmp) cc_final: 0.5273 (mtp) outliers start: 19 outliers final: 10 residues processed: 329 average time/residue: 0.2318 time to fit residues: 106.1594 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 : 1.099 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 10.0000 chunk 60 optimal weight: 0.0270 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: 7.9990 chunk 8 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.167115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.133581 restraints weight = 14788.468| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 1.83 r_work: 0.3556 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2547 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= 0.189 Angle : 0.640 14.062 14002 Z= 0.328 Chirality : 0.041 0.199 1618 Planarity : 0.005 0.050 1764 Dihedral : 4.985 32.034 1412 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.70 % Allowed : 19.42 % Favored : 77.88 % 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: -0.94 (0.23), residues: 1313 helix: 0.32 (0.17), residues: 992 sheet: None (None), residues: 0 loop : -3.59 (0.30), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 21 HIS 0.002 0.001 HIS F 142 PHE 0.013 0.001 PHE D 203 TYR 0.018 0.002 TYR G 155 ARG 0.005 0.000 ARG E 89 *********************** 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 347 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 317 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 124 PRO cc_start: 0.7639 (Cg_exo) cc_final: 0.7110 (Cg_endo) REVERT: E 161 MET cc_start: 0.7962 (OUTLIER) cc_final: 0.7278 (mpp) REVERT: E 240 MET cc_start: 0.8052 (tmm) cc_final: 0.7563 (tmm) REVERT: C 47 MET cc_start: 0.8120 (mmm) cc_final: 0.7825 (mmm) REVERT: C 250 PRO cc_start: 0.8358 (Cg_exo) cc_final: 0.8071 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7043 (mt-10) REVERT: D 62 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6796 (pp) REVERT: D 82 GLN cc_start: 0.8128 (mt0) cc_final: 0.7760 (tt0) REVERT: D 238 ARG cc_start: 0.7817 (mmp-170) cc_final: 0.7498 (mmm160) REVERT: F 23 MET cc_start: 0.7357 (mpp) cc_final: 0.6641 (mpp) REVERT: F 50 MET cc_start: 0.8253 (mmm) cc_final: 0.7998 (mmm) REVERT: F 75 MET cc_start: 0.6790 (ptt) cc_final: 0.6404 (ptm) REVERT: F 112 LYS cc_start: 0.7813 (tttt) cc_final: 0.6995 (tmtt) REVERT: F 131 MET cc_start: 0.7849 (mmt) cc_final: 0.7283 (mmm) REVERT: F 222 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8181 (mm-30) REVERT: F 238 ARG cc_start: 0.7919 (tpm170) cc_final: 0.7632 (tmt170) REVERT: G 50 MET cc_start: 0.8838 (mmm) cc_final: 0.8274 (mmm) REVERT: G 75 MET cc_start: 0.4668 (mmm) cc_final: 0.3856 (mmt) REVERT: G 111 MET cc_start: 0.6930 (mpp) cc_final: 0.6449 (mpp) REVERT: G 131 MET cc_start: 0.6191 (mmp) cc_final: 0.5109 (mtp) REVERT: G 132 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7268 (mm-30) outliers start: 30 outliers final: 16 residues processed: 334 average time/residue: 0.2196 time to fit residues: 102.3179 Evaluate side-chains 297 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 279 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 172 LEU 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 252 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 122 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 0.0570 chunk 65 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.168200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134750 restraints weight = 14634.394| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.81 r_work: 0.3574 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10387 Z= 0.185 Angle : 0.634 14.118 14002 Z= 0.323 Chirality : 0.041 0.196 1618 Planarity : 0.005 0.049 1764 Dihedral : 4.887 34.760 1412 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.06 % Allowed : 21.67 % Favored : 75.27 % 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: -0.60 (0.24), residues: 1313 helix: 0.57 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -3.47 (0.30), residues: 322 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 0.013 0.001 PHE D 203 TYR 0.028 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** 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 337 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 303 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7154 (OUTLIER) cc_final: 0.6897 (tp) REVERT: E 161 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7410 (mpp) REVERT: E 240 MET cc_start: 0.8094 (tmm) cc_final: 0.7694 (tmm) REVERT: C 172 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7219 (mt) REVERT: C 241 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7131 (tt0) REVERT: C 250 PRO cc_start: 0.8375 (Cg_exo) cc_final: 0.8119 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7052 (mt-10) REVERT: D 82 GLN cc_start: 0.8160 (mt0) cc_final: 0.7924 (tt0) REVERT: D 132 GLU cc_start: 0.7351 (tp30) cc_final: 0.7100 (tp30) REVERT: D 238 ARG cc_start: 0.7826 (mmp-170) cc_final: 0.7520 (mmm160) REVERT: F 23 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6793 (mpp) REVERT: F 75 MET cc_start: 0.6757 (ptt) cc_final: 0.6459 (ptm) REVERT: F 112 LYS cc_start: 0.7788 (tttt) cc_final: 0.6964 (tmtt) REVERT: F 131 MET cc_start: 0.7823 (mmt) cc_final: 0.7331 (mmm) REVERT: F 238 ARG cc_start: 0.7895 (tpm170) cc_final: 0.7626 (tmt170) REVERT: G 33 PHE cc_start: 0.8248 (m-80) cc_final: 0.7969 (m-80) REVERT: G 50 MET cc_start: 0.8737 (mmm) cc_final: 0.8248 (mmm) REVERT: G 75 MET cc_start: 0.4668 (mmm) cc_final: 0.3937 (mmt) REVERT: G 111 MET cc_start: 0.6862 (mpp) cc_final: 0.6364 (mpp) REVERT: G 131 MET cc_start: 0.6123 (mmp) cc_final: 0.5080 (mtt) REVERT: G 212 PHE cc_start: 0.7678 (t80) cc_final: 0.7476 (t80) REVERT: G 222 GLU cc_start: 0.7823 (tp30) cc_final: 0.7251 (tp30) outliers start: 34 outliers final: 22 residues processed: 314 average time/residue: 0.2078 time to fit residues: 92.5882 Evaluate side-chains 309 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 283 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 172 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 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 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 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 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 60 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 129 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 232 GLN C 170 GLN F 170 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.165233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131756 restraints weight = 14763.999| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 1.80 r_work: 0.3533 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10387 Z= 0.235 Angle : 0.659 13.928 14002 Z= 0.334 Chirality : 0.043 0.210 1618 Planarity : 0.005 0.049 1764 Dihedral : 5.008 38.847 1412 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 4.05 % Allowed : 21.94 % Favored : 74.01 % 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: -0.54 (0.24), residues: 1313 helix: 0.58 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -3.25 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.012 0.002 PHE D 203 TYR 0.042 0.002 TYR C 110 ARG 0.007 0.000 ARG E 89 *********************** 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 333 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 288 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: E 78 ILE cc_start: 0.7159 (OUTLIER) cc_final: 0.6957 (tp) REVERT: E 94 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6102 (pp20) REVERT: E 161 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7517 (mpp) REVERT: E 240 MET cc_start: 0.8017 (tmm) cc_final: 0.7577 (tmm) REVERT: C 56 MET cc_start: 0.6466 (mmm) cc_final: 0.6164 (mmt) REVERT: C 241 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7341 (tt0) REVERT: C 250 PRO cc_start: 0.8367 (Cg_exo) cc_final: 0.8153 (Cg_endo) REVERT: C 252 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7135 (mt-10) REVERT: D 62 LEU cc_start: 0.7309 (OUTLIER) cc_final: 0.6750 (pp) REVERT: D 132 GLU cc_start: 0.7319 (tp30) cc_final: 0.7099 (tp30) REVERT: D 252 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8353 (tp30) REVERT: F 23 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.6615 (mpp) REVERT: F 112 LYS cc_start: 0.7879 (tttt) cc_final: 0.7090 (tmtt) REVERT: F 131 MET cc_start: 0.7837 (mmt) cc_final: 0.7354 (mmm) REVERT: F 238 ARG cc_start: 0.7818 (tpm170) cc_final: 0.7614 (tmt170) REVERT: G 50 MET cc_start: 0.8729 (mmm) cc_final: 0.8324 (mmm) REVERT: G 75 MET cc_start: 0.4818 (mmm) cc_final: 0.3988 (mmt) REVERT: G 111 MET cc_start: 0.6832 (mpp) cc_final: 0.6287 (mpp) REVERT: G 131 MET cc_start: 0.6192 (mmp) cc_final: 0.5106 (mtt) outliers start: 45 outliers final: 32 residues processed: 311 average time/residue: 0.2055 time to fit residues: 90.9595 Evaluate side-chains 305 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 267 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 161 MET Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 172 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 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 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: 0.9990 chunk 116 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN F 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.168010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134665 restraints weight = 14694.272| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.80 r_work: 0.3566 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10387 Z= 0.190 Angle : 0.639 13.738 14002 Z= 0.326 Chirality : 0.042 0.214 1618 Planarity : 0.005 0.043 1764 Dihedral : 4.860 45.668 1412 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 3.24 % Allowed : 24.10 % 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: -0.37 (0.24), residues: 1313 helix: 0.70 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -3.23 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.013 0.001 PHE D 203 TYR 0.038 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** 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 337 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 301 time to evaluate : 1.184 Fit side-chains revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.6110 (pp20) REVERT: E 124 PRO cc_start: 0.7644 (Cg_exo) cc_final: 0.7276 (Cg_endo) REVERT: E 161 MET cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (mpp) REVERT: E 240 MET cc_start: 0.8013 (tmm) cc_final: 0.7608 (tmm) REVERT: E 244 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8631 (mm) REVERT: C 56 MET cc_start: 0.6623 (mmm) cc_final: 0.6362 (mmt) REVERT: C 241 GLU cc_start: 0.7620 (tm-30) cc_final: 0.7245 (tt0) REVERT: D 62 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6857 (pp) REVERT: D 132 GLU cc_start: 0.7305 (tp30) cc_final: 0.7085 (tp30) REVERT: F 23 MET cc_start: 0.7371 (OUTLIER) cc_final: 0.6646 (mpp) REVERT: F 112 LYS cc_start: 0.7836 (tttt) cc_final: 0.6993 (tmtt) REVERT: F 131 MET cc_start: 0.7801 (mmt) cc_final: 0.7409 (mmm) REVERT: G 33 PHE cc_start: 0.8241 (m-10) cc_final: 0.8036 (m-80) REVERT: G 50 MET cc_start: 0.8659 (mmm) cc_final: 0.8222 (mmm) REVERT: G 75 MET cc_start: 0.4802 (mmm) cc_final: 0.4595 (mmt) REVERT: G 111 MET cc_start: 0.6799 (mpp) cc_final: 0.6302 (mpp) REVERT: G 131 MET cc_start: 0.6025 (mmp) cc_final: 0.5075 (mtt) REVERT: G 241 GLU cc_start: 0.7155 (mp0) cc_final: 0.6823 (mp0) outliers start: 36 outliers final: 25 residues processed: 318 average time/residue: 0.2157 time to fit residues: 96.8798 Evaluate side-chains 308 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 30 LEU 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 161 MET Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 244 LEU 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 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 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: 0.0980 chunk 115 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 104 optimal weight: 0.0370 chunk 127 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 73 ASN C 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.170568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.137149 restraints weight = 14850.473| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.81 r_work: 0.3595 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3538 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= 0.180 Angle : 0.647 13.548 14002 Z= 0.331 Chirality : 0.042 0.202 1618 Planarity : 0.005 0.043 1764 Dihedral : 4.797 45.448 1412 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.88 % Allowed : 24.28 % Favored : 72.84 % 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: -0.18 (0.24), residues: 1313 helix: 0.83 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -3.13 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 21 HIS 0.001 0.001 HIS G 142 PHE 0.012 0.001 PHE D 203 TYR 0.028 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** 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 344 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 312 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: E 73 ASN cc_start: 0.7863 (m-40) cc_final: 0.7612 (m110) REVERT: E 94 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.6074 (pp20) REVERT: E 112 LYS cc_start: 0.7155 (tptm) cc_final: 0.6344 (tttm) REVERT: E 187 LYS cc_start: 0.8941 (tmtt) cc_final: 0.8666 (tppt) REVERT: E 240 MET cc_start: 0.7869 (tmm) cc_final: 0.7466 (tmm) REVERT: D 62 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6836 (pp) REVERT: D 101 ASP cc_start: 0.7593 (p0) cc_final: 0.7360 (t0) REVERT: D 112 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7429 (mttm) REVERT: D 132 GLU cc_start: 0.7362 (tp30) cc_final: 0.7145 (tp30) REVERT: F 16 PHE cc_start: 0.7271 (m-80) cc_final: 0.7016 (m-80) REVERT: F 23 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.6596 (mpp) REVERT: F 75 MET cc_start: 0.6089 (ptm) cc_final: 0.5530 (mmm) REVERT: F 112 LYS cc_start: 0.7863 (tttt) cc_final: 0.7055 (tmtt) REVERT: F 131 MET cc_start: 0.7742 (mmt) cc_final: 0.7434 (mmm) REVERT: G 50 MET cc_start: 0.8628 (mmm) cc_final: 0.8207 (mmm) REVERT: G 75 MET cc_start: 0.4766 (mmm) cc_final: 0.4555 (mmt) REVERT: G 111 MET cc_start: 0.6856 (mpp) cc_final: 0.6301 (mpp) REVERT: G 131 MET cc_start: 0.6104 (mmp) cc_final: 0.5233 (mtt) outliers start: 32 outliers final: 26 residues processed: 330 average time/residue: 0.2049 time to fit residues: 96.5663 Evaluate side-chains 309 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain C residue 81 ILE Chi-restraints excluded: chain C residue 90 LYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 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 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 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 148 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 98 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 0.0980 chunk 107 optimal weight: 0.0070 chunk 74 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 GLN F 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.170783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137434 restraints weight = 14822.990| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 1.81 r_work: 0.3596 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3736 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= 0.187 Angle : 0.669 13.486 14002 Z= 0.339 Chirality : 0.042 0.190 1618 Planarity : 0.005 0.045 1764 Dihedral : 4.739 44.701 1412 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.42 % Allowed : 24.19 % 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: -0.11 (0.24), residues: 1313 helix: 0.89 (0.17), residues: 982 sheet: None (None), residues: 0 loop : -3.04 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.033 0.002 PHE B 33 TYR 0.024 0.002 TYR C 110 ARG 0.006 0.000 ARG E 89 *********************** 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 342 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 304 time to evaluate : 1.258 Fit side-chains revert: symmetry clash REVERT: A 40 PHE cc_start: 0.5184 (p90) cc_final: 0.4298 (t80) REVERT: E 73 ASN cc_start: 0.7849 (m-40) cc_final: 0.7598 (m110) REVERT: E 94 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6029 (pp20) REVERT: E 112 LYS cc_start: 0.7214 (tptm) cc_final: 0.6320 (tttm) REVERT: E 172 LEU cc_start: 0.8900 (pp) cc_final: 0.8385 (mt) REVERT: C 56 MET cc_start: 0.6395 (mmm) cc_final: 0.6046 (mmt) REVERT: C 241 GLU cc_start: 0.7828 (tm-30) cc_final: 0.7155 (tt0) REVERT: D 62 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6863 (pp) REVERT: D 112 LYS cc_start: 0.7912 (mtmt) cc_final: 0.7503 (mttm) REVERT: F 16 PHE cc_start: 0.7192 (m-80) cc_final: 0.6655 (m-80) REVERT: F 23 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7053 (mtm) REVERT: F 47 MET cc_start: 0.7988 (tpt) cc_final: 0.7711 (tpt) REVERT: F 75 MET cc_start: 0.6035 (ptm) cc_final: 0.5597 (mmp) REVERT: F 112 LYS cc_start: 0.8208 (tttt) cc_final: 0.7272 (tmtt) REVERT: F 131 MET cc_start: 0.7763 (mmt) cc_final: 0.7459 (mmm) REVERT: G 50 MET cc_start: 0.8597 (mmm) cc_final: 0.8174 (mmm) REVERT: G 111 MET cc_start: 0.6797 (mpp) cc_final: 0.6323 (mpp) REVERT: G 131 MET cc_start: 0.5981 (mmp) cc_final: 0.4990 (mtt) outliers start: 38 outliers final: 31 residues processed: 322 average time/residue: 0.2019 time to fit residues: 92.9773 Evaluate side-chains 318 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 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 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 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 20 LEU 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 148 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: 0.7980 chunk 87 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 101 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 GLN F 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.171713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.138348 restraints weight = 14776.113| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 1.83 r_work: 0.3610 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10387 Z= 0.205 Angle : 0.713 13.374 14002 Z= 0.360 Chirality : 0.044 0.280 1618 Planarity : 0.005 0.046 1764 Dihedral : 4.777 46.340 1412 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 3.51 % Allowed : 24.64 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.09 (0.24), residues: 1313 helix: 0.89 (0.17), residues: 981 sheet: None (None), residues: 0 loop : -2.97 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 21 HIS 0.002 0.001 HIS C 142 PHE 0.031 0.002 PHE B 33 TYR 0.025 0.002 TYR G 155 ARG 0.007 0.000 ARG E 89 *********************** 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 343 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 304 time to evaluate : 1.260 Fit side-chains REVERT: A 40 PHE cc_start: 0.5201 (p90) cc_final: 0.4307 (t80) REVERT: E 94 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6087 (pp20) REVERT: E 112 LYS cc_start: 0.7201 (tptm) cc_final: 0.6291 (tttm) REVERT: E 172 LEU cc_start: 0.8874 (pp) cc_final: 0.8349 (mt) REVERT: C 56 MET cc_start: 0.6428 (mmm) cc_final: 0.6067 (mmt) REVERT: D 62 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6789 (pp) REVERT: D 112 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7535 (mttm) REVERT: F 23 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.7084 (mtm) REVERT: F 75 MET cc_start: 0.6010 (ptm) cc_final: 0.5646 (mmp) REVERT: F 112 LYS cc_start: 0.8173 (tttt) cc_final: 0.7261 (tmtt) REVERT: F 131 MET cc_start: 0.7732 (mmt) cc_final: 0.7461 (mmm) REVERT: G 50 MET cc_start: 0.8598 (mmm) cc_final: 0.8202 (mmm) REVERT: G 111 MET cc_start: 0.6867 (mpp) cc_final: 0.6350 (mpp) REVERT: G 131 MET cc_start: 0.5921 (mmp) cc_final: 0.4916 (mtt) outliers start: 39 outliers final: 30 residues processed: 322 average time/residue: 0.2090 time to fit residues: 98.2403 Evaluate side-chains 318 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 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 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 185 MET 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 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 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 30 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 236 ASN Chi-restraints excluded: chain G residue 256 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 99 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 GLN F 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.171102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.137956 restraints weight = 14750.510| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 1.82 r_work: 0.3603 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10387 Z= 0.210 Angle : 0.748 20.763 14002 Z= 0.374 Chirality : 0.043 0.268 1618 Planarity : 0.005 0.046 1764 Dihedral : 4.736 45.435 1412 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.51 % Allowed : 25.54 % Favored : 70.95 % 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: -0.11 (0.24), residues: 1313 helix: 0.92 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -3.02 (0.31), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 21 HIS 0.002 0.001 HIS C 142 PHE 0.033 0.002 PHE B 33 TYR 0.030 0.002 TYR G 155 ARG 0.004 0.000 ARG E 89 ********************** 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 336 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 297 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 94 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.5963 (pp20) REVERT: E 112 LYS cc_start: 0.7214 (tptm) cc_final: 0.6291 (tttm) REVERT: E 172 LEU cc_start: 0.8876 (pp) cc_final: 0.8344 (mt) REVERT: E 231 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8224 (mp) REVERT: C 56 MET cc_start: 0.6381 (mmm) cc_final: 0.6028 (mmt) REVERT: C 241 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7433 (tt0) REVERT: D 62 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6827 (pp) REVERT: D 112 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7510 (mttm) REVERT: D 131 MET cc_start: 0.8066 (mmm) cc_final: 0.7740 (mmm) REVERT: F 75 MET cc_start: 0.6273 (ptm) cc_final: 0.5613 (mmp) REVERT: F 112 LYS cc_start: 0.8181 (tttt) cc_final: 0.7261 (tmtt) REVERT: F 185 MET cc_start: 0.6875 (ttm) cc_final: 0.6548 (ttm) REVERT: G 50 MET cc_start: 0.8652 (mmm) cc_final: 0.8162 (mmm) REVERT: G 111 MET cc_start: 0.6815 (mpp) cc_final: 0.6296 (mpp) REVERT: G 131 MET cc_start: 0.5929 (mmp) cc_final: 0.4846 (mtt) outliers start: 39 outliers final: 30 residues processed: 317 average time/residue: 0.1958 time to fit residues: 89.4848 Evaluate side-chains 322 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 231 ILE Chi-restraints excluded: chain E residue 239 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 171 MET Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain D residue 40 PHE Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 223 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 G residue 14 LEU Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 23 MET Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 138 MET Chi-restraints excluded: chain G residue 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: 0.5980 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 170 GLN F 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.169247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.135756 restraints weight = 14629.817| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.82 r_work: 0.3609 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10387 Z= 0.239 Angle : 0.771 18.780 14002 Z= 0.382 Chirality : 0.045 0.247 1618 Planarity : 0.005 0.046 1764 Dihedral : 4.806 45.245 1412 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 3.42 % Allowed : 25.81 % 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: -0.22 (0.24), residues: 1313 helix: 0.80 (0.17), residues: 974 sheet: None (None), residues: 0 loop : -2.96 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 21 HIS 0.002 0.001 HIS G 142 PHE 0.035 0.002 PHE B 33 TYR 0.027 0.002 TYR C 110 ARG 0.002 0.000 ARG E 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5819.61 seconds wall clock time: 103 minutes 42.57 seconds (6222.57 seconds total)