Starting phenix.real_space_refine on Fri Aug 7 01:24:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.map" model { file = "/net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ofu_70443/08_2026/9ofu_70443.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 66 5.49 5 S 71 5.16 5 C 6151 2.51 5 N 1775 2.21 5 O 1990 1.98 5 H 8591 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18644 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "F" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 685 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "C" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 4609 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain breaks: 4 Chain: "D" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 4035 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 11, 'TRANS': 234} Chain breaks: 7 Chain: "A" Number of atoms: 4640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4640 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 4 Chain: "B" Number of atoms: 4007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 4007 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain breaks: 7 Time building chain proxies: 3.59, per 1000 atoms: 0.19 Number of scatterers: 18644 At special positions: 0 Unit cell: (121.18, 122.01, 116.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 71 16.00 P 66 15.00 O 1990 8.00 N 1775 7.00 C 6151 6.00 H 8591 1.00 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: 1.65 Conformation dependent library (CDL) restraints added in 604.3 milliseconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 12 sheets defined 45.9% alpha, 22.7% beta 30 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'C' and resid 3 through 23 Processing helix chain 'C' and resid 26 through 31 removed outlier: 3.910A pdb=" N SER C 31 " --> pdb=" O HIS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 54 Processing helix chain 'C' and resid 65 through 68 Processing helix chain 'C' and resid 69 through 75 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.109A pdb=" N TYR C 98 " --> pdb=" O ASN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 162 through 166 Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.516A pdb=" N ILE C 212 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 242 removed outlier: 3.690A pdb=" N LEU C 241 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.651A pdb=" N LEU C 249 " --> pdb=" O GLU C 245 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 250 " --> pdb=" O PRO C 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 245 through 250' Processing helix chain 'C' and resid 254 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.633A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N MET C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C 274 " --> pdb=" O HIS C 270 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR C 275 " --> pdb=" O HIS C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 26 removed outlier: 3.652A pdb=" N MET D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 53 Processing helix chain 'D' and resid 70 through 82 Processing helix chain 'D' and resid 102 through 108 Processing helix chain 'D' and resid 110 through 115 removed outlier: 4.131A pdb=" N TRP D 114 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 127 through 135 Processing helix chain 'D' and resid 289 through 295 Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.581A pdb=" N LEU D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 329 removed outlier: 3.854A pdb=" N PHE D 322 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLN D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 23 Processing helix chain 'A' and resid 26 through 33 removed outlier: 3.814A pdb=" N HIS A 32 " --> pdb=" O ASN A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 54 removed outlier: 3.732A pdb=" N ALA A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 removed outlier: 4.301A pdb=" N CYS A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 69' Processing helix chain 'A' and resid 69 through 75 removed outlier: 4.147A pdb=" N LYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.899A pdb=" N TYR A 98 " --> pdb=" O ASN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.514A pdb=" N LEU A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 162 through 166 Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.554A pdb=" N ILE A 212 " --> pdb=" O PRO A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.862A pdb=" N LEU A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 250 " --> pdb=" O PRO A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 245 through 250' Processing helix chain 'A' and resid 253 through 257 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.790A pdb=" N LEU A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 37 through 53 Processing helix chain 'B' and resid 70 through 82 Processing helix chain 'B' and resid 102 through 108 removed outlier: 3.554A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.821A pdb=" N TRP B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 126 No H-bonds generated for 'chain 'B' and resid 124 through 126' Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 305 through 310 removed outlier: 4.256A pdb=" N PHE B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.734A pdb=" N VAL B 325 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N VAL B 326 " --> pdb=" O PHE B 322 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS B 327 " --> pdb=" O GLN B 323 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 80 through 81 removed outlier: 3.619A pdb=" N VAL C 200 " --> pdb=" O HIS C 176 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS C 176 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 175 " --> pdb=" O ARG C 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 231 through 234 removed outlier: 5.899A pdb=" N ARG C 224 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS C 234 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 222 " --> pdb=" O CYS C 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 223 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 316 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY C 292 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ALA C 288 " --> pdb=" O GLY C 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 231 through 234 removed outlier: 5.899A pdb=" N ARG C 224 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N CYS C 234 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 222 " --> pdb=" O CYS C 234 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 223 " --> pdb=" O CYS C 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS C 316 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS C 313 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 96 through 99 removed outlier: 3.507A pdb=" N ALA D 249 " --> pdb=" O PHE D 87 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 272 through 275 removed outlier: 3.664A pdb=" N PHE D 273 " --> pdb=" O ASN D 371 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN D 371 " --> pdb=" O PHE D 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER D 275 " --> pdb=" O CYS D 369 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 336 through 337 removed outlier: 3.713A pdb=" N MET D 349 " --> pdb=" O PHE D 337 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 91 removed outlier: 6.499A pdb=" N MET A 88 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR A 83 " --> pdb=" O MET A 88 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 90 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS A 203 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 196 " --> pdb=" O TYR A 180 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 200 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 174 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 204 " --> pdb=" O HIS A 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 231 through 234 removed outlier: 6.292A pdb=" N ARG A 224 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS A 234 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 222 " --> pdb=" O CYS A 234 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 231 through 234 removed outlier: 6.292A pdb=" N ARG A 224 " --> pdb=" O SER A 232 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N CYS A 234 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU A 222 " --> pdb=" O CYS A 234 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET A 286 " --> pdb=" O VAL A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'B' and resid 285 through 286 removed outlier: 3.511A pdb=" N PHE B 285 " --> pdb=" O ARG B 276 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS B 369 " --> pdb=" O SER B 275 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 336 through 338 removed outlier: 3.683A pdb=" N PHE B 337 " --> pdb=" O MET B 349 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1062 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 77 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 8562 1.02 - 1.21: 31 1.21 - 1.41: 4350 1.41 - 1.61: 5931 1.61 - 1.81: 113 Bond restraints: 18987 Sorted by residual: bond pdb=" NE ARG B 276 " pdb=" HE ARG B 276 " ideal model delta sigma weight residual 0.860 0.970 -0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" C3' DC E 10 " pdb=" C2' DC E 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 bond pdb=" C3' DC F 52 " pdb=" C2' DC F 52 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.67e+00 bond pdb=" C3' DA F 37 " pdb=" C2' DA F 37 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.83e+00 ... (remaining 18982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.03: 33732 6.03 - 12.07: 3 12.07 - 18.10: 0 18.10 - 24.13: 2 24.13 - 30.17: 4 Bond angle restraints: 33741 Sorted by residual: angle pdb="HG22 THR A 102 " pdb=" CG2 THR A 102 " pdb="HG23 THR A 102 " ideal model delta sigma weight residual 109.00 78.83 30.17 3.00e+00 1.11e-01 1.01e+02 angle pdb="HG21 THR A 102 " pdb=" CG2 THR A 102 " pdb="HG22 THR A 102 " ideal model delta sigma weight residual 109.00 78.92 30.08 3.00e+00 1.11e-01 1.01e+02 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG23 THR A 102 " ideal model delta sigma weight residual 110.00 81.87 28.13 3.00e+00 1.11e-01 8.79e+01 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG21 THR A 102 " ideal model delta sigma weight residual 110.00 81.98 28.02 3.00e+00 1.11e-01 8.73e+01 angle pdb=" CB THR A 102 " pdb=" CG2 THR A 102 " pdb="HG22 THR A 102 " ideal model delta sigma weight residual 110.00 132.45 -22.45 3.00e+00 1.11e-01 5.60e+01 ... (remaining 33736 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.36: 8120 27.36 - 54.73: 716 54.73 - 82.09: 101 82.09 - 109.46: 7 109.46 - 136.82: 1 Dihedral angle restraints: 8945 sinusoidal: 5173 harmonic: 3772 Sorted by residual: dihedral pdb=" C THR C 83 " pdb=" N THR C 83 " pdb=" CA THR C 83 " pdb=" CB THR C 83 " ideal model delta harmonic sigma weight residual -122.00 -132.14 10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" C4' DC F 52 " pdb=" C3' DC F 52 " pdb=" O3' DC F 52 " pdb=" P DA F 53 " ideal model delta sinusoidal sigma weight residual 220.00 83.18 136.82 1 3.50e+01 8.16e-04 1.36e+01 dihedral pdb=" CA PRO A 117 " pdb=" C PRO A 117 " pdb=" N CYS A 118 " pdb=" CA CYS A 118 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 8942 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1377 0.064 - 0.127: 208 0.127 - 0.191: 12 0.191 - 0.254: 0 0.254 - 0.318: 1 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CA THR C 83 " pdb=" N THR C 83 " pdb=" C THR C 83 " pdb=" CB THR C 83 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA ILE C 91 " pdb=" N ILE C 91 " pdb=" C ILE C 91 " pdb=" CB ILE C 91 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE C 202 " pdb=" N ILE C 202 " pdb=" C ILE C 202 " pdb=" CB ILE C 202 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 ... (remaining 1595 not shown) Planarity restraints: 2579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN C 283 " -0.188 2.00e-02 2.50e+03 4.00e-01 2.41e+03 pdb=" CD GLN C 283 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN C 283 " 0.177 2.00e-02 2.50e+03 pdb=" NE2 GLN C 283 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 283 " 0.671 2.00e-02 2.50e+03 pdb="HE22 GLN C 283 " -0.667 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 103 " -0.161 2.00e-02 2.50e+03 1.83e-01 5.03e+02 pdb=" CD GLN A 103 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN A 103 " 0.158 2.00e-02 2.50e+03 pdb=" NE2 GLN A 103 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 103 " 0.274 2.00e-02 2.50e+03 pdb="HE22 GLN A 103 " -0.275 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 299 " -0.072 2.00e-02 2.50e+03 7.22e-02 7.81e+01 pdb=" CD GLN A 299 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 299 " 0.056 2.00e-02 2.50e+03 pdb=" NE2 GLN A 299 " 0.008 2.00e-02 2.50e+03 pdb="HE21 GLN A 299 " -0.112 2.00e-02 2.50e+03 pdb="HE22 GLN A 299 " 0.099 2.00e-02 2.50e+03 ... (remaining 2576 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.11: 451 2.11 - 2.73: 30984 2.73 - 3.36: 50753 3.36 - 3.98: 64554 3.98 - 4.60: 100961 Nonbonded interactions: 247703 Sorted by model distance: nonbonded pdb=" HE3 MET A 99 " pdb=" HB3 MET A 150 " model vdw 1.490 2.440 nonbonded pdb=" HB3 LEU A 261 " pdb="HH21 ARG A 285 " model vdw 1.495 2.270 nonbonded pdb=" HD1 HIS A 259 " pdb=" H LEU A 261 " model vdw 1.508 2.100 nonbonded pdb=" HE2 MET A 99 " pdb=" HE1 MET A 150 " model vdw 1.512 2.440 nonbonded pdb="HG22 VAL C 81 " pdb=" HB ILE C 89 " model vdw 1.541 2.440 ... (remaining 247698 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' and (resid 1 through 54 or resid 65 through 129 or resid 141 through \ 180 or resid 195 through 324)) selection = (chain 'C' and (resid 1 through 180 or resid 195 through 212 or resid 218 throug \ h 324)) } ncs_group { reference = (chain 'B' and (resid 6 through 177 or resid 210 through 253 or resid 271 throug \ h 309 or resid 313 through 373)) selection = (chain 'D' and (resid 6 through 27 or resid 35 through 88 or resid 93 through 13 \ 4 or resid 171 through 221 or resid 247 through 253 or resid 271 through 373)) } 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 group one per residue 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: 5.310 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: 0.130 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 21.150 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 : 0.005 0.036 10396 Z= 0.330 Angle : 0.681 7.976 14304 Z= 0.464 Chirality : 0.044 0.318 1598 Planarity : 0.004 0.043 1575 Dihedral : 20.090 136.820 4005 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.28), residues: 1014 helix: 1.01 (0.28), residues: 353 sheet: -2.03 (0.32), residues: 244 loop : -0.02 (0.33), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 276 TYR 0.018 0.002 TYR C 180 PHE 0.014 0.001 PHE D 283 TRP 0.031 0.002 TRP D 348 HIS 0.007 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.33 (10396) covalent geometry : angle 0.68106 / 0.46 (14304) hydrogen bonds : bond 0.18120 / 19.88 ( 449) hydrogen bonds : angle 8.36695 / 10.95 ( 1216) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 SER cc_start: 0.7951 (t) cc_final: 0.7557 (m) REVERT: C 161 MET cc_start: 0.7075 (tpp) cc_final: 0.6862 (tpp) REVERT: D 49 MET cc_start: 0.7313 (mmm) cc_final: 0.6629 (mmm) REVERT: A 72 LEU cc_start: 0.6784 (tp) cc_final: 0.6528 (tp) REVERT: A 310 GLN cc_start: 0.6407 (mm110) cc_final: 0.5588 (pm20) REVERT: B 23 SER cc_start: 0.8719 (p) cc_final: 0.8276 (m) REVERT: B 25 MET cc_start: 0.8195 (tpp) cc_final: 0.7992 (tpp) REVERT: B 274 ILE cc_start: 0.8127 (tp) cc_final: 0.7789 (tp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2066 time to fit residues: 77.4208 Evaluate side-chains 193 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 270 HIS A 208 HIS ** B 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.202191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.165444 restraints weight = 37228.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.168122 restraints weight = 32608.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.169868 restraints weight = 26104.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.170213 restraints weight = 18984.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.170582 restraints weight = 17720.017| |-----------------------------------------------------------------------------| r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10396 Z= 0.174 Angle : 0.599 6.699 14304 Z= 0.337 Chirality : 0.041 0.194 1598 Planarity : 0.005 0.058 1575 Dihedral : 21.754 132.889 1862 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.93 % Allowed : 18.97 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.27), residues: 1014 helix: 1.06 (0.27), residues: 355 sheet: -2.00 (0.30), residues: 255 loop : -0.08 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 49 TYR 0.021 0.002 TYR C 180 PHE 0.014 0.002 PHE D 173 TRP 0.013 0.001 TRP D 348 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (10396) covalent geometry : angle 0.59856 / 0.34 (14304) hydrogen bonds : bond 0.05065 / 5.45 ( 449) hydrogen bonds : angle 6.44508 / 8.08 ( 1216) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 SER cc_start: 0.7951 (t) cc_final: 0.7643 (m) REVERT: A 72 LEU cc_start: 0.6910 (tp) cc_final: 0.6598 (tp) REVERT: B 287 ASP cc_start: 0.7663 (OUTLIER) cc_final: 0.7338 (m-30) outliers start: 19 outliers final: 12 residues processed: 213 average time/residue: 0.2187 time to fit residues: 65.4323 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.199837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.162500 restraints weight = 37158.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165197 restraints weight = 34049.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.166851 restraints weight = 26908.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.167268 restraints weight = 19685.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.167832 restraints weight = 18364.096| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10396 Z= 0.167 Angle : 0.563 7.836 14304 Z= 0.315 Chirality : 0.040 0.179 1598 Planarity : 0.004 0.051 1575 Dihedral : 21.786 130.033 1862 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.13 % Allowed : 19.68 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.27), residues: 1014 helix: 1.07 (0.28), residues: 364 sheet: -1.94 (0.30), residues: 242 loop : -0.46 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 276 TYR 0.012 0.002 TYR A 90 PHE 0.013 0.002 PHE A 221 TRP 0.009 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (10396) covalent geometry : angle 0.56310 / 0.31 (14304) hydrogen bonds : bond 0.04513 / 4.86 ( 449) hydrogen bonds : angle 5.98208 / 7.55 ( 1216) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 145 SER cc_start: 0.8151 (t) cc_final: 0.7733 (m) REVERT: C 299 GLN cc_start: 0.8405 (tt0) cc_final: 0.7771 (tm-30) REVERT: D 99 VAL cc_start: 0.8549 (p) cc_final: 0.8193 (t) REVERT: A 72 LEU cc_start: 0.6935 (tp) cc_final: 0.6647 (tp) outliers start: 21 outliers final: 18 residues processed: 210 average time/residue: 0.2061 time to fit residues: 61.9469 Evaluate side-chains 204 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 265 HIS C 270 HIS ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.194206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.156192 restraints weight = 37669.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157125 restraints weight = 36835.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.159172 restraints weight = 35130.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.159832 restraints weight = 24050.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.160244 restraints weight = 23151.732| |-----------------------------------------------------------------------------| r_work (final): 0.4004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 10396 Z= 0.255 Angle : 0.631 6.061 14304 Z= 0.354 Chirality : 0.042 0.186 1598 Planarity : 0.005 0.052 1575 Dihedral : 21.883 128.757 1862 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.96 % Allowed : 19.88 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.26), residues: 1014 helix: 0.77 (0.27), residues: 363 sheet: -2.28 (0.28), residues: 259 loop : -0.87 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 276 TYR 0.012 0.002 TYR B 120 PHE 0.018 0.002 PHE D 283 TRP 0.006 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00563 / 0.25 (10396) covalent geometry : angle 0.63138 / 0.35 (14304) hydrogen bonds : bond 0.04445 / 4.78 ( 449) hydrogen bonds : angle 5.94737 / 7.46 ( 1216) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7517 (t) REVERT: C 88 MET cc_start: 0.8152 (mmm) cc_final: 0.7526 (mtt) REVERT: C 145 SER cc_start: 0.8463 (t) cc_final: 0.8010 (m) REVERT: C 299 GLN cc_start: 0.8686 (tt0) cc_final: 0.8082 (tm-30) REVERT: D 99 VAL cc_start: 0.8529 (p) cc_final: 0.8218 (t) REVERT: D 355 THR cc_start: 0.7355 (OUTLIER) cc_final: 0.6836 (p) REVERT: A 72 LEU cc_start: 0.7071 (tp) cc_final: 0.6825 (tp) REVERT: A 198 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7880 (m) outliers start: 39 outliers final: 30 residues processed: 208 average time/residue: 0.1902 time to fit residues: 58.2115 Evaluate side-chains 208 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 3 ASP Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 223 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS B 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.191971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.154439 restraints weight = 38043.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.154312 restraints weight = 35138.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157223 restraints weight = 33600.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.157367 restraints weight = 22495.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.157719 restraints weight = 21119.324| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10396 Z= 0.157 Angle : 0.549 5.978 14304 Z= 0.306 Chirality : 0.039 0.175 1598 Planarity : 0.004 0.050 1575 Dihedral : 21.856 127.619 1862 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.55 % Allowed : 20.49 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.26), residues: 1014 helix: 0.96 (0.27), residues: 364 sheet: -2.02 (0.29), residues: 244 loop : -0.86 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.012 0.001 TYR A 293 PHE 0.013 0.002 PHE A 221 TRP 0.005 0.001 TRP D 348 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (10396) covalent geometry : angle 0.54880 / 0.31 (14304) hydrogen bonds : bond 0.03781 / 4.07 ( 449) hydrogen bonds : angle 5.68720 / 7.14 ( 1216) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7680 (OUTLIER) cc_final: 0.7440 (t) REVERT: C 88 MET cc_start: 0.8407 (mmm) cc_final: 0.7748 (mtt) REVERT: C 145 SER cc_start: 0.8475 (t) cc_final: 0.7969 (m) REVERT: C 299 GLN cc_start: 0.8631 (tt0) cc_final: 0.8080 (tm-30) REVERT: D 99 VAL cc_start: 0.8548 (p) cc_final: 0.8272 (t) REVERT: D 355 THR cc_start: 0.7267 (OUTLIER) cc_final: 0.6839 (p) REVERT: A 72 LEU cc_start: 0.6948 (tp) cc_final: 0.6695 (tp) REVERT: A 198 CYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7915 (m) REVERT: B 42 LEU cc_start: 0.8267 (mt) cc_final: 0.8003 (mt) outliers start: 35 outliers final: 26 residues processed: 200 average time/residue: 0.1642 time to fit residues: 48.1384 Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain D residue 356 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 4 optimal weight: 30.0000 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.189123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151882 restraints weight = 38056.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151391 restraints weight = 37811.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153861 restraints weight = 37519.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.154377 restraints weight = 25348.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.155039 restraints weight = 25786.211| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10396 Z= 0.220 Angle : 0.598 6.328 14304 Z= 0.333 Chirality : 0.040 0.182 1598 Planarity : 0.004 0.052 1575 Dihedral : 21.915 125.633 1862 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.40 % Favored : 92.50 % Rotamer: Outliers : 3.85 % Allowed : 20.69 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.26), residues: 1014 helix: 0.87 (0.28), residues: 358 sheet: -2.24 (0.29), residues: 251 loop : -0.87 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 276 TYR 0.010 0.002 TYR C 45 PHE 0.017 0.002 PHE D 283 TRP 0.005 0.001 TRP A 295 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (10396) covalent geometry : angle 0.59774 / 0.33 (14304) hydrogen bonds : bond 0.04064 / 4.34 ( 449) hydrogen bonds : angle 5.68391 / 7.12 ( 1216) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7536 (t) REVERT: C 88 MET cc_start: 0.8142 (mmm) cc_final: 0.7433 (mtt) REVERT: C 145 SER cc_start: 0.8433 (t) cc_final: 0.7979 (m) REVERT: D 99 VAL cc_start: 0.8529 (p) cc_final: 0.8230 (t) REVERT: D 355 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7197 (p) REVERT: A 72 LEU cc_start: 0.7055 (tp) cc_final: 0.6848 (tp) outliers start: 38 outliers final: 33 residues processed: 193 average time/residue: 0.1631 time to fit residues: 45.9822 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain D residue 355 THR Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 354 PHE Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 100 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 30.0000 chunk 63 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.190836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.153796 restraints weight = 38143.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.154218 restraints weight = 34168.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157238 restraints weight = 30310.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157093 restraints weight = 21407.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.157415 restraints weight = 20137.111| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10396 Z= 0.152 Angle : 0.547 8.404 14304 Z= 0.302 Chirality : 0.039 0.174 1598 Planarity : 0.004 0.052 1575 Dihedral : 21.895 123.823 1862 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.45 % Allowed : 21.81 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.26), residues: 1014 helix: 0.90 (0.27), residues: 364 sheet: -2.02 (0.30), residues: 236 loop : -0.97 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 276 TYR 0.019 0.001 TYR A 293 PHE 0.021 0.002 PHE B 283 TRP 0.005 0.001 TRP A 295 HIS 0.006 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (10396) covalent geometry : angle 0.54677 / 0.30 (14304) hydrogen bonds : bond 0.03596 / 3.84 ( 449) hydrogen bonds : angle 5.52554 / 6.89 ( 1216) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7728 (OUTLIER) cc_final: 0.7448 (t) REVERT: C 88 MET cc_start: 0.8349 (mmm) cc_final: 0.7599 (mtt) REVERT: C 145 SER cc_start: 0.8400 (t) cc_final: 0.7953 (m) REVERT: D 99 VAL cc_start: 0.8510 (p) cc_final: 0.8231 (t) REVERT: A 72 LEU cc_start: 0.6991 (tp) cc_final: 0.6754 (tp) REVERT: A 198 CYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7927 (m) outliers start: 34 outliers final: 29 residues processed: 190 average time/residue: 0.1758 time to fit residues: 48.7467 Evaluate side-chains 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 HIS C 270 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.190947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.153149 restraints weight = 37928.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.153177 restraints weight = 36019.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.156033 restraints weight = 31466.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.156236 restraints weight = 22089.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.156574 restraints weight = 20701.153| |-----------------------------------------------------------------------------| r_work (final): 0.3955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10396 Z= 0.141 Angle : 0.536 6.113 14304 Z= 0.298 Chirality : 0.039 0.172 1598 Planarity : 0.004 0.052 1575 Dihedral : 21.875 121.277 1862 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.55 % Allowed : 21.50 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.27), residues: 1014 helix: 1.08 (0.28), residues: 364 sheet: -1.91 (0.31), residues: 231 loop : -0.95 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 276 TYR 0.011 0.001 TYR C 180 PHE 0.013 0.001 PHE D 283 TRP 0.005 0.001 TRP A 295 HIS 0.007 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (10396) covalent geometry : angle 0.53647 / 0.30 (14304) hydrogen bonds : bond 0.03448 / 3.67 ( 449) hydrogen bonds : angle 5.41283 / 6.80 ( 1216) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7433 (t) REVERT: C 88 MET cc_start: 0.8155 (mmm) cc_final: 0.7320 (mtt) REVERT: C 145 SER cc_start: 0.8401 (t) cc_final: 0.7955 (m) REVERT: D 99 VAL cc_start: 0.8538 (p) cc_final: 0.8263 (t) REVERT: A 72 LEU cc_start: 0.6989 (tp) cc_final: 0.6756 (tp) REVERT: A 198 CYS cc_start: 0.8245 (OUTLIER) cc_final: 0.7861 (m) outliers start: 35 outliers final: 30 residues processed: 188 average time/residue: 0.1661 time to fit residues: 45.5997 Evaluate side-chains 201 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 101 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 20.0000 chunk 52 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.191440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.154271 restraints weight = 37912.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.153836 restraints weight = 34751.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.156872 restraints weight = 33091.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.156911 restraints weight = 22302.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.157262 restraints weight = 20848.812| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10396 Z= 0.132 Angle : 0.525 5.985 14304 Z= 0.290 Chirality : 0.038 0.170 1598 Planarity : 0.004 0.053 1575 Dihedral : 21.838 116.277 1862 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.35 % Allowed : 21.91 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.27), residues: 1014 helix: 1.24 (0.28), residues: 364 sheet: -1.89 (0.31), residues: 241 loop : -0.79 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 276 TYR 0.014 0.001 TYR C 180 PHE 0.013 0.001 PHE D 283 TRP 0.006 0.001 TRP A 295 HIS 0.010 0.001 HIS C 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10396) covalent geometry : angle 0.52539 / 0.29 (14304) hydrogen bonds : bond 0.03305 / 3.50 ( 449) hydrogen bonds : angle 5.27495 / 6.60 ( 1216) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 175 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7415 (t) REVERT: C 88 MET cc_start: 0.8280 (mmm) cc_final: 0.7496 (mtt) REVERT: C 145 SER cc_start: 0.8429 (t) cc_final: 0.7978 (m) REVERT: D 99 VAL cc_start: 0.8517 (p) cc_final: 0.8260 (t) REVERT: A 72 LEU cc_start: 0.6954 (tp) cc_final: 0.6721 (tp) REVERT: A 198 CYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7793 (m) outliers start: 33 outliers final: 28 residues processed: 193 average time/residue: 0.1965 time to fit residues: 55.1992 Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.190912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153659 restraints weight = 37909.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.153208 restraints weight = 34479.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.156173 restraints weight = 33699.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.156305 restraints weight = 22589.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156655 restraints weight = 21004.475| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10396 Z= 0.135 Angle : 0.523 5.732 14304 Z= 0.290 Chirality : 0.038 0.168 1598 Planarity : 0.004 0.052 1575 Dihedral : 21.790 112.088 1862 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.35 % Allowed : 21.50 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.27), residues: 1014 helix: 1.40 (0.29), residues: 358 sheet: -1.73 (0.32), residues: 231 loop : -0.74 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 276 TYR 0.013 0.001 TYR A 293 PHE 0.013 0.001 PHE D 283 TRP 0.005 0.001 TRP A 295 HIS 0.011 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (10396) covalent geometry : angle 0.52341 / 0.29 (14304) hydrogen bonds : bond 0.03270 / 3.48 ( 449) hydrogen bonds : angle 5.23808 / 6.59 ( 1216) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 THR cc_start: 0.7699 (OUTLIER) cc_final: 0.7437 (t) REVERT: C 88 MET cc_start: 0.8137 (mmm) cc_final: 0.7275 (mtt) REVERT: C 145 SER cc_start: 0.8423 (t) cc_final: 0.7977 (m) REVERT: D 99 VAL cc_start: 0.8513 (p) cc_final: 0.8268 (t) REVERT: A 72 LEU cc_start: 0.6949 (tp) cc_final: 0.6729 (tp) REVERT: A 198 CYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7759 (m) outliers start: 33 outliers final: 28 residues processed: 189 average time/residue: 0.1774 time to fit residues: 48.8514 Evaluate side-chains 199 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain C residue 25 LEU Chi-restraints excluded: chain C residue 42 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 173 CYS Chi-restraints excluded: chain C residue 210 SER Chi-restraints excluded: chain C residue 217 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 273 MET Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 44 MET Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 290 CYS Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain D residue 354 PHE Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 76 ASP Chi-restraints excluded: chain A residue 180 TYR Chi-restraints excluded: chain A residue 198 CYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain B residue 4 HIS Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 287 ASP Chi-restraints excluded: chain B residue 355 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.191240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.153625 restraints weight = 37910.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153046 restraints weight = 33556.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.155691 restraints weight = 33498.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.155998 restraints weight = 23115.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.156587 restraints weight = 21573.211| |-----------------------------------------------------------------------------| r_work (final): 0.3956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10396 Z= 0.133 Angle : 0.519 5.192 14304 Z= 0.286 Chirality : 0.038 0.169 1598 Planarity : 0.004 0.054 1575 Dihedral : 21.733 107.344 1862 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.55 % Allowed : 21.50 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.27), residues: 1014 helix: 1.43 (0.29), residues: 358 sheet: -1.84 (0.32), residues: 231 loop : -0.66 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 132 TYR 0.011 0.001 TYR A 90 PHE 0.013 0.001 PHE D 283 TRP 0.004 0.001 TRP D 348 HIS 0.010 0.001 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10396) covalent geometry : angle 0.51886 / 0.29 (14304) hydrogen bonds : bond 0.03225 / 3.44 ( 449) hydrogen bonds : angle 5.18845 / 6.53 ( 1216) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2953.89 seconds wall clock time: 51 minutes 17.80 seconds (3077.80 seconds total)