Starting phenix.real_space_refine on Thu Sep 18 17:36:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.cif Found real_map, /net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9of2_70418/09_2025/9of2_70418.map" } resolution = 3.7 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= 0.002 sd= 0.038 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 54 5.49 5 S 81 5.16 5 C 6237 2.51 5 N 1781 2.21 5 O 1996 1.98 5 H 8765 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 545 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 4874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 4874 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 4 Chain: "D" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 4092 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 10, 'TRANS': 245} Chain breaks: 6 Chain: "E" Number of atoms: 4771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4771 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 3 Chain: "F" Number of atoms: 4070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 4070 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 9, 'TRANS': 242} Chain breaks: 6 Time building chain proxies: 3.87, per 1000 atoms: 0.20 Number of scatterers: 18914 At special positions: 0 Unit cell: (96.216, 112.252, 123.224, 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 81 16.00 P 54 15.00 O 1996 8.00 N 1781 7.00 C 6237 6.00 H 8765 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: 1.69 Conformation dependent library (CDL) restraints added in 505.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 10 sheets defined 42.4% alpha, 23.9% beta 20 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.28 Creating SS restraints... Processing helix chain 'C' and resid 15 through 38 removed outlier: 3.561A pdb=" N ASP C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 44 through 51 removed outlier: 3.966A pdb=" N HIS C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 73 Processing helix chain 'C' and resid 89 through 95 removed outlier: 4.184A pdb=" N LYS C 93 " --> pdb=" O ASN C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 120 removed outlier: 4.281A pdb=" N PHE C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 127 Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.975A pdb=" N THR C 135 " --> pdb=" O PHE C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 140 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 184 through 188 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.525A pdb=" N MET C 235 " --> pdb=" O PRO C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 265 removed outlier: 4.444A pdb=" N GLU C 263 " --> pdb=" O ASP C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 280 Processing helix chain 'C' and resid 282 through 284 No H-bonds generated for 'chain 'C' and resid 282 through 284' Processing helix chain 'C' and resid 285 through 300 Processing helix chain 'C' and resid 355 through 359 Processing helix chain 'D' and resid 94 through 116 Processing helix chain 'D' and resid 128 through 142 removed outlier: 3.803A pdb=" N SER D 141 " --> pdb=" O SER D 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 173 removed outlier: 3.879A pdb=" N LYS D 165 " --> pdb=" O ASP D 161 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N HIS D 166 " --> pdb=" O GLN D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 removed outlier: 3.579A pdb=" N VAL D 196 " --> pdb=" O SER D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 205 removed outlier: 3.627A pdb=" N TRP D 204 " --> pdb=" O PRO D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 removed outlier: 3.652A pdb=" N VAL D 213 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 226 removed outlier: 3.596A pdb=" N LEU D 221 " --> pdb=" O ASP D 217 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D 223 " --> pdb=" O ASP D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 387 through 392 removed outlier: 3.846A pdb=" N LEU D 391 " --> pdb=" O GLN D 387 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 392' Processing helix chain 'D' and resid 404 through 416 removed outlier: 3.800A pdb=" N LEU D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 36 removed outlier: 3.637A pdb=" N ARG E 27 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 36 " --> pdb=" O GLU E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 54 through 74 removed outlier: 3.713A pdb=" N SER E 62 " --> pdb=" O ARG E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 90 through 95 Processing helix chain 'E' and resid 114 through 119 removed outlier: 4.129A pdb=" N PHE E 118 " --> pdb=" O ASN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 127 removed outlier: 4.198A pdb=" N THR E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 Processing helix chain 'E' and resid 136 through 138 No H-bonds generated for 'chain 'E' and resid 136 through 138' Processing helix chain 'E' and resid 139 through 148 removed outlier: 3.542A pdb=" N ILE E 143 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER E 148 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.759A pdb=" N MET E 235 " --> pdb=" O PRO E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 265 removed outlier: 3.517A pdb=" N LEU E 264 " --> pdb=" O ARG E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 272 removed outlier: 3.572A pdb=" N LEU E 272 " --> pdb=" O PRO E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 276 through 280 Processing helix chain 'E' and resid 282 through 284 No H-bonds generated for 'chain 'E' and resid 282 through 284' Processing helix chain 'E' and resid 285 through 299 Processing helix chain 'F' and resid 95 through 116 Processing helix chain 'F' and resid 129 through 142 removed outlier: 3.535A pdb=" N ARG F 133 " --> pdb=" O LEU F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 172 removed outlier: 3.643A pdb=" N GLU F 170 " --> pdb=" O HIS F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 194 removed outlier: 3.511A pdb=" N THR F 194 " --> pdb=" O ASP F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 191 through 194' Processing helix chain 'F' and resid 208 through 213 removed outlier: 3.998A pdb=" N VAL F 213 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 216 No H-bonds generated for 'chain 'F' and resid 214 through 216' Processing helix chain 'F' and resid 217 through 226 Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 395 through 400 removed outlier: 3.920A pdb=" N PHE F 399 " --> pdb=" O ASN F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 403 No H-bonds generated for 'chain 'F' and resid 401 through 403' Processing helix chain 'F' and resid 404 through 416 removed outlier: 4.144A pdb=" N VAL F 416 " --> pdb=" O PHE F 412 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 108 through 111 removed outlier: 3.906A pdb=" N PHE C 110 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 223 " --> pdb=" O GLN C 198 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR C 196 " --> pdb=" O MET C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 254 through 257 removed outlier: 6.667A pdb=" N ARG C 247 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N CYS C 257 " --> pdb=" O LEU C 245 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N LEU C 245 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N CYS C 336 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 340 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN C 322 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL C 302 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 307 through 310 Processing sheet with id=AA4, first strand: chain 'D' and resid 186 through 189 removed outlier: 6.709A pdb=" N VAL D 186 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER D 180 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR D 188 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 177 " --> pdb=" O ALA D 339 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 304 " --> pdb=" O MET D 267 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS D 265 " --> pdb=" O VAL D 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 364 through 367 removed outlier: 4.248A pdb=" N TYR D 456 " --> pdb=" O PHE D 446 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 364 through 367 removed outlier: 4.248A pdb=" N TYR D 456 " --> pdb=" O PHE D 446 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N MET D 439 " --> pdb=" O PHE D 427 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE D 427 " --> pdb=" O MET D 439 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL D 425 " --> pdb=" O THR D 441 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL D 422 " --> pdb=" O SER F 424 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N MET F 426 " --> pdb=" O VAL D 422 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N SER D 424 " --> pdb=" O MET F 426 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE F 427 " --> pdb=" O MET F 439 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER F 442 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 460 " --> pdb=" O SER F 442 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N TYR F 456 " --> pdb=" O PHE F 446 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.334A pdb=" N PHE E 110 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 223 " --> pdb=" O GLN E 198 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN E 198 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR E 196 " --> pdb=" O MET E 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.981A pdb=" N ILE E 326 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 337 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 324 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS E 339 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN E 322 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN E 341 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU E 320 " --> pdb=" O ASN E 341 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL E 343 " --> pdb=" O TRP E 318 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TRP E 318 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL E 302 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 254 through 257 removed outlier: 6.981A pdb=" N ILE E 326 " --> pdb=" O GLN E 335 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE E 337 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR E 324 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N CYS E 339 " --> pdb=" O GLN E 322 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLN E 322 " --> pdb=" O CYS E 339 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN E 341 " --> pdb=" O GLU E 320 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLU E 320 " --> pdb=" O ASN E 341 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL E 343 " --> pdb=" O TRP E 318 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N TRP E 318 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 186 through 189 removed outlier: 6.772A pdb=" N VAL F 186 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N SER F 180 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR F 188 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 339 " --> pdb=" O PHE F 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 309 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY F 310 " --> pdb=" O ARG F 261 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 98 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.45 Time building geometry restraints manager: 2.27 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: 8726 1.02 - 1.22: 42 1.22 - 1.42: 4320 1.42 - 1.61: 6010 1.61 - 1.81: 126 Bond restraints: 19224 Sorted by residual: bond pdb=" ND2 ASN F 198 " pdb="HD21 ASN F 198 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" ND2 ASN F 198 " pdb="HD22 ASN F 198 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" O3' DG B 10 " pdb=" P DC B 11 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.50e-02 4.44e+03 6.15e+00 bond pdb=" CA LEU E 69 " pdb=" C LEU E 69 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.30e-02 5.92e+03 2.58e+00 bond pdb=" O3' DA A 40 " pdb=" P DG A 41 " ideal model delta sigma weight residual 1.607 1.629 -0.022 1.50e-02 4.44e+03 2.21e+00 ... (remaining 19219 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 32949 1.18 - 2.37: 1100 2.37 - 3.55: 91 3.55 - 4.74: 28 4.74 - 5.92: 8 Bond angle restraints: 34176 Sorted by residual: angle pdb=" N ASN F 198 " pdb=" CA ASN F 198 " pdb=" C ASN F 198 " ideal model delta sigma weight residual 111.39 116.55 -5.16 1.38e+00 5.25e-01 1.40e+01 angle pdb=" O3' DC A 42 " pdb=" C3' DC A 42 " pdb=" C2' DC A 42 " ideal model delta sigma weight residual 111.50 106.10 5.40 1.50e+00 4.44e-01 1.30e+01 angle pdb=" N LEU E 69 " pdb=" CA LEU E 69 " pdb=" C LEU E 69 " ideal model delta sigma weight residual 111.28 107.70 3.58 1.09e+00 8.42e-01 1.08e+01 angle pdb=" C ASN F 198 " pdb=" N GLN F 199 " pdb=" CA GLN F 199 " ideal model delta sigma weight residual 123.11 117.70 5.41 1.79e+00 3.12e-01 9.12e+00 angle pdb=" C4' DC A 42 " pdb=" C3' DC A 42 " pdb=" O3' DC A 42 " ideal model delta sigma weight residual 110.00 114.42 -4.42 1.50e+00 4.44e-01 8.67e+00 ... (remaining 34171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 8143 25.39 - 50.79: 768 50.79 - 76.18: 160 76.18 - 101.57: 13 101.57 - 126.97: 1 Dihedral angle restraints: 9085 sinusoidal: 5176 harmonic: 3909 Sorted by residual: dihedral pdb=" CA HIS D 214 " pdb=" C HIS D 214 " pdb=" N PRO D 215 " pdb=" CA PRO D 215 " ideal model delta harmonic sigma weight residual 180.00 -161.90 -18.10 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA TYR E 35 " pdb=" C TYR E 35 " pdb=" N GLU E 36 " pdb=" CA GLU E 36 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" C4' DA A 40 " pdb=" C3' DA A 40 " pdb=" O3' DA A 40 " pdb=" P DG A 41 " ideal model delta sinusoidal sigma weight residual 220.00 93.03 126.97 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 9082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1076 0.029 - 0.057: 346 0.057 - 0.086: 82 0.086 - 0.114: 84 0.114 - 0.143: 22 Chirality restraints: 1610 Sorted by residual: chirality pdb=" C3' DC B 21 " pdb=" C4' DC B 21 " pdb=" O3' DC B 21 " pdb=" C2' DC B 21 " both_signs ideal model delta sigma weight residual False -2.66 -2.80 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE E 237 " pdb=" N ILE E 237 " pdb=" C ILE E 237 " pdb=" CB ILE E 237 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" P DC B 11 " pdb=" OP1 DC B 11 " pdb=" OP2 DC B 11 " pdb=" O5' DC B 11 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 1607 not shown) Planarity restraints: 2667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 198 " -0.176 2.00e-02 2.50e+03 1.76e-01 4.64e+02 pdb=" CG ASN F 198 " 0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN F 198 " 0.168 2.00e-02 2.50e+03 pdb=" ND2 ASN F 198 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN F 198 " 0.249 2.00e-02 2.50e+03 pdb="HD22 ASN F 198 " -0.253 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 198 " 0.019 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" N GLN F 199 " -0.063 2.00e-02 2.50e+03 pdb=" CA GLN F 199 " 0.015 2.00e-02 2.50e+03 pdb=" H GLN F 199 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 311 " -0.013 2.00e-02 2.50e+03 2.39e-02 5.72e+00 pdb=" N LYS C 312 " 0.041 2.00e-02 2.50e+03 pdb=" CA LYS C 312 " -0.010 2.00e-02 2.50e+03 pdb=" H LYS C 312 " -0.018 2.00e-02 2.50e+03 ... (remaining 2664 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 1859 2.24 - 2.83: 38225 2.83 - 3.42: 43949 3.42 - 4.01: 61197 4.01 - 4.60: 93249 Nonbonded interactions: 238479 Sorted by model distance: nonbonded pdb=" OE1 GLU C 17 " pdb=" H GLU C 17 " model vdw 1.649 2.450 nonbonded pdb=" H SER E 249 " pdb=" O LYS E 253 " model vdw 1.652 2.450 nonbonded pdb=" O GLN C 123 " pdb=" HG1 THR C 127 " model vdw 1.676 2.450 nonbonded pdb=" HB2 SER C 304 " pdb="HG21 THR C 321 " model vdw 1.678 2.440 nonbonded pdb=" O GLN E 123 " pdb=" HG1 THR E 127 " model vdw 1.697 2.450 ... (remaining 238474 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 'C' and ((resid 20 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid \ 21 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name OD2)) or (resid 22 and (name N or name CA or name C or name O or name CB \ )) or resid 23 through 74 or resid 87 through 203 or resid 219 through 359)) selection = (chain 'E' and (resid 20 through 178 or (resid 179 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2)) or (resid 180 and (name N or name CA or name C or name O )) or re \ sid 181 through 327 or (resid 328 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name ND2)) or (resid 329 and (name N or name C \ A or name C or name O or name CB or name CG or name CD )) or resid 333 through 3 \ 59)) } ncs_group { reference = (chain 'D' and (resid 94 through 118 or (resid 126 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD )) or (resid 127 and (name N or n \ ame CA or name C or name O or name CB or name CG or name OD1 or name OD2)) or re \ sid 128 through 269 or resid 303 through 464)) selection = (chain 'F' and (resid 94 through 142 or resid 156 through 314 or resid 335 throu \ gh 429 or (resid 430 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name NE or name CZ or name NH1 or name NH2)) or resid 431 th \ rough 464)) } 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: 5.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 21.660 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.003 0.040 10459 Z= 0.140 Angle : 0.501 5.922 14329 Z= 0.285 Chirality : 0.038 0.143 1610 Planarity : 0.002 0.039 1626 Dihedral : 21.040 126.967 4002 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.00 % Allowed : 25.63 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.29), residues: 1069 helix: 2.24 (0.31), residues: 346 sheet: -1.09 (0.37), residues: 240 loop : 0.21 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 26 TYR 0.004 0.001 TYR C 316 PHE 0.004 0.001 PHE C 98 TRP 0.002 0.000 TRP D 438 HIS 0.003 0.000 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00298 (10459) covalent geometry : angle 0.50133 (14329) hydrogen bonds : bond 0.22613 ( 412) hydrogen bonds : angle 9.32339 ( 1121) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.530 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: D 115 MET cc_start: 0.8936 (tpp) cc_final: 0.8683 (mmm) REVERT: D 159 LEU cc_start: 0.8489 (mm) cc_final: 0.8286 (mm) REVERT: D 160 THR cc_start: 0.8872 (p) cc_final: 0.8643 (p) REVERT: E 119 MET cc_start: 0.8921 (mpp) cc_final: 0.8434 (mmt) REVERT: E 252 MET cc_start: 0.8510 (mmp) cc_final: 0.8205 (tpt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2560 time to fit residues: 76.1306 Evaluate side-chains 116 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.112309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.088195 restraints weight = 53215.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091956 restraints weight = 25728.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.094502 restraints weight = 16231.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.096009 restraints weight = 11884.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097137 restraints weight = 9775.835| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 10459 Z= 0.218 Angle : 0.555 5.421 14329 Z= 0.310 Chirality : 0.041 0.152 1610 Planarity : 0.004 0.038 1626 Dihedral : 18.844 136.994 1771 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.90 % Allowed : 23.69 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.28), residues: 1069 helix: 1.67 (0.30), residues: 354 sheet: -1.36 (0.32), residues: 277 loop : -0.24 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 27 TYR 0.008 0.001 TYR F 311 PHE 0.013 0.002 PHE D 177 TRP 0.010 0.001 TRP E 190 HIS 0.004 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00504 (10459) covalent geometry : angle 0.55464 (14329) hydrogen bonds : bond 0.04764 ( 412) hydrogen bonds : angle 5.61348 ( 1121) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 0.601 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: C 289 MET cc_start: 0.9276 (mmm) cc_final: 0.9018 (mmm) REVERT: D 115 MET cc_start: 0.8874 (tpp) cc_final: 0.8656 (mmm) REVERT: D 214 HIS cc_start: 0.7046 (OUTLIER) cc_final: 0.6416 (p-80) REVERT: E 32 GLU cc_start: 0.7941 (tp30) cc_final: 0.7547 (tp30) REVERT: E 119 MET cc_start: 0.9106 (mpp) cc_final: 0.8734 (mmt) REVERT: E 291 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8494 (ttmm) REVERT: F 134 MET cc_start: 0.8519 (mtm) cc_final: 0.8315 (mtm) outliers start: 30 outliers final: 17 residues processed: 136 average time/residue: 0.2356 time to fit residues: 44.2389 Evaluate side-chains 117 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 374 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 400 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 441 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 10 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094284 restraints weight = 51367.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098349 restraints weight = 24794.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.100954 restraints weight = 15506.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.102593 restraints weight = 11374.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.103529 restraints weight = 9238.851| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10459 Z= 0.144 Angle : 0.473 4.816 14329 Z= 0.261 Chirality : 0.038 0.165 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.415 137.386 1771 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.93 % Allowed : 23.89 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.28), residues: 1069 helix: 1.57 (0.30), residues: 364 sheet: -1.37 (0.31), residues: 283 loop : -0.34 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 102 TYR 0.007 0.001 TYR C 327 PHE 0.011 0.001 PHE E 244 TRP 0.006 0.001 TRP E 190 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00328 (10459) covalent geometry : angle 0.47252 (14329) hydrogen bonds : bond 0.03962 ( 412) hydrogen bonds : angle 5.04878 ( 1121) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.498 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: C 289 MET cc_start: 0.9249 (mmm) cc_final: 0.9015 (mmm) REVERT: D 115 MET cc_start: 0.8894 (tpp) cc_final: 0.8666 (mmm) REVERT: E 119 MET cc_start: 0.9080 (mpp) cc_final: 0.8701 (mmt) REVERT: E 179 ARG cc_start: 0.8075 (mtm180) cc_final: 0.7819 (mtp180) outliers start: 20 outliers final: 14 residues processed: 115 average time/residue: 0.2524 time to fit residues: 38.9605 Evaluate side-chains 107 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 183 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 167 LEU Chi-restraints excluded: chain F residue 400 CYS Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 45 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN D 447 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.114292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.089343 restraints weight = 51250.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093268 restraints weight = 25066.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095817 restraints weight = 15962.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097488 restraints weight = 11853.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098570 restraints weight = 9665.372| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10459 Z= 0.212 Angle : 0.523 4.396 14329 Z= 0.291 Chirality : 0.040 0.159 1610 Planarity : 0.004 0.037 1626 Dihedral : 18.225 147.402 1771 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.71 % Allowed : 24.27 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.27), residues: 1069 helix: 1.36 (0.29), residues: 356 sheet: -1.43 (0.31), residues: 276 loop : -0.58 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 261 TYR 0.009 0.001 TYR C 281 PHE 0.015 0.002 PHE E 244 TRP 0.007 0.001 TRP E 190 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00494 (10459) covalent geometry : angle 0.52349 (14329) hydrogen bonds : bond 0.04360 ( 412) hydrogen bonds : angle 4.98274 ( 1121) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 115 MET cc_start: 0.8851 (tpp) cc_final: 0.8615 (mmm) outliers start: 28 outliers final: 21 residues processed: 118 average time/residue: 0.2533 time to fit residues: 40.9495 Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Chi-restraints excluded: chain F residue 441 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.112764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.089103 restraints weight = 51685.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.092709 restraints weight = 24995.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.095103 restraints weight = 15964.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.096666 restraints weight = 11762.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097568 restraints weight = 9576.008| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10459 Z= 0.160 Angle : 0.474 4.179 14329 Z= 0.262 Chirality : 0.038 0.152 1610 Planarity : 0.003 0.038 1626 Dihedral : 18.143 147.866 1771 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.13 % Allowed : 24.66 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.27), residues: 1069 helix: 1.48 (0.30), residues: 354 sheet: -1.50 (0.31), residues: 287 loop : -0.41 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 185 TYR 0.006 0.001 TYR C 91 PHE 0.011 0.001 PHE F 363 TRP 0.005 0.001 TRP F 315 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00367 (10459) covalent geometry : angle 0.47362 (14329) hydrogen bonds : bond 0.03691 ( 412) hydrogen bonds : angle 4.73010 ( 1121) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 289 MET cc_start: 0.9259 (mmm) cc_final: 0.9043 (mmm) REVERT: D 343 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8085 (mp) outliers start: 22 outliers final: 17 residues processed: 103 average time/residue: 0.2429 time to fit residues: 35.1369 Evaluate side-chains 99 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 0.0070 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 22 optimal weight: 0.0040 chunk 112 optimal weight: 0.6980 overall best weight: 0.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.088789 restraints weight = 50987.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.092670 restraints weight = 25003.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.095204 restraints weight = 15862.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096755 restraints weight = 11717.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097816 restraints weight = 9659.230| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10459 Z= 0.098 Angle : 0.432 3.987 14329 Z= 0.236 Chirality : 0.038 0.152 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.036 150.143 1771 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.93 % Allowed : 24.66 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.28), residues: 1069 helix: 1.70 (0.30), residues: 358 sheet: -1.34 (0.31), residues: 282 loop : -0.27 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 440 TYR 0.006 0.001 TYR C 307 PHE 0.008 0.001 PHE D 177 TRP 0.005 0.001 TRP E 190 HIS 0.004 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00221 (10459) covalent geometry : angle 0.43238 (14329) hydrogen bonds : bond 0.02946 ( 412) hydrogen bonds : angle 4.42937 ( 1121) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.562 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: D 343 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8041 (mp) outliers start: 20 outliers final: 13 residues processed: 106 average time/residue: 0.2346 time to fit residues: 34.8439 Evaluate side-chains 99 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 408 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 2 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 102 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.115515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.090901 restraints weight = 51200.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094655 restraints weight = 25176.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097119 restraints weight = 16030.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098718 restraints weight = 11887.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099620 restraints weight = 9712.635| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10459 Z= 0.185 Angle : 0.484 4.207 14329 Z= 0.268 Chirality : 0.038 0.152 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.172 150.727 1771 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.42 % Allowed : 24.37 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.28), residues: 1069 helix: 1.56 (0.30), residues: 354 sheet: -1.48 (0.31), residues: 287 loop : -0.44 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 261 TYR 0.007 0.001 TYR E 316 PHE 0.014 0.001 PHE E 244 TRP 0.007 0.001 TRP F 315 HIS 0.004 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00432 (10459) covalent geometry : angle 0.48423 (14329) hydrogen bonds : bond 0.03878 ( 412) hydrogen bonds : angle 4.58768 ( 1121) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8109 (mp) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.2577 time to fit residues: 38.5594 Evaluate side-chains 103 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 241 SER Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 365 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.3980 chunk 110 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 97 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.115697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091166 restraints weight = 50263.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094974 restraints weight = 24371.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097464 restraints weight = 15497.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.099034 restraints weight = 11477.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.100098 restraints weight = 9432.153| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10459 Z= 0.106 Angle : 0.440 5.477 14329 Z= 0.240 Chirality : 0.037 0.147 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.124 152.084 1771 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.74 % Allowed : 24.85 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.28), residues: 1069 helix: 1.71 (0.30), residues: 358 sheet: -1.36 (0.31), residues: 290 loop : -0.32 (0.33), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 27 TYR 0.005 0.001 TYR C 307 PHE 0.010 0.001 PHE F 363 TRP 0.005 0.001 TRP F 438 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00240 (10459) covalent geometry : angle 0.43968 (14329) hydrogen bonds : bond 0.03084 ( 412) hydrogen bonds : angle 4.34476 ( 1121) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 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: D 343 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8069 (mp) outliers start: 18 outliers final: 16 residues processed: 101 average time/residue: 0.2200 time to fit residues: 31.8089 Evaluate side-chains 98 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 344 GLN Chi-restraints excluded: chain F residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 76 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.113505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088630 restraints weight = 51567.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.092350 restraints weight = 25309.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094828 restraints weight = 16314.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096421 restraints weight = 12166.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097296 restraints weight = 9990.947| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10459 Z= 0.208 Angle : 0.494 4.200 14329 Z= 0.273 Chirality : 0.039 0.152 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.206 151.789 1771 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.22 % Allowed : 24.56 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.28), residues: 1069 helix: 1.50 (0.30), residues: 360 sheet: -1.56 (0.31), residues: 288 loop : -0.42 (0.32), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 27 TYR 0.007 0.001 TYR E 316 PHE 0.014 0.002 PHE E 244 TRP 0.007 0.001 TRP F 438 HIS 0.003 0.001 HIS E 194 Details of bonding type rmsd covalent geometry : bond 0.00484 (10459) covalent geometry : angle 0.49363 (14329) hydrogen bonds : bond 0.03924 ( 412) hydrogen bonds : angle 4.55467 ( 1121) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 343 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8137 (mp) REVERT: F 157 SER cc_start: 0.8990 (m) cc_final: 0.8785 (t) outliers start: 23 outliers final: 19 residues processed: 99 average time/residue: 0.2200 time to fit residues: 31.1538 Evaluate side-chains 102 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 109 ILE Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 90 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 79 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.116015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.091264 restraints weight = 50670.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.095126 restraints weight = 24745.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.097663 restraints weight = 15780.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099234 restraints weight = 11680.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.100238 restraints weight = 9614.157| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10459 Z= 0.105 Angle : 0.442 6.620 14329 Z= 0.240 Chirality : 0.037 0.148 1610 Planarity : 0.003 0.037 1626 Dihedral : 18.164 152.055 1771 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.55 % Allowed : 25.53 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.28), residues: 1069 helix: 1.73 (0.30), residues: 358 sheet: -1.33 (0.31), residues: 289 loop : -0.36 (0.33), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 27 TYR 0.006 0.001 TYR C 307 PHE 0.010 0.001 PHE F 363 TRP 0.006 0.001 TRP F 438 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00237 (10459) covalent geometry : angle 0.44224 (14329) hydrogen bonds : bond 0.03009 ( 412) hydrogen bonds : angle 4.29293 ( 1121) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2138 Ramachandran restraints generated. 1069 Oldfield, 0 Emsley, 1069 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.549 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: C 302 VAL cc_start: 0.9414 (p) cc_final: 0.9189 (t) REVERT: D 343 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8096 (mp) REVERT: D 433 ASN cc_start: 0.8893 (m-40) cc_final: 0.8318 (p0) outliers start: 16 outliers final: 14 residues processed: 100 average time/residue: 0.2179 time to fit residues: 31.0530 Evaluate side-chains 102 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 THR Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 174 CYS Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain D residue 165 LYS Chi-restraints excluded: chain D residue 214 HIS Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 SER Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 174 CYS Chi-restraints excluded: chain E residue 353 VAL Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 340 ILE Chi-restraints excluded: chain F residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.114091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089298 restraints weight = 50698.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093156 restraints weight = 24893.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.095700 restraints weight = 15846.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097310 restraints weight = 11685.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098203 restraints weight = 9563.459| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.5113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10459 Z= 0.158 Angle : 0.476 9.966 14329 Z= 0.258 Chirality : 0.038 0.150 1610 Planarity : 0.003 0.036 1626 Dihedral : 18.230 151.753 1771 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.84 % Allowed : 25.53 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.28), residues: 1069 helix: 1.66 (0.30), residues: 358 sheet: -1.41 (0.31), residues: 286 loop : -0.27 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 27 TYR 0.005 0.001 TYR C 202 PHE 0.012 0.001 PHE E 244 TRP 0.006 0.001 TRP F 438 HIS 0.003 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00369 (10459) covalent geometry : angle 0.47617 (14329) hydrogen bonds : bond 0.03466 ( 412) hydrogen bonds : angle 4.39594 ( 1121) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2925.98 seconds wall clock time: 50 minutes 49.54 seconds (3049.54 seconds total)