Starting phenix.real_space_refine on Sat Feb 7 20:28:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.map" model { file = "/net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ml3_48346/02_2026/9ml3_48346.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.290 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: 5 Type Number sf(0) Gaussians S 101 5.16 5 C 11509 2.51 5 N 3023 2.21 5 O 3436 1.98 5 H 17555 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35624 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 6348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6348 Classifications: {'peptide': 406} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain breaks: 4 Chain: "B" Number of atoms: 6430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6430 Classifications: {'peptide': 412} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 386} Chain breaks: 3 Chain: "C" Number of atoms: 6458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 6458 Classifications: {'peptide': 414} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 388} Chain breaks: 2 Chain: "D" Number of atoms: 6444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6444 Classifications: {'peptide': 413} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 387} Chain breaks: 3 Chain: "E" Number of atoms: 6444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 6444 Classifications: {'peptide': 413} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 25, 'TRANS': 387} Chain breaks: 3 Chain: "H" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1925 Classifications: {'peptide': 124} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "L" Number of atoms: 1575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1575 Classifications: {'peptide': 110} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Time building chain proxies: 6.36, per 1000 atoms: 0.18 Number of scatterers: 35624 At special positions: 0 Unit cell: (117.81, 118.932, 132.396, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 O 3436 8.00 N 3023 7.00 C 11509 6.00 H 17555 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: 2.76 Conformation dependent library (CDL) restraints added in 913.3 milliseconds 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4238 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 31 sheets defined 15.6% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 294 through 299 removed outlier: 4.295A pdb=" N ASN A 299 " --> pdb=" O SER A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 410 through 413 removed outlier: 3.568A pdb=" N LEU A 413 " --> pdb=" O SER A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 413' Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.035A pdb=" N ASN B 145 " --> pdb=" O ASP B 142 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 146 " --> pdb=" O THR B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 146' Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 247 through 254 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.862A pdb=" N TYR B 290 " --> pdb=" O ASP B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.820A pdb=" N THR B 297 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ASN B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 398 through 409 Processing helix chain 'B' and resid 409 through 416 removed outlier: 4.319A pdb=" N LEU B 413 " --> pdb=" O ASN B 409 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TRP B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 475 Processing helix chain 'B' and resid 476 through 486 Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 93 through 97 Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.533A pdb=" N TYR C 290 " --> pdb=" O ASP C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 299 removed outlier: 4.192A pdb=" N ASN C 299 " --> pdb=" O SER C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.717A pdb=" N GLU C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 475 removed outlier: 3.751A pdb=" N GLN C 475 " --> pdb=" O ASP C 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 475' Processing helix chain 'C' and resid 476 through 486 Processing helix chain 'D' and resid 37 through 41 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.813A pdb=" N THR D 297 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN D 299 " --> pdb=" O SER D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 370 through 372 No H-bonds generated for 'chain 'D' and resid 370 through 372' Processing helix chain 'D' and resid 398 through 409 Processing helix chain 'D' and resid 410 through 416 removed outlier: 3.732A pdb=" N GLU D 414 " --> pdb=" O SER D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 475 Processing helix chain 'D' and resid 476 through 486 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 93 through 97 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 247 through 254 Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.777A pdb=" N TYR E 290 " --> pdb=" O ASP E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.985A pdb=" N THR E 297 " --> pdb=" O SER E 294 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASN E 299 " --> pdb=" O SER E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 372 No H-bonds generated for 'chain 'E' and resid 370 through 372' Processing helix chain 'E' and resid 398 through 409 Processing helix chain 'E' and resid 410 through 416 removed outlier: 3.869A pdb=" N GLU E 414 " --> pdb=" O SER E 410 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 472 through 475 removed outlier: 3.654A pdb=" N GLN E 475 " --> pdb=" O ASP E 472 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 472 through 475' Processing helix chain 'E' and resid 476 through 486 removed outlier: 3.532A pdb=" N LEU E 484 " --> pdb=" O ARG E 480 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 removed outlier: 4.092A pdb=" N SER H 65 " --> pdb=" O SER H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 52 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 43 through 52 current: chain 'A' and resid 324 through 325 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 324 through 325 current: chain 'A' and resid 374 through 396 No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.548A pdb=" N ILE A 66 " --> pdb=" O LEU A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 461 through 464 removed outlier: 3.649A pdb=" N PHE A 262 " --> pdb=" O ILE A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 137 removed outlier: 4.258A pdb=" N LEU A 136 " --> pdb=" O GLU A 159 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU A 159 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 202 through 208 removed outlier: 5.638A pdb=" N TRP A 183 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N CYS A 243 " --> pdb=" O TRP A 183 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET A 214 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 275 removed outlier: 3.853A pdb=" N HIS A 273 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 280 through 281 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 280 through 281 current: chain 'E' and resid 324 through 325 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 324 through 325 current: chain 'E' and resid 374 through 396 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 314 through 315 current: chain 'B' and resid 262 through 276 removed outlier: 6.654A pdb=" N THR B 308 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LEU B 274 " --> pdb=" O PHE B 306 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE B 306 " --> pdb=" O LEU B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 43 through 52 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 43 through 52 current: chain 'B' and resid 374 through 396 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AB2, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.975A pdb=" N LEU B 136 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU B 159 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.082A pdb=" N TRP B 183 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS B 243 " --> pdb=" O TRP B 183 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET B 214 " --> pdb=" O LYS B 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 314 through 315 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 314 through 315 current: chain 'C' and resid 262 through 275 removed outlier: 6.724A pdb=" N THR C 308 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 274 " --> pdb=" O PHE C 306 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N PHE C 306 " --> pdb=" O LEU C 274 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 43 through 52 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 43 through 52 current: chain 'C' and resid 325 through 326 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 325 through 326 current: chain 'C' and resid 374 through 396 Processing sheet with id=AB6, first strand: chain 'C' and resid 132 through 137 removed outlier: 4.089A pdb=" N LEU C 136 " --> pdb=" O GLU C 159 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU C 159 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 202 through 208 removed outlier: 5.908A pdb=" N TRP C 183 " --> pdb=" O CYS C 243 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N CYS C 243 " --> pdb=" O TRP C 183 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET C 214 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 314 through 315 removed outlier: 3.572A pdb=" N PHE D 262 " --> pdb=" O ILE D 173 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL D 86 " --> pdb=" O TRP D 461 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D 463 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ARG D 88 " --> pdb=" O VAL D 463 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 43 through 52 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 43 through 52 current: chain 'D' and resid 324 through 325 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 324 through 325 current: chain 'D' and resid 374 through 396 No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 131 through 137 removed outlier: 3.609A pdb=" N SER D 132 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU D 136 " --> pdb=" O GLU D 159 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N GLU D 159 " --> pdb=" O LEU D 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 202 through 208 removed outlier: 5.893A pdb=" N TRP D 183 " --> pdb=" O CYS D 243 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS D 243 " --> pdb=" O TRP D 183 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET D 214 " --> pdb=" O LYS D 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 273 through 276 removed outlier: 3.854A pdb=" N HIS D 273 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE D 306 " --> pdb=" O PHE D 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 314 through 315 removed outlier: 7.139A pdb=" N VAL E 463 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG E 88 " --> pdb=" O VAL E 463 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 66 through 67 removed outlier: 6.735A pdb=" N ILE E 66 " --> pdb=" O LEU E 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 131 through 138 removed outlier: 3.827A pdb=" N LEU E 136 " --> pdb=" O GLU E 159 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N GLU E 159 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.722A pdb=" N ARG H 100D" --> pdb=" O TRP H 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 202 through 208 removed outlier: 5.850A pdb=" N TRP E 183 " --> pdb=" O CYS E 243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N CYS E 243 " --> pdb=" O TRP E 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N MET E 214 " --> pdb=" O LYS E 244 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 273 through 276 removed outlier: 4.057A pdb=" N HIS E 273 " --> pdb=" O THR E 308 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE E 306 " --> pdb=" O PHE E 275 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AD2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.715A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N TRP H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD4, first strand: chain 'L' and resid 34 through 38 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 46 current: chain 'L' and resid 96 through 98 328 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.85 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17080 1.03 - 1.23: 501 1.23 - 1.42: 7994 1.42 - 1.62: 10357 1.62 - 1.81: 148 Bond restraints: 36080 Sorted by residual: bond pdb=" CZ ARG L 61 " pdb=" NH2 ARG L 61 " ideal model delta sigma weight residual 1.330 1.228 0.102 1.30e-02 5.92e+03 6.12e+01 bond pdb=" CD1 PHE L 62 " pdb=" HD1 PHE L 62 " ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N GLN L 17 " pdb=" H GLN L 17 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N THR L 24 " pdb=" H THR L 24 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.63e+01 bond pdb=" N LYS H 43 " pdb=" H LYS H 43 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 36075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 63581 2.09 - 4.17: 857 4.17 - 6.26: 414 6.26 - 8.35: 142 8.35 - 10.44: 19 Bond angle restraints: 65013 Sorted by residual: angle pdb=" C SER L 63 " pdb=" N GLY L 64 " pdb=" CA GLY L 64 " ideal model delta sigma weight residual 122.18 129.24 -7.06 6.90e-01 2.10e+00 1.05e+02 angle pdb=" CA PHE L 98 " pdb=" CB PHE L 98 " pdb=" CG PHE L 98 " ideal model delta sigma weight residual 113.80 120.85 -7.05 1.00e+00 1.00e+00 4.97e+01 angle pdb=" CA PHE L 62 " pdb=" CB PHE L 62 " pdb=" CG PHE L 62 " ideal model delta sigma weight residual 113.80 120.56 -6.76 1.00e+00 1.00e+00 4.57e+01 angle pdb=" C ARG H 38 " pdb=" N GLN H 39 " pdb=" CA GLN H 39 " ideal model delta sigma weight residual 123.15 130.75 -7.60 1.21e+00 6.83e-01 3.95e+01 angle pdb=" C THR L 74 " pdb=" N ILE L 75 " pdb=" CA ILE L 75 " ideal model delta sigma weight residual 123.12 131.27 -8.15 1.30e+00 5.92e-01 3.93e+01 ... (remaining 65008 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15580 17.99 - 35.97: 1183 35.97 - 53.96: 339 53.96 - 71.95: 95 71.95 - 89.93: 30 Dihedral angle restraints: 17227 sinusoidal: 9239 harmonic: 7988 Sorted by residual: dihedral pdb=" CA CYS L 23 " pdb=" C CYS L 23 " pdb=" N THR L 24 " pdb=" CA THR L 24 " ideal model delta harmonic sigma weight residual -180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C GLN L 79 " pdb=" N GLN L 79 " pdb=" CA GLN L 79 " pdb=" CB GLN L 79 " ideal model delta harmonic sigma weight residual -122.60 -133.67 11.07 0 2.50e+00 1.60e-01 1.96e+01 dihedral pdb=" CA SER L 22 " pdb=" C SER L 22 " pdb=" N CYS L 23 " pdb=" CA CYS L 23 " ideal model delta harmonic sigma weight residual -180.00 -158.63 -21.37 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 17224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 2683 0.150 - 0.299: 2 0.299 - 0.449: 9 0.449 - 0.599: 43 0.599 - 0.749: 9 Chirality restraints: 2746 Sorted by residual: chirality pdb=" CG LEU H 45 " pdb=" CB LEU H 45 " pdb=" CD1 LEU H 45 " pdb=" CD2 LEU H 45 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CG LEU L 47 " pdb=" CB LEU L 47 " pdb=" CD1 LEU L 47 " pdb=" CD2 LEU L 47 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CG LEU L 4 " pdb=" CB LEU L 4 " pdb=" CD1 LEU L 4 " pdb=" CD2 LEU L 4 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 2743 not shown) Planarity restraints: 5395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN L 6 " -0.012 2.00e-02 2.50e+03 5.99e-02 5.39e+01 pdb=" CD GLN L 6 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN L 6 " 0.048 2.00e-02 2.50e+03 pdb=" NE2 GLN L 6 " -0.108 2.00e-02 2.50e+03 pdb="HE21 GLN L 6 " 0.084 2.00e-02 2.50e+03 pdb="HE22 GLN L 6 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 100 " -0.030 2.00e-02 2.50e+03 5.41e-02 2.92e+01 pdb=" N GLY L 101 " 0.093 2.00e-02 2.50e+03 pdb=" CA GLY L 101 " -0.027 2.00e-02 2.50e+03 pdb=" H GLY L 101 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 20 " 0.025 2.00e-02 2.50e+03 4.61e-02 2.12e+01 pdb=" N ILE L 21 " -0.080 2.00e-02 2.50e+03 pdb=" CA ILE L 21 " 0.022 2.00e-02 2.50e+03 pdb=" H ILE L 21 " 0.032 2.00e-02 2.50e+03 ... (remaining 5392 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.36: 12864 2.36 - 2.92: 79220 2.92 - 3.48: 89974 3.48 - 4.04: 130453 4.04 - 4.60: 189657 Nonbonded interactions: 502168 Sorted by model distance: nonbonded pdb=" OE2 GLU L 83 " pdb=" H VAL L 106 " model vdw 1.806 2.450 nonbonded pdb=" O GLY L 13 " pdb=" H LEU L 106A" model vdw 1.810 2.450 nonbonded pdb=" HA ASN B 106 " pdb="HD21 ASN B 106 " model vdw 1.835 2.270 nonbonded pdb=" H ASP A 415 " pdb=" H TRP A 416 " model vdw 1.844 2.100 nonbonded pdb=" HG3 GLN L 6 " pdb=" H THR L 100 " model vdw 1.847 2.270 ... (remaining 502163 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 34 through 150 or resid 154 through 187 or resid 194 throu \ gh 416 or resid 453 through 485)) selection = (chain 'C' and (resid 34 through 71 or resid 73 through 150 or resid 154 through \ 187 or resid 194 through 416 or resid 453 through 485)) selection = (chain 'D' and (resid 34 through 150 or resid 154 through 187 or resid 194 throu \ gh 416 or resid 453 through 485)) selection = (chain 'E' and (resid 34 through 150 or resid 154 through 187 or resid 194 throu \ gh 416 or resid 453 through 485)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.260 Extract box with map and model: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 31.380 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 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 : 0.009 0.140 18525 Z= 0.467 Angle : 0.848 10.234 25173 Z= 0.507 Chirality : 0.093 0.749 2746 Planarity : 0.004 0.062 3259 Dihedral : 14.354 89.932 6718 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.55 % Allowed : 8.89 % Favored : 90.56 % Cbeta Deviations : 0.71 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.18), residues: 2248 helix: -0.04 (0.37), residues: 221 sheet: -1.14 (0.19), residues: 691 loop : -0.19 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 266 TYR 0.034 0.001 TYR L 86 PHE 0.026 0.001 PHE L 98 TRP 0.033 0.001 TRP L 35 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00911 (18525) covalent geometry : angle 0.84822 (25173) hydrogen bonds : bond 0.21150 ( 328) hydrogen bonds : angle 8.34967 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8823 (tp) cc_final: 0.8408 (mt) REVERT: A 106 ASN cc_start: 0.7374 (t0) cc_final: 0.7007 (t0) REVERT: A 329 ARG cc_start: 0.8826 (ttm170) cc_final: 0.8559 (ttm-80) REVERT: A 366 GLU cc_start: 0.8062 (mp0) cc_final: 0.7647 (mp0) REVERT: B 72 ASN cc_start: 0.7646 (t0) cc_final: 0.7252 (t0) REVERT: B 198 ASP cc_start: 0.8337 (m-30) cc_final: 0.7949 (m-30) REVERT: B 402 MET cc_start: 0.6395 (mmm) cc_final: 0.5748 (tmt) REVERT: C 457 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8266 (ttpp) REVERT: D 181 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.7477 (pp20) REVERT: D 195 GLN cc_start: 0.8100 (mp-120) cc_final: 0.7782 (mp10) REVERT: D 222 MET cc_start: 0.9126 (ptm) cc_final: 0.8861 (ptm) REVERT: D 414 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7607 (mm-30) REVERT: H 38 ARG cc_start: 0.6654 (ptt180) cc_final: 0.6377 (ptt180) REVERT: H 69 MET cc_start: 0.6838 (mmm) cc_final: 0.6603 (mmm) REVERT: L 5 THR cc_start: 0.8870 (m) cc_final: 0.8664 (p) REVERT: L 21 ILE cc_start: 0.7111 (mm) cc_final: 0.6899 (tp) REVERT: L 31 ASP cc_start: 0.7895 (p0) cc_final: 0.7585 (p0) REVERT: L 45 LYS cc_start: 0.6622 (tppt) cc_final: 0.6377 (tttm) REVERT: L 69 ASP cc_start: 0.8019 (m-30) cc_final: 0.7440 (m-30) outliers start: 11 outliers final: 8 residues processed: 151 average time/residue: 1.4157 time to fit residues: 239.1326 Evaluate side-chains 151 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN B 106 ASN C 106 ASN C 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.107425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.075902 restraints weight = 80127.247| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.48 r_work: 0.2859 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18525 Z= 0.177 Angle : 0.512 5.140 25173 Z= 0.263 Chirality : 0.045 0.143 2746 Planarity : 0.004 0.045 3259 Dihedral : 4.887 53.483 2486 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.90 % Allowed : 8.69 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2248 helix: -0.24 (0.35), residues: 231 sheet: -0.96 (0.19), residues: 695 loop : -0.26 (0.17), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 266 TYR 0.009 0.001 TYR D 263 PHE 0.013 0.001 PHE D 262 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00427 (18525) covalent geometry : angle 0.51180 (25173) hydrogen bonds : bond 0.04856 ( 328) hydrogen bonds : angle 6.29933 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8706 (tp) cc_final: 0.8290 (mt) REVERT: A 106 ASN cc_start: 0.7209 (t0) cc_final: 0.6838 (t0) REVERT: A 159 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: A 329 ARG cc_start: 0.8873 (ttm170) cc_final: 0.8581 (ttm-80) REVERT: B 72 ASN cc_start: 0.7627 (t0) cc_final: 0.7248 (t0) REVERT: B 198 ASP cc_start: 0.8229 (m-30) cc_final: 0.7808 (m-30) REVERT: B 402 MET cc_start: 0.6145 (mmm) cc_final: 0.5509 (tmt) REVERT: C 457 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8256 (ttpp) REVERT: D 181 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8108 (pt0) REVERT: D 195 GLN cc_start: 0.8043 (mp-120) cc_final: 0.7738 (mp10) REVERT: D 222 MET cc_start: 0.9103 (ptm) cc_final: 0.8890 (ptm) REVERT: D 414 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7529 (mm-30) REVERT: H 38 ARG cc_start: 0.6492 (ptt180) cc_final: 0.6245 (ptt180) REVERT: L 31 ASP cc_start: 0.7797 (p0) cc_final: 0.7486 (p0) REVERT: L 45 LYS cc_start: 0.6507 (tppt) cc_final: 0.6297 (tttm) REVERT: L 69 ASP cc_start: 0.7813 (m-30) cc_final: 0.7076 (m-30) REVERT: L 103 LYS cc_start: 0.6452 (pptt) cc_final: 0.6194 (ptpp) outliers start: 18 outliers final: 10 residues processed: 156 average time/residue: 1.3046 time to fit residues: 228.3333 Evaluate side-chains 153 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 40 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 169 GLN D 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.076021 restraints weight = 80042.543| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.48 r_work: 0.2863 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18525 Z= 0.162 Angle : 0.492 4.918 25173 Z= 0.250 Chirality : 0.044 0.140 2746 Planarity : 0.004 0.044 3259 Dihedral : 4.615 54.736 2475 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.85 % Allowed : 9.69 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.17), residues: 2248 helix: -0.22 (0.35), residues: 231 sheet: -0.91 (0.19), residues: 689 loop : -0.26 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 266 TYR 0.008 0.001 TYR E 263 PHE 0.011 0.001 PHE D 262 TRP 0.010 0.001 TRP H 7 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00397 (18525) covalent geometry : angle 0.49167 (25173) hydrogen bonds : bond 0.03818 ( 328) hydrogen bonds : angle 5.83279 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8725 (tp) cc_final: 0.8319 (mt) REVERT: A 106 ASN cc_start: 0.7137 (t0) cc_final: 0.6693 (t0) REVERT: A 329 ARG cc_start: 0.8884 (ttm170) cc_final: 0.8599 (ttm-80) REVERT: B 72 ASN cc_start: 0.7754 (t0) cc_final: 0.7399 (t0) REVERT: B 198 ASP cc_start: 0.8243 (m-30) cc_final: 0.7831 (m-30) REVERT: B 402 MET cc_start: 0.6177 (mmm) cc_final: 0.5524 (tmt) REVERT: C 457 LYS cc_start: 0.8614 (ttpp) cc_final: 0.8299 (ttpp) REVERT: D 195 GLN cc_start: 0.8082 (mp-120) cc_final: 0.7765 (mp10) REVERT: D 222 MET cc_start: 0.9139 (ptm) cc_final: 0.8926 (ptm) REVERT: D 414 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7474 (mm-30) REVERT: H 46 ASP cc_start: 0.6916 (m-30) cc_final: 0.6431 (t0) REVERT: L 21 ILE cc_start: 0.6868 (mm) cc_final: 0.6579 (tp) REVERT: L 31 ASP cc_start: 0.7817 (p0) cc_final: 0.7447 (p0) REVERT: L 69 ASP cc_start: 0.7943 (m-30) cc_final: 0.7265 (m-30) REVERT: L 103 LYS cc_start: 0.6421 (pptt) cc_final: 0.6195 (ptpp) outliers start: 17 outliers final: 10 residues processed: 158 average time/residue: 1.3759 time to fit residues: 243.0853 Evaluate side-chains 149 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 ARG Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 325 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 120 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN B 304 ASN C 72 ASN D 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.075233 restraints weight = 80199.997| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.44 r_work: 0.2840 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18525 Z= 0.237 Angle : 0.520 4.908 25173 Z= 0.266 Chirality : 0.046 0.141 2746 Planarity : 0.004 0.049 3259 Dihedral : 4.673 57.050 2473 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.15 % Allowed : 10.08 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.17), residues: 2248 helix: -0.16 (0.35), residues: 231 sheet: -0.93 (0.19), residues: 689 loop : -0.33 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 266 TYR 0.011 0.001 TYR D 263 PHE 0.013 0.001 PHE D 262 TRP 0.010 0.001 TRP H 7 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00581 (18525) covalent geometry : angle 0.51967 (25173) hydrogen bonds : bond 0.03801 ( 328) hydrogen bonds : angle 5.65273 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8656 (tp) cc_final: 0.8247 (mt) REVERT: A 106 ASN cc_start: 0.7045 (t0) cc_final: 0.6599 (t0) REVERT: A 159 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7972 (pt0) REVERT: A 329 ARG cc_start: 0.8912 (ttm170) cc_final: 0.8626 (ttm-80) REVERT: B 72 ASN cc_start: 0.7756 (t0) cc_final: 0.7392 (t0) REVERT: B 198 ASP cc_start: 0.8211 (m-30) cc_final: 0.7864 (m-30) REVERT: B 402 MET cc_start: 0.6245 (mmm) cc_final: 0.5638 (tmt) REVERT: C 457 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8330 (ttpp) REVERT: D 195 GLN cc_start: 0.8095 (mp-120) cc_final: 0.7772 (mp10) REVERT: D 222 MET cc_start: 0.9097 (ptm) cc_final: 0.8837 (ptm) REVERT: D 414 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7543 (mm-30) REVERT: H 46 ASP cc_start: 0.6845 (m-30) cc_final: 0.6394 (t0) REVERT: L 21 ILE cc_start: 0.6966 (mm) cc_final: 0.6675 (tp) REVERT: L 31 ASP cc_start: 0.7721 (p0) cc_final: 0.7377 (p0) REVERT: L 69 ASP cc_start: 0.7834 (m-30) cc_final: 0.7159 (m-30) REVERT: L 103 LYS cc_start: 0.6475 (pptt) cc_final: 0.6265 (ptpp) outliers start: 23 outliers final: 14 residues processed: 156 average time/residue: 1.3374 time to fit residues: 234.5170 Evaluate side-chains 152 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 95 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 217 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 216 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 197 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 139 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN D 106 ASN D 464 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.106490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075415 restraints weight = 80134.720| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 2.44 r_work: 0.2794 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2671 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 18525 Z= 0.190 Angle : 0.505 4.549 25173 Z= 0.256 Chirality : 0.045 0.138 2746 Planarity : 0.004 0.049 3259 Dihedral : 4.636 59.220 2473 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.15 % Allowed : 10.53 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.17), residues: 2248 helix: 0.11 (0.36), residues: 219 sheet: -0.93 (0.19), residues: 697 loop : -0.32 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 266 TYR 0.009 0.001 TYR C 325 PHE 0.013 0.001 PHE D 262 TRP 0.009 0.001 TRP H 7 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00467 (18525) covalent geometry : angle 0.50483 (25173) hydrogen bonds : bond 0.03460 ( 328) hydrogen bonds : angle 5.49235 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8743 (tp) cc_final: 0.8369 (mt) REVERT: A 106 ASN cc_start: 0.7096 (t0) cc_final: 0.6630 (t0) REVERT: A 159 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8075 (pt0) REVERT: A 329 ARG cc_start: 0.8899 (ttm170) cc_final: 0.8629 (ttm-80) REVERT: B 72 ASN cc_start: 0.7806 (t0) cc_final: 0.7435 (t0) REVERT: B 198 ASP cc_start: 0.8536 (m-30) cc_final: 0.8181 (m-30) REVERT: B 402 MET cc_start: 0.6368 (mmm) cc_final: 0.5728 (tmt) REVERT: C 358 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8019 (pt) REVERT: C 457 LYS cc_start: 0.8753 (ttpp) cc_final: 0.8442 (ttpp) REVERT: D 195 GLN cc_start: 0.8149 (mp-120) cc_final: 0.7804 (mp10) REVERT: D 222 MET cc_start: 0.9164 (ptm) cc_final: 0.8933 (ptm) REVERT: D 414 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7607 (mm-30) REVERT: E 366 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: H 46 ASP cc_start: 0.6863 (m-30) cc_final: 0.6450 (t0) REVERT: L 31 ASP cc_start: 0.7813 (p0) cc_final: 0.7445 (p0) REVERT: L 69 ASP cc_start: 0.8042 (m-30) cc_final: 0.7370 (m-30) REVERT: L 103 LYS cc_start: 0.6533 (pptt) cc_final: 0.6324 (ptpp) outliers start: 23 outliers final: 13 residues processed: 162 average time/residue: 1.2399 time to fit residues: 226.8943 Evaluate side-chains 159 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 209 optimal weight: 5.9990 chunk 163 optimal weight: 0.0980 chunk 75 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 208 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN C 72 ASN D 106 ASN D 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.073052 restraints weight = 80963.740| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.46 r_work: 0.2837 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18525 Z= 0.211 Angle : 0.509 5.028 25173 Z= 0.259 Chirality : 0.045 0.139 2746 Planarity : 0.004 0.063 3259 Dihedral : 4.659 57.985 2473 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.00 % Allowed : 11.28 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.17), residues: 2248 helix: 0.16 (0.36), residues: 219 sheet: -0.92 (0.19), residues: 693 loop : -0.37 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 266 TYR 0.010 0.001 TYR D 263 PHE 0.015 0.001 PHE A 104 TRP 0.009 0.001 TRP H 7 HIS 0.004 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00516 (18525) covalent geometry : angle 0.50892 (25173) hydrogen bonds : bond 0.03469 ( 328) hydrogen bonds : angle 5.39579 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8726 (tp) cc_final: 0.8354 (mt) REVERT: A 106 ASN cc_start: 0.7046 (t0) cc_final: 0.6579 (t0) REVERT: A 159 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: A 329 ARG cc_start: 0.8932 (ttm170) cc_final: 0.8657 (ttm-80) REVERT: B 72 ASN cc_start: 0.7794 (t0) cc_final: 0.7432 (t0) REVERT: B 198 ASP cc_start: 0.8487 (m-30) cc_final: 0.8127 (m-30) REVERT: B 402 MET cc_start: 0.6295 (mmm) cc_final: 0.5653 (tmt) REVERT: C 358 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8000 (pt) REVERT: C 457 LYS cc_start: 0.8718 (ttpp) cc_final: 0.8409 (ttpp) REVERT: D 195 GLN cc_start: 0.8125 (mp-120) cc_final: 0.7782 (mp10) REVERT: D 222 MET cc_start: 0.9126 (ptm) cc_final: 0.8888 (ptm) REVERT: D 414 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7578 (mm-30) REVERT: E 366 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: H 46 ASP cc_start: 0.6847 (m-30) cc_final: 0.6420 (t0) REVERT: L 31 ASP cc_start: 0.7737 (p0) cc_final: 0.7385 (p0) REVERT: L 37 GLN cc_start: 0.6659 (tt0) cc_final: 0.5784 (tm-30) REVERT: L 69 ASP cc_start: 0.8013 (m-30) cc_final: 0.7366 (m-30) REVERT: L 103 LYS cc_start: 0.6532 (pptt) cc_final: 0.6313 (ptpp) outliers start: 20 outliers final: 12 residues processed: 154 average time/residue: 1.2616 time to fit residues: 219.0040 Evaluate side-chains 156 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 122 optimal weight: 5.9990 chunk 161 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 186 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 196 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN C 304 ASN D 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.104983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.073404 restraints weight = 80978.830| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.50 r_work: 0.2793 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18525 Z= 0.165 Angle : 0.493 7.892 25173 Z= 0.249 Chirality : 0.044 0.139 2746 Planarity : 0.004 0.069 3259 Dihedral : 4.562 54.452 2473 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.90 % Allowed : 11.83 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2248 helix: 0.22 (0.37), residues: 219 sheet: -0.87 (0.19), residues: 693 loop : -0.33 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 266 TYR 0.009 0.001 TYR C 325 PHE 0.018 0.001 PHE A 104 TRP 0.009 0.001 TRP H 7 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00404 (18525) covalent geometry : angle 0.49265 (25173) hydrogen bonds : bond 0.03232 ( 328) hydrogen bonds : angle 5.26794 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8738 (tp) cc_final: 0.8376 (mt) REVERT: A 106 ASN cc_start: 0.7159 (t0) cc_final: 0.6738 (t0) REVERT: A 159 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8086 (pt0) REVERT: A 329 ARG cc_start: 0.8904 (ttm170) cc_final: 0.8636 (ttm-80) REVERT: B 72 ASN cc_start: 0.7821 (t0) cc_final: 0.7472 (t0) REVERT: B 198 ASP cc_start: 0.8503 (m-30) cc_final: 0.8137 (m-30) REVERT: B 402 MET cc_start: 0.6334 (mmm) cc_final: 0.5643 (tmt) REVERT: C 358 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8080 (pt) REVERT: C 457 LYS cc_start: 0.8779 (ttpp) cc_final: 0.8466 (ttpp) REVERT: D 195 GLN cc_start: 0.8134 (mp-120) cc_final: 0.7778 (mp10) REVERT: D 222 MET cc_start: 0.9157 (ptm) cc_final: 0.8936 (ptm) REVERT: D 414 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7599 (mm-30) REVERT: E 366 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: H 46 ASP cc_start: 0.6862 (m-30) cc_final: 0.6462 (t0) REVERT: L 31 ASP cc_start: 0.7829 (p0) cc_final: 0.7430 (p0) REVERT: L 37 GLN cc_start: 0.6686 (tt0) cc_final: 0.5804 (tm-30) REVERT: L 69 ASP cc_start: 0.8095 (m-30) cc_final: 0.7462 (m-30) REVERT: L 103 LYS cc_start: 0.6646 (pptt) cc_final: 0.6401 (ptpp) outliers start: 18 outliers final: 14 residues processed: 159 average time/residue: 1.3755 time to fit residues: 246.0408 Evaluate side-chains 161 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 23 optimal weight: 5.9990 chunk 177 optimal weight: 0.0170 chunk 73 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN B 106 ASN D 106 ASN D 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.106242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075390 restraints weight = 80257.866| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.43 r_work: 0.2841 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2717 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18525 Z= 0.187 Angle : 0.497 5.551 25173 Z= 0.252 Chirality : 0.045 0.139 2746 Planarity : 0.004 0.048 3259 Dihedral : 4.542 49.130 2473 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.20 % Allowed : 11.78 % Favored : 87.02 % 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 are not related in a simple way. whole: -0.78 (0.17), residues: 2248 helix: 0.28 (0.37), residues: 219 sheet: -0.89 (0.19), residues: 693 loop : -0.35 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 266 TYR 0.010 0.001 TYR C 325 PHE 0.022 0.001 PHE A 104 TRP 0.008 0.001 TRP H 7 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00460 (18525) covalent geometry : angle 0.49701 (25173) hydrogen bonds : bond 0.03281 ( 328) hydrogen bonds : angle 5.19243 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8685 (tp) cc_final: 0.8323 (mt) REVERT: A 106 ASN cc_start: 0.7042 (t0) cc_final: 0.6627 (t0) REVERT: A 159 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: A 329 ARG cc_start: 0.8942 (ttm170) cc_final: 0.8668 (ttm-80) REVERT: B 72 ASN cc_start: 0.7796 (t0) cc_final: 0.7432 (t0) REVERT: B 198 ASP cc_start: 0.8414 (m-30) cc_final: 0.8036 (m-30) REVERT: B 402 MET cc_start: 0.6220 (mmm) cc_final: 0.5548 (tmt) REVERT: C 358 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7931 (pt) REVERT: D 195 GLN cc_start: 0.8082 (mp-120) cc_final: 0.7735 (mp10) REVERT: D 222 MET cc_start: 0.9084 (ptm) cc_final: 0.8848 (ptm) REVERT: D 414 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7545 (mm-30) REVERT: E 366 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: H 46 ASP cc_start: 0.6883 (m-30) cc_final: 0.6376 (t0) REVERT: L 31 ASP cc_start: 0.7704 (p0) cc_final: 0.7309 (p0) REVERT: L 37 GLN cc_start: 0.6602 (tt0) cc_final: 0.5771 (tm-30) REVERT: L 69 ASP cc_start: 0.7972 (m-30) cc_final: 0.7323 (m-30) REVERT: L 103 LYS cc_start: 0.6661 (pptt) cc_final: 0.6444 (ptpp) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 1.3028 time to fit residues: 237.6008 Evaluate side-chains 158 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 208 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 ASN D 106 ASN E 206 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.075300 restraints weight = 80175.484| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.42 r_work: 0.2791 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18525 Z= 0.194 Angle : 0.504 5.816 25173 Z= 0.255 Chirality : 0.045 0.139 2746 Planarity : 0.004 0.082 3259 Dihedral : 4.544 44.080 2473 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.00 % Allowed : 12.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.17), residues: 2248 helix: 0.29 (0.37), residues: 219 sheet: -0.89 (0.19), residues: 693 loop : -0.36 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG B 266 TYR 0.010 0.001 TYR C 325 PHE 0.024 0.001 PHE A 104 TRP 0.006 0.001 TRP H 7 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00475 (18525) covalent geometry : angle 0.50366 (25173) hydrogen bonds : bond 0.03267 ( 328) hydrogen bonds : angle 5.18373 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8736 (tp) cc_final: 0.8390 (mt) REVERT: A 106 ASN cc_start: 0.7169 (t0) cc_final: 0.6744 (t0) REVERT: A 159 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8091 (pt0) REVERT: A 329 ARG cc_start: 0.8908 (ttm170) cc_final: 0.8651 (ttm-80) REVERT: A 356 MET cc_start: 0.8752 (mtm) cc_final: 0.8514 (mtm) REVERT: B 72 ASN cc_start: 0.7829 (t0) cc_final: 0.7455 (t0) REVERT: B 198 ASP cc_start: 0.8507 (m-30) cc_final: 0.8149 (m-30) REVERT: B 402 MET cc_start: 0.6347 (mmm) cc_final: 0.5654 (tmt) REVERT: C 358 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8097 (pt) REVERT: C 457 LYS cc_start: 0.8804 (ttpp) cc_final: 0.8494 (ttpp) REVERT: D 195 GLN cc_start: 0.8139 (mp-120) cc_final: 0.7777 (mp10) REVERT: D 222 MET cc_start: 0.9144 (ptm) cc_final: 0.8927 (ptm) REVERT: D 414 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7613 (mm-30) REVERT: E 195 GLN cc_start: 0.7334 (pt0) cc_final: 0.6929 (pp30) REVERT: E 366 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: H 46 ASP cc_start: 0.6926 (m-30) cc_final: 0.6432 (t0) REVERT: L 31 ASP cc_start: 0.7787 (p0) cc_final: 0.7306 (p0) REVERT: L 37 GLN cc_start: 0.6639 (tt0) cc_final: 0.5793 (tm-30) REVERT: L 69 ASP cc_start: 0.8158 (m-30) cc_final: 0.7467 (m-30) REVERT: L 103 LYS cc_start: 0.6815 (pptt) cc_final: 0.6562 (ptpp) outliers start: 20 outliers final: 15 residues processed: 154 average time/residue: 1.2468 time to fit residues: 217.1972 Evaluate side-chains 157 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 73 LYS Chi-restraints excluded: chain B residue 159 GLU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 67 LYS Chi-restraints excluded: chain E residue 325 TYR Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 114 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 184 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 183 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN D 106 ASN H 3 GLN H 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.076537 restraints weight = 79801.957| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.48 r_work: 0.2865 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18525 Z= 0.093 Angle : 0.466 5.760 25173 Z= 0.234 Chirality : 0.044 0.142 2746 Planarity : 0.004 0.074 3259 Dihedral : 4.272 38.161 2473 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 12.73 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2248 helix: 0.38 (0.37), residues: 219 sheet: -0.77 (0.19), residues: 699 loop : -0.23 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 266 TYR 0.007 0.001 TYR C 325 PHE 0.025 0.001 PHE A 104 TRP 0.008 0.000 TRP H 7 HIS 0.002 0.001 HIS A 182 Details of bonding type rmsd covalent geometry : bond 0.00229 (18525) covalent geometry : angle 0.46562 (25173) hydrogen bonds : bond 0.02830 ( 328) hydrogen bonds : angle 5.02338 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4496 Ramachandran restraints generated. 2248 Oldfield, 0 Emsley, 2248 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 82 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.862 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: A 75 LEU cc_start: 0.8705 (tp) cc_final: 0.8347 (mt) REVERT: A 106 ASN cc_start: 0.7015 (t0) cc_final: 0.6599 (t0) REVERT: A 159 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: A 329 ARG cc_start: 0.8906 (ttm170) cc_final: 0.8636 (ttm-80) REVERT: A 356 MET cc_start: 0.8695 (mtm) cc_final: 0.8485 (mtm) REVERT: B 198 ASP cc_start: 0.8371 (m-30) cc_final: 0.7978 (m-30) REVERT: B 402 MET cc_start: 0.6228 (mmm) cc_final: 0.5548 (tmt) REVERT: C 358 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7932 (pt) REVERT: D 181 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8531 (pt0) REVERT: D 195 GLN cc_start: 0.8032 (mp-120) cc_final: 0.7632 (mp10) REVERT: D 414 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7520 (mm-30) REVERT: E 195 GLN cc_start: 0.7252 (pt0) cc_final: 0.6953 (pp30) REVERT: E 366 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6833 (mp0) REVERT: H 46 ASP cc_start: 0.6868 (m-30) cc_final: 0.6370 (t0) REVERT: L 31 ASP cc_start: 0.7705 (p0) cc_final: 0.7301 (p0) REVERT: L 37 GLN cc_start: 0.6529 (tt0) cc_final: 0.5686 (tm-30) REVERT: L 69 ASP cc_start: 0.8004 (m-30) cc_final: 0.7371 (m-30) REVERT: L 103 LYS cc_start: 0.6864 (pptt) cc_final: 0.6603 (ptpp) outliers start: 16 outliers final: 9 residues processed: 160 average time/residue: 1.3333 time to fit residues: 240.4123 Evaluate side-chains 156 residues out of total 2003 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 GLU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 410 SER Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 216 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 66 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain H residue 69 MET Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 227 random chunks: chunk 122 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 84 optimal weight: 0.0980 chunk 127 optimal weight: 0.6980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN D 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.075464 restraints weight = 80157.292| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 2.47 r_work: 0.2799 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18525 Z= 0.168 Angle : 0.487 5.465 25173 Z= 0.246 Chirality : 0.044 0.139 2746 Planarity : 0.004 0.072 3259 Dihedral : 4.343 35.899 2473 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.60 % Favored : 96.35 % Rotamer: Outliers : 0.95 % Allowed : 12.73 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2248 helix: 0.42 (0.37), residues: 219 sheet: -0.80 (0.19), residues: 699 loop : -0.28 (0.17), residues: 1330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 266 TYR 0.010 0.001 TYR C 325 PHE 0.027 0.001 PHE A 104 TRP 0.005 0.001 TRP H 7 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00414 (18525) covalent geometry : angle 0.48691 (25173) hydrogen bonds : bond 0.03072 ( 328) hydrogen bonds : angle 5.00417 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9423.12 seconds wall clock time: 160 minutes 10.78 seconds (9610.78 seconds total)